* using log directory 'd:/Rcompile/CRANpkg/local/2.11/RBrownie.Rcheck' * using R version 2.11.1 Patched (2010-07-29 r52657) * using session charset: ISO8859-1 * checking for file 'RBrownie/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'RBrownie' version '0.1.1' * checking package name space information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking whether package 'RBrownie' can be installed ... OK * checking package directory ... OK * checking for portable file names ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking R files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the name space can be loaded with stated dependencies ... OK * checking whether the name space can be unloaded cleanly ... OK * checking for unstated dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE tipdate.ci: no visible binding for '<<-' assignment to 'cipos' tipdate.ci: no visible binding for '<<-' assignment to 'citype' tipdate.ci: no visible binding for '<<-' assignment to 'cinode' tipdate.ci : addlen: no visible binding for '<<-' assignment to 'cipos' tipdate.ci : addlen: no visible binding for global variable 'cipos' tipdate.ci : addtype: no visible binding for '<<-' assignment to 'citype' tipdate.ci : addtype: no visible binding for global variable 'citype' tipdate.ci : addnode: no visible binding for '<<-' assignment to 'cinode' tipdate.ci : addnode: no visible binding for global variable 'cinode' tipdate.ci: no visible binding for global variable 'cipos' tipdate.ci: no visible binding for global variable 'citype' * checking Rd files ... NOTE prepare_Rd: RBrownie.Rd:204-206: Dropping empty section \references prepare_Rd: addCensored.Rd:63-65: Dropping empty section \note prepare_Rd: addCensored.Rd:57-59: Dropping empty section \references prepare_Rd: addCensored.Rd:74-76: Dropping empty section \examples prepare_Rd: addChoose.Rd:46-48: Dropping empty section \note prepare_Rd: addChoose.Rd:40-42: Dropping empty section \references prepare_Rd: addChoose.Rd:52-54: Dropping empty section \seealso prepare_Rd: addDiscrete.Rd:114-116: Dropping empty section \note prepare_Rd: addDiscrete.Rd:111-113: Dropping empty section \author prepare_Rd: addDiscrete.Rd:108-110: Dropping empty section \references prepare_Rd: addDiscrete.Rd:120-122: Dropping empty section \seealso prepare_Rd: addEndLog.Rd:23-29: Dropping empty section \value prepare_Rd: addEndLog.Rd:36-38: Dropping empty section \note prepare_Rd: addEndLog.Rd:45-47: Dropping empty section \examples prepare_Rd: addHS.Rd:131-133: Dropping empty section \note prepare_Rd: addHS.Rd:125-127: Dropping empty section \references prepare_Rd: addHS.Rd:137-139: Dropping empty section \seealso prepare_Rd: addLiteral.Rd:34-36: Dropping empty section \note prepare_Rd: addLiteral.Rd:40-42: Dropping empty section \seealso prepare_Rd: addModel.Rd:56-58: Dropping empty section \note prepare_Rd: addModel.Rd:50-52: Dropping empty section \references prepare_Rd: addModel.Rd:62-64: Dropping empty section \seealso prepare_Rd: addModel.Rd:65-67: Dropping empty section \examples prepare_Rd: addNonCensored.Rd:62-64: Dropping empty section \note prepare_Rd: addNumopt.Rd:63-65: Dropping empty section \note prepare_Rd: addNumopt.Rd:57-59: Dropping empty section \references prepare_Rd: addNumopt.Rd:69-71: Dropping empty section \seealso prepare_Rd: addOpt.Rd:53-55: Dropping empty section \note prepare_Rd: addOpt.Rd:59-61: Dropping empty section \seealso prepare_Rd: addStartLog.Rd:51-53: Dropping empty section \note prepare_Rd: addStartLog.Rd:45-47: Dropping empty section \references prepare_Rd: addSubNode.Rd:46-48: Dropping empty section \note prepare_Rd: addSubNode.Rd:43-45: Dropping empty section \author prepare_Rd: addSubNode.Rd:40-42: Dropping empty section \references prepare_Rd: addSubNode.Rd:56-59: Dropping empty section \examples prepare_Rd: addTipvariance.Rd:42-44: Dropping empty section \note prepare_Rd: addTipvariance.Rd:36-38: Dropping empty section \references prepare_Rd: addTipvariance.Rd:48-50: Dropping empty section \seealso prepare_Rd: addcmd.binary.Rd:25-27: Dropping empty section \details prepare_Rd: addcmd.binary.Rd:28-34: Dropping empty section \value prepare_Rd: addcmd.binary.Rd:41-43: Dropping empty section \note prepare_Rd: addcmd.binary.Rd:35-37: Dropping empty section \references prepare_Rd: addcmd.binary.Rd:47-49: Dropping empty section \seealso prepare_Rd: addcmd.binary.Rd:50-52: Dropping empty section \examples prepare_Rd: addcmd.freq.Rd:28-30: Dropping empty section \details prepare_Rd: addcmd.freq.Rd:31-37: Dropping empty section \value prepare_Rd: addcmd.freq.Rd:44-46: Dropping empty section \note prepare_Rd: addcmd.freq.Rd:38-40: Dropping empty section \references prepare_Rd: addcmd.freq.Rd:50-52: Dropping empty section \seealso prepare_Rd: addcmd.freq.Rd:53-55: Dropping empty section \examples prepare_Rd: addcmd.literal.Rd:25-27: Dropping empty section \details prepare_Rd: addcmd.literal.Rd:28-34: Dropping empty section \value prepare_Rd: addcmd.literal.Rd:41-43: Dropping empty section \note prepare_Rd: addcmd.literal.Rd:35-37: Dropping empty section \references prepare_Rd: addcmd.literal.Rd:47-49: Dropping empty section \seealso prepare_Rd: addcmd.literal.Rd:50-52: Dropping empty section \examples prepare_Rd: addcmd.model.continuous.Rd:22-24: Dropping empty section \details prepare_Rd: addcmd.model.continuous.Rd:25-31: Dropping empty section \value prepare_Rd: addcmd.model.continuous.Rd:38-40: Dropping empty section \note prepare_Rd: addcmd.model.continuous.Rd:32-34: Dropping empty section \references prepare_Rd: addcmd.model.continuous.Rd:44-46: Dropping empty section \seealso prepare_Rd: addcmd.model.continuous.Rd:47-49: Dropping empty section \examples prepare_Rd: addcmd.model.discrete.Rd:28-30: Dropping empty section \details prepare_Rd: addcmd.model.discrete.Rd:31-37: Dropping empty section \value prepare_Rd: addcmd.model.discrete.Rd:44-46: Dropping empty section \note prepare_Rd: addcmd.model.discrete.Rd:38-40: Dropping empty section \references prepare_Rd: addcmd.model.discrete.Rd:50-52: Dropping empty section \seealso prepare_Rd: addcmd.model.discrete.Rd:53-55: Dropping empty section \examples prepare_Rd: addcmd.states.Rd:25-27: Dropping empty section \details prepare_Rd: addcmd.states.Rd:28-34: Dropping empty section \value prepare_Rd: addcmd.states.Rd:41-43: Dropping empty section \note prepare_Rd: addcmd.states.Rd:35-37: Dropping empty section \references prepare_Rd: addcmd.states.Rd:47-49: Dropping empty section \seealso prepare_Rd: addcmd.states.Rd:50-52: Dropping empty section \examples prepare_Rd: addcmd.taxaset.Rd:25-27: Dropping empty section \details prepare_Rd: addcmd.taxaset.Rd:28-34: Dropping empty section \value prepare_Rd: addcmd.taxaset.Rd:41-43: Dropping empty section \note prepare_Rd: addcmd.taxaset.Rd:35-37: Dropping empty section \references prepare_Rd: addcmd.taxaset.Rd:47-49: Dropping empty section \seealso prepare_Rd: addcmd.taxaset.Rd:50-52: Dropping empty section \examples prepare_Rd: addcmd.tvtype.Rd:22-24: Dropping empty section \details prepare_Rd: addcmd.tvtype.Rd:25-31: Dropping empty section \value prepare_Rd: addcmd.tvtype.Rd:38-40: Dropping empty section \note prepare_Rd: addcmd.tvtype.Rd:32-34: Dropping empty section \references prepare_Rd: addcmd.tvtype.Rd:44-46: Dropping empty section \seealso prepare_Rd: addcmd.tvtype.Rd:47-49: Dropping empty section \examples prepare_Rd: areTaxaMono.Rd:34-36: Dropping empty section \note prepare_Rd: areTaxaMono.Rd:28-30: Dropping empty section \references prepare_Rd: areTaxaMutex.Rd:34-36: Dropping empty section \note prepare_Rd: areTaxaMutex.Rd:28-30: Dropping empty section \references prepare_Rd: areTaxaMutex.Rd:40-42: Dropping empty section \seealso prepare_Rd: areTaxaPara.Rd:37-39: Dropping empty section \note prepare_Rd: areTaxaPara.Rd:31-33: Dropping empty section \references prepare_Rd: areTaxaPara.Rd:43-45: Dropping empty section \seealso prepare_Rd: as.contData.Rd:33-35: Dropping empty section \note prepare_Rd: as.contData.Rd:30-32: Dropping empty section \author prepare_Rd: as.contData.Rd:27-29: Dropping empty section \references prepare_Rd: as.contData.Rd:39-41: Dropping empty section \seealso prepare_Rd: as.discData.Rd:34-36: Dropping empty section \note prepare_Rd: as.discData.Rd:28-30: Dropping empty section \references prepare_Rd: as.discData.Rd:40-42: Dropping empty section \seealso prepare_Rd: brownie-class.Rd:98: Dropping empty section \note prepare_Rd: brownie-class.Rd:96: Dropping empty section \references prepare_Rd: brownie.datatypes.Rd:14-16: Dropping empty section \details prepare_Rd: brownie.datatypes.Rd:17-23: Dropping empty section \value prepare_Rd: brownie.datatypes.Rd:30-32: Dropping empty section \note prepare_Rd: brownie.datatypes.Rd:27-29: Dropping empty section \author prepare_Rd: brownie.datatypes.Rd:24-26: Dropping empty section \references prepare_Rd: brownie.datatypes.Rd:36-38: Dropping empty section \seealso prepare_Rd: brownie.freqs.Rd:19-21: Dropping empty section \details prepare_Rd: brownie.freqs.Rd:22-28: Dropping empty section \value prepare_Rd: brownie.freqs.Rd:35-37: Dropping empty section \note prepare_Rd: brownie.freqs.Rd:29-31: Dropping empty section \references prepare_Rd: brownie.freqs.Rd:41-43: Dropping empty section \seealso prepare_Rd: brownie.freqs.Rd:44-46: Dropping empty section \examples prepare_Rd: brownie.models.continuous.Rd:19-21: Dropping empty section \details prepare_Rd: brownie.models.continuous.Rd:22-28: Dropping empty section \value prepare_Rd: brownie.models.continuous.Rd:35-37: Dropping empty section \note prepare_Rd: brownie.models.continuous.Rd:29-31: Dropping empty section \references prepare_Rd: brownie.models.continuous.Rd:41-43: Dropping empty section \seealso prepare_Rd: brownie.models.continuous.Rd:44-46: Dropping empty section \examples prepare_Rd: brownie.models.discrete.Rd:19-21: Dropping empty section \details prepare_Rd: brownie.models.discrete.Rd:22-28: Dropping empty section \value prepare_Rd: brownie.models.discrete.Rd:35-37: Dropping empty section \note prepare_Rd: brownie.models.discrete.Rd:29-31: Dropping empty section \references prepare_Rd: brownie.models.discrete.Rd:41-43: Dropping empty section \seealso prepare_Rd: brownie.models.discrete.Rd:44-46: Dropping empty section \examples prepare_Rd: brownie.tvtypes.Rd:19-21: Dropping empty section \details prepare_Rd: brownie.tvtypes.Rd:22-24: Dropping empty section \value prepare_Rd: brownie.tvtypes.Rd:31-33: Dropping empty section \note prepare_Rd: brownie.tvtypes.Rd:25-27: Dropping empty section \references prepare_Rd: brownie.tvtypes.Rd:37-39: Dropping empty section \seealso prepare_Rd: brownie.tvtypes.Rd:40-42: Dropping empty section \examples prepare_Rd: check.empty.Rd:31-33: Dropping empty section \note prepare_Rd: check.empty.Rd:25-27: Dropping empty section \references prepare_Rd: check.empty.Rd:37-39: Dropping empty section \seealso prepare_Rd: check.freq.Rd:19-21: Dropping empty section \details prepare_Rd: check.freq.Rd:22-28: Dropping empty section \value prepare_Rd: check.freq.Rd:35-37: Dropping empty section \note prepare_Rd: check.freq.Rd:29-31: Dropping empty section \references prepare_Rd: check.freq.Rd:41-43: Dropping empty section \seealso prepare_Rd: check.freq.Rd:44-46: Dropping empty section \examples prepare_Rd: check.statevector.Rd:34-36: Dropping empty section \note prepare_Rd: check.statevector.Rd:28-30: Dropping empty section \references prepare_Rd: check.statevector.Rd:40-42: Dropping empty section \seealso prepare_Rd: check.statevector.Rd:43-45: Dropping empty section \examples prepare_Rd: checkBrownie.Rd:19-21: Dropping empty section \details prepare_Rd: checkBrownie.Rd:22-28: Dropping empty section \value prepare_Rd: checkBrownie.Rd:35-37: Dropping empty section \note prepare_Rd: checkBrownie.Rd:29-31: Dropping empty section \references prepare_Rd: checkBrownie.Rd:41-43: Dropping empty section \seealso prepare_Rd: checkBrownie.Rd:44-46: Dropping empty section \examples prepare_Rd: checkCommands.Rd:19-21: Dropping empty section \details prepare_Rd: checkCommands.Rd:22-28: Dropping empty section \value prepare_Rd: checkCommands.Rd:35-37: Dropping empty section \note prepare_Rd: checkCommands.Rd:29-31: Dropping empty section \references prepare_Rd: checkCommands.Rd:41-43: Dropping empty section \seealso prepare_Rd: checkCommands.Rd:44-45: Dropping empty section \examples prepare_Rd: checkDataTypes.Rd:19-21: Dropping empty section \details prepare_Rd: checkDataTypes.Rd:22-28: Dropping empty section \value prepare_Rd: checkDataTypes.Rd:35-36: Dropping empty section \note prepare_Rd: checkDataTypes.Rd:29-31: Dropping empty section \references prepare_Rd: checkDataTypes.Rd:40-41: Dropping empty section \seealso prepare_Rd: checkDataTypes.Rd:42-43: Dropping empty section \examples prepare_Rd: checkMono.Rd:37-39: Dropping empty section \note prepare_Rd: checkMono.Rd:31-33: Dropping empty section \references prepare_Rd: checkPara.Rd:37-39: Dropping empty section \note prepare_Rd: checkPara.Rd:31-33: Dropping empty section \references prepare_Rd: checkval.dummy.Rd:19-21: Dropping empty section \details prepare_Rd: checkval.dummy.Rd:22-28: Dropping empty section \value prepare_Rd: checkval.dummy.Rd:35-37: Dropping empty section \note prepare_Rd: checkval.dummy.Rd:29-31: Dropping empty section \references prepare_Rd: checkval.dummy.Rd:41-43: Dropping empty section \seealso prepare_Rd: checkval.dummy.Rd:44-46: Dropping empty section \examples prepare_Rd: checkval.integer.Rd:19-21: Dropping empty section \details prepare_Rd: checkval.integer.Rd:22-28: Dropping empty section \value prepare_Rd: checkval.integer.Rd:35-37: Dropping empty section \note prepare_Rd: checkval.integer.Rd:29-31: Dropping empty section \references prepare_Rd: checkval.integer.Rd:41-43: Dropping empty section \seealso prepare_Rd: checkval.integer.Rd:44-46: Dropping empty section \examples prepare_Rd: checkval.model.continuous.Rd:19-21: Dropping empty section \details prepare_Rd: checkval.model.continuous.Rd:22-28: Dropping empty section \value prepare_Rd: checkval.model.continuous.Rd:35-37: Dropping empty section \note prepare_Rd: checkval.model.continuous.Rd:29-31: Dropping empty section \references prepare_Rd: checkval.model.continuous.Rd:41-43: Dropping empty section \seealso prepare_Rd: checkval.model.continuous.Rd:44-46: Dropping empty section \examples prepare_Rd: checkval.model.discrete.Rd:19-21: Dropping empty section \details prepare_Rd: checkval.model.discrete.Rd:22-28: Dropping empty section \value prepare_Rd: checkval.model.discrete.Rd:35-37: Dropping empty section \note prepare_Rd: checkval.model.discrete.Rd:29-31: Dropping empty section \references prepare_Rd: checkval.model.discrete.Rd:41-43: Dropping empty section \seealso prepare_Rd: checkval.model.discrete.Rd:44-46: Dropping empty section \examples prepare_Rd: checkval.ratemat.Rd:22-24: Dropping empty section \details prepare_Rd: checkval.ratemat.Rd:25-31: Dropping empty section \value prepare_Rd: checkval.ratemat.Rd:38-40: Dropping empty section \note prepare_Rd: checkval.ratemat.Rd:32-34: Dropping empty section \references prepare_Rd: checkval.ratemat.Rd:44-46: Dropping empty section \seealso prepare_Rd: checkval.ratemat.Rd:47-49: Dropping empty section \examples prepare_Rd: checkval.yesno.Rd:19-21: Dropping empty section \details prepare_Rd: checkval.yesno.Rd:22-28: Dropping empty section \value prepare_Rd: checkval.yesno.Rd:35-37: Dropping empty section \note prepare_Rd: checkval.yesno.Rd:29-31: Dropping empty section \references prepare_Rd: checkval.yesno.Rd:41-43: Dropping empty section \seealso prepare_Rd: checkval.yesno.Rd:44-46: Dropping empty section \examples prepare_Rd: collapse.singletons.Rd:19-21: Dropping empty section \details prepare_Rd: collapse.singletons.Rd:31-33: Dropping empty section \note prepare_Rd: collapse.singletons.Rd:25-27: Dropping empty section \references prepare_Rd: collapse.subnodes.Rd:36-38: Dropping empty section \examples prepare_Rd: collapse.to.singles.Rd:34-36: Dropping empty section \note prepare_Rd: collapse.to.singles.Rd:28-30: Dropping empty section \references prepare_Rd: collapse.to.singles.Rd:40-42: Dropping empty section \seealso prepare_Rd: contData.Rd:14-16: Dropping empty section \details prepare_Rd: contData.Rd:17-23: Dropping empty section \value prepare_Rd: contData.Rd:30-32: Dropping empty section \note prepare_Rd: contData.Rd:24-26: Dropping empty section \references prepare_Rd: contData.Rd:36-38: Dropping empty section \seealso prepare_Rd: contData.Rd:39-41: Dropping empty section \examples prepare_Rd: discData.Rd:14-16: Dropping empty section \details prepare_Rd: discData.Rd:17-23: Dropping empty section \value prepare_Rd: discData.Rd:30-32: Dropping empty section \note prepare_Rd: discData.Rd:24-26: Dropping empty section \references prepare_Rd: discData.Rd:36-38: Dropping empty section \seealso prepare_Rd: discData.Rd:39-41: Dropping empty section \examples prepare_Rd: execute.brownie.Rd:32-34: Dropping empty section \note prepare_Rd: execute.brownie.Rd:26-28: Dropping empty section \references prepare_Rd: expand.singles.Rd:34-36: Dropping empty section \note prepare_Rd: expand.singles.Rd:28-30: Dropping empty section \references prepare_Rd: expand.singles.Rd:40-42: Dropping empty section \seealso prepare_Rd: genericData.Rd:14-16: Dropping empty section \details prepare_Rd: genericData.Rd:17-23: Dropping empty section \value prepare_Rd: genericData.Rd:30-32: Dropping empty section \note prepare_Rd: genericData.Rd:24-26: Dropping empty section \references prepare_Rd: genericData.Rd:39-41: Dropping empty section \examples prepare_Rd: geospiza_ext.Rd:21-23: Dropping empty section \references prepare_Rd: get.left.right.Rd:22-24: Dropping empty section \details prepare_Rd: get.left.right.Rd:34-36: Dropping empty section \note prepare_Rd: get.left.right.Rd:28-30: Dropping empty section \references prepare_Rd: get.left.right.Rd:40-42: Dropping empty section \seealso prepare_Rd: get.nexus.comments.Rd:22-24: Dropping empty section \details prepare_Rd: get.nexus.comments.Rd:25-31: Dropping empty section \value prepare_Rd: get.nexus.comments.Rd:38-40: Dropping empty section \note prepare_Rd: get.nexus.comments.Rd:32-34: Dropping empty section \references prepare_Rd: get.nexus.comments.Rd:44-46: Dropping empty section \seealso prepare_Rd: get.nexus.comments.Rd:47-49: Dropping empty section \examples prepare_Rd: get.nodenames.Rd:19-20: Dropping empty section \details prepare_Rd: get.nodenames.Rd:30-32: Dropping empty section \note prepare_Rd: get.nodenames.Rd:24-26: Dropping empty section \references prepare_Rd: get.nodenames.Rd:36-38: Dropping empty section \seealso prepare_Rd: get.nodenames.Rd:39-40: Dropping empty section \examples prepare_Rd: get.tree.weights.Rd:31-33: Dropping empty section \details prepare_Rd: get.tree.weights.Rd:43-45: Dropping empty section \note prepare_Rd: get.tree.weights.Rd:37-39: Dropping empty section \references prepare_Rd: get.tree.weights.Rd:49-51: Dropping empty section \seealso prepare_Rd: get.tree.weights.Rd:52-54: Dropping empty section \examples prepare_Rd: getEmptyDataFrame.Rd:34-36: Dropping empty section \note prepare_Rd: getEmptyDataFrame.Rd:28-30: Dropping empty section \references prepare_Rd: getEmptyDataFrame.Rd:40-42: Dropping empty section \seealso prepare_Rd: getEmptyDataFrame.Rd:43-45: Dropping empty section \examples prepare_Rd: getSubNodeData.Rd:22-24: Dropping empty section \details prepare_Rd: getSubNodeData.Rd:34-36: Dropping empty section \note prepare_Rd: getSubNodeData.Rd:28-30: Dropping empty section \references prepare_Rd: getSubNodeData.Rd:40-42: Dropping empty section \seealso prepare_Rd: getSubNodeEdgeInds.Rd:22-24: Dropping empty section \value prepare_Rd: getSubNodeEdgeInds.Rd:31-33: Dropping empty section \note prepare_Rd: getSubNodeEdgeInds.Rd:25-27: Dropping empty section \references prepare_Rd: getSubNodeEdgeInds.Rd:37-39: Dropping empty section \seealso prepare_Rd: getSubNodePosish.Rd:19-21: Dropping empty section \details prepare_Rd: getSubNodePosish.Rd:31-33: Dropping empty section \note prepare_Rd: getSubNodePosish.Rd:25-27: Dropping empty section \references prepare_Rd: getSubNodePosish.Rd:37-39: Dropping empty section \seealso prepare_Rd: has.block.Rd:25-27: Dropping empty section \details prepare_Rd: has.block.Rd:37-39: Dropping empty section \note prepare_Rd: has.block.Rd:31-33: Dropping empty section \references prepare_Rd: has.block.Rd:43-45: Dropping empty section \seealso prepare_Rd: has.block.Rd:46-48: Dropping empty section \examples prepare_Rd: has.characters2.Rd:34-36: Dropping empty section \note prepare_Rd: has.characters2.Rd:28-30: Dropping empty section \references prepare_Rd: has.characters2.Rd:40-42: Dropping empty section \seealso prepare_Rd: has.characters2.Rd:43-45: Dropping empty section \examples prepare_Rd: has.weights.Rd:34-36: Dropping empty section \note prepare_Rd: has.weights.Rd:28-30: Dropping empty section \references prepare_Rd: has.weights.Rd:40-42: Dropping empty section \seealso prepare_Rd: has.weights.Rd:43-45: Dropping empty section \examples prepare_Rd: hasCommands.Rd:31-33: Dropping empty section \note prepare_Rd: hasCommands.Rd:25-27: Dropping empty section \references prepare_Rd: haschar.Rd:22-24: Dropping empty section \details prepare_Rd: haschar.Rd:25-27: Dropping empty section \value prepare_Rd: haschar.Rd:34-36: Dropping empty section \note prepare_Rd: haschar.Rd:28-30: Dropping empty section \references prepare_Rd: haschar.Rd:40-42: Dropping empty section \seealso prepare_Rd: haschar.Rd:43-45: Dropping empty section \examples prepare_Rd: is.binary.Rd:19-21: Dropping empty section \details prepare_Rd: is.binary.Rd:22-24: Dropping empty section \value prepare_Rd: is.binary.Rd:31-33: Dropping empty section \note prepare_Rd: is.binary.Rd:25-27: Dropping empty section \references prepare_Rd: is.binary.Rd:37-39: Dropping empty section \seealso prepare_Rd: is.binary.Rd:40-41: Dropping empty section \examples prepare_Rd: is.contData.Rd:18-20: Dropping empty section \details prepare_Rd: is.contData.Rd:21-23: Dropping empty section \value prepare_Rd: is.contData.Rd:30-32: Dropping empty section \note prepare_Rd: is.contData.Rd:24-26: Dropping empty section \references prepare_Rd: is.contData.Rd:36-38: Dropping empty section \seealso prepare_Rd: is.contData.Rd:39-40: Dropping empty section \examples prepare_Rd: is.discData.Rd:19-21: Dropping empty section \details prepare_Rd: is.discData.Rd:22-28: Dropping empty section \value prepare_Rd: is.discData.Rd:35-37: Dropping empty section \note prepare_Rd: is.discData.Rd:29-31: Dropping empty section \references prepare_Rd: is.discData.Rd:41-43: Dropping empty section \seealso prepare_Rd: is.discData.Rd:44-46: Dropping empty section \examples prepare_Rd: is.simmap.Rd:40-42: Dropping empty section \note prepare_Rd: is.simmap.Rd:34-36: Dropping empty section \references prepare_Rd: is.simmap.Rd:46-48: Dropping empty section \seealso prepare_Rd: is.taxaname.internal.Rd:19-21: Dropping empty section \details prepare_Rd: is.taxaname.internal.Rd:22-28: Dropping empty section \value prepare_Rd: is.taxaname.internal.Rd:35-37: Dropping empty section \note prepare_Rd: is.taxaname.internal.Rd:29-31: Dropping empty section \references prepare_Rd: is.taxaname.internal.Rd:41-43: Dropping empty section \seealso prepare_Rd: is.taxaname.internal.Rd:44-46: Dropping empty section \examples prepare_Rd: is_valid_datatype.Rd:19-21: Dropping empty section \details prepare_Rd: is_valid_datatype.Rd:22-28: Dropping empty section \value prepare_Rd: is_valid_datatype.Rd:35-37: Dropping empty section \note prepare_Rd: is_valid_datatype.Rd:32-34: Dropping empty section \author prepare_Rd: is_valid_datatype.Rd:29-31: Dropping empty section \references prepare_Rd: is_valid_datatype.Rd:41-43: Dropping empty section \seealso prepare_Rd: is_valid_datatype.Rd:44-45: Dropping empty section \examples prepare_Rd: is_valid_datatype_bound.Rd:19-21: Dropping empty section \details prepare_Rd: is_valid_datatype_bound.Rd:22-28: Dropping empty section \value prepare_Rd: is_valid_datatype_bound.Rd:35-37: Dropping empty section \note prepare_Rd: is_valid_datatype_bound.Rd:32-34: Dropping empty section \author prepare_Rd: is_valid_datatype_bound.Rd:29-31: Dropping empty section \references prepare_Rd: is_valid_datatype_bound.Rd:41-43: Dropping empty section \seealso prepare_Rd: is_valid_datatype_bound.Rd:44-45: Dropping empty section \examples prepare_Rd: is_valid_datatype_prob.Rd:19-21: Dropping empty section \details prepare_Rd: is_valid_datatype_prob.Rd:22-28: Dropping empty section \value prepare_Rd: is_valid_datatype_prob.Rd:35-37: Dropping empty section \note prepare_Rd: is_valid_datatype_prob.Rd:32-34: Dropping empty section \author prepare_Rd: is_valid_datatype_prob.Rd:29-31: Dropping empty section \references prepare_Rd: is_valid_datatype_prob.Rd:41-43: Dropping empty section \seealso prepare_Rd: is_valid_datatype_prob.Rd:44-46: Dropping empty section \examples prepare_Rd: isback.Rd:22-24: Dropping empty section \details prepare_Rd: isback.Rd:25-31: Dropping empty section \value prepare_Rd: isback.Rd:38-40: Dropping empty section \note prepare_Rd: isback.Rd:32-34: Dropping empty section \references prepare_Rd: isback.Rd:44-46: Dropping empty section \seealso prepare_Rd: isback.Rd:47-49: Dropping empty section \examples prepare_Rd: match.order.Rd:22-24: Dropping empty section \details prepare_Rd: match.order.Rd:25-31: Dropping empty section \value prepare_Rd: match.order.Rd:38-40: Dropping empty section \note prepare_Rd: match.order.Rd:35-37: Dropping empty section \author prepare_Rd: match.order.Rd:32-34: Dropping empty section \references prepare_Rd: match.order.Rd:44-46: Dropping empty section \seealso prepare_Rd: match.order.Rd:47-48: Dropping empty section \examples prepare_Rd: nSubNodes.Rd:19-20: Dropping empty section \details prepare_Rd: nSubNodes.Rd:29-31: Dropping empty section \note prepare_Rd: nSubNodes.Rd:24-25: Dropping empty section \references prepare_Rd: nSubNodes.Rd:33-34: Dropping empty section \seealso prepare_Rd: newlabels.v15.Rd:25-27: Dropping empty section \details prepare_Rd: newlabels.v15.Rd:37-39: Dropping empty section \note prepare_Rd: newlabels.v15.Rd:34-36: Dropping empty section \author prepare_Rd: newlabels.v15.Rd:31-33: Dropping empty section \references prepare_Rd: newlabels.v15.Rd:47-49: Dropping empty section \examples prepare_Rd: newlabels.v1x.Rd:28-30: Dropping empty section \details prepare_Rd: newlabels.v1x.Rd:44-46: Dropping empty section \examples prepare_Rd: parrot.Rd:20-21: Dropping empty section \references prepare_Rd: phyextPlot.Rd:62-63: Dropping empty section \value prepare_Rd: phyextPlot.Rd:69-70: Dropping empty section \note prepare_Rd: phyextPlot.Rd:64-65: Dropping empty section \references prepare_Rd: phyextPlot.Rd:74-76: Dropping empty section \seealso prepare_Rd: phylo4d_ext-class.Rd:80: Dropping empty section \note prepare_Rd: plot.censored.Rd:43-45: Dropping empty section \value prepare_Rd: plot.censored.Rd:52-54: Dropping empty section \note prepare_Rd: plot.censored.Rd:46-48: Dropping empty section \references prepare_Rd: plot.censored.Rd:58-60: Dropping empty section \seealso prepare_Rd: plot.taxaset.Rd:40-42: Dropping empty section \details prepare_Rd: plot.taxaset.Rd:43-49: Dropping empty section \value prepare_Rd: plot.taxaset.Rd:56-58: Dropping empty section \note prepare_Rd: plot.taxaset.Rd:50-52: Dropping empty section \references prepare_Rd: plot.taxaset.Rd:62-64: Dropping empty section \seealso prepare_Rd: rcpp_hello_world.Rd:14-16: Dropping empty section \details prepare_Rd: rcpp_hello_world.Rd:17-23: Dropping empty section \value prepare_Rd: rcpp_hello_world.Rd:30-32: Dropping empty section \note prepare_Rd: rcpp_hello_world.Rd:24-26: Dropping empty section \references prepare_Rd: rcpp_hello_world.Rd:36-38: Dropping empty section \seealso prepare_Rd: rcpp_hello_world.Rd:39-41: Dropping empty section \examples prepare_Rd: read.analysis.output.Rd:42-44: Dropping empty section \note prepare_Rd: read.analysis.output.Rd:36-38: Dropping empty section \references prepare_Rd: read.analysis.output.Rd:46-48: Dropping empty section \seealso prepare_Rd: read.analysis.output.Rd:49-51: Dropping empty section \examples prepare_Rd: read.brownie.string.Rd:22-24: Dropping empty section \details prepare_Rd: read.brownie.string.Rd:25-29: Dropping empty section \value prepare_Rd: read.brownie.string.Rd:36-38: Dropping empty section \note prepare_Rd: read.brownie.string.Rd:30-32: Dropping empty section \references prepare_Rd: read.brownie.string.Rd:42-44: Dropping empty section \seealso prepare_Rd: read.characters2.Rd:34-36: Dropping empty section \note prepare_Rd: read.characters2.Rd:28-30: Dropping empty section \references prepare_Rd: read.characters2.Rd:43-45: Dropping empty section \examples prepare_Rd: read.continuous.output.Rd:37-39: Dropping empty section \note prepare_Rd: read.continuous.output.Rd:31-33: Dropping empty section \references prepare_Rd: read.continuous.output.Rd:46-48: Dropping empty section \examples prepare_Rd: read.discrete.output.Rd:42-44: Dropping empty section \note prepare_Rd: read.discrete.output.Rd:36-38: Dropping empty section \references prepare_Rd: read.discrete.output.Rd:52-54: Dropping empty section \examples prepare_Rd: read.nexus.block.Rd:43-45: Dropping empty section \note prepare_Rd: read.nexus.block.Rd:37-39: Dropping empty section \references prepare_Rd: read.nexus.block.Rd:49-51: Dropping empty section \seealso prepare_Rd: read.nexus.block.Rd:52-54: Dropping empty section \examples prepare_Rd: read.nexus.simmap.Rd:40-42: Dropping empty section \note prepare_Rd: read.nexus.simmap.Rd:34-36: Dropping empty section \references prepare_Rd: read.nexus.simmap.Rd:46-48: Dropping empty section \seealso prepare_Rd: read.nexus.simmap.Rd:49-51: Dropping empty section \examples prepare_Rd: read.ratetest.output.Rd:37-39: Dropping empty section \note prepare_Rd: read.ratetest.output.Rd:31-33: Dropping empty section \references prepare_Rd: read.ratetest.output.Rd:46-48: Dropping empty section \examples prepare_Rd: read.simmap.Rd:31-33: Dropping empty section \details prepare_Rd: read.simmap.Rd:43-45: Dropping empty section \note prepare_Rd: read.simmap.Rd:37-39: Dropping empty section \references prepare_Rd: read.simmap.Rd:49-51: Dropping empty section \seealso prepare_Rd: read.simmap.new.Rd:29-30: Dropping empty section \value prepare_Rd: read.simmap.new.Rd:37-39: Dropping empty section \note prepare_Rd: read.simmap.new.Rd:34-36: Dropping empty section \author prepare_Rd: read.simmap.new.Rd:31-33: Dropping empty section \references prepare_Rd: read.simmap.new.Rd:43-45: Dropping empty section \seealso prepare_Rd: readBrownie.Rd:33-35: Dropping empty section \note prepare_Rd: readBrownie.Rd:27-29: Dropping empty section \references prepare_Rd: readBrownie.Rd:39-41: Dropping empty section \seealso prepare_Rd: rm.ending.Rd:19-21: Dropping empty section \details prepare_Rd: rm.ending.Rd:22-28: Dropping empty section \value prepare_Rd: rm.ending.Rd:35-37: Dropping empty section \note prepare_Rd: rm.ending.Rd:29-31: Dropping empty section \references prepare_Rd: rm.ending.Rd:41-43: Dropping empty section \seealso prepare_Rd: rm.ending.Rd:44-46: Dropping empty section \examples prepare_Rd: run.analysis.Rd:34-36: Dropping empty section \note prepare_Rd: run.analysis.Rd:28-30: Dropping empty section \references prepare_Rd: run.analysis.Rd:45-47: Dropping empty section \examples prepare_Rd: run.asis.Rd:44-46: Dropping empty section \note prepare_Rd: run.asis.Rd:38-40: Dropping empty section \references prepare_Rd: runCensored.Rd:45-47: Dropping empty section \note prepare_Rd: runCensored.Rd:39-41: Dropping empty section \references prepare_Rd: runDiscrete.Rd:61-63: Dropping empty section \note prepare_Rd: runDiscrete.Rd:55-57: Dropping empty section \references prepare_Rd: runNonCensored.Rd:65-67: Dropping empty section \note prepare_Rd: runNonCensored.Rd:59-61: Dropping empty section \references prepare_Rd: scan.textout.Rd:35-37: Dropping empty section \note prepare_Rd: scan.textout.Rd:29-31: Dropping empty section \references prepare_Rd: scan.textout.Rd:41-43: Dropping empty section \seealso prepare_Rd: scan.treesout.Rd:31-33: Dropping empty section \note prepare_Rd: scan.treesout.Rd:25-27: Dropping empty section \references prepare_Rd: scan.treesout.Rd:37-39: Dropping empty section \seealso prepare_Rd: showBrownie.Rd:14-16: Dropping empty section \details prepare_Rd: showBrownie.Rd:26-28: Dropping empty section \note prepare_Rd: showBrownie.Rd:20-22: Dropping empty section \references prepare_Rd: showBrownie.Rd:32-34: Dropping empty section \seealso prepare_Rd: showBrownie.Rd:35-37: Dropping empty section \examples prepare_Rd: showSubNodes.Rd:31-33: Dropping empty section \note prepare_Rd: showSubNodes.Rd:25-27: Dropping empty section \references prepare_Rd: showSubNodes.Rd:37-39: Dropping empty section \seealso prepare_Rd: strip.Rd:25-27: Dropping empty section \details prepare_Rd: strip.Rd:28-34: Dropping empty section \value prepare_Rd: strip.Rd:41-43: Dropping empty section \note prepare_Rd: strip.Rd:38-40: Dropping empty section \author prepare_Rd: strip.Rd:35-37: Dropping empty section \references prepare_Rd: strip.Rd:47-49: Dropping empty section \seealso prepare_Rd: summaryCont.Rd:37-39: Dropping empty section \note prepare_Rd: summaryCont.Rd:31-33: Dropping empty section \references prepare_Rd: summaryCont.Rd:43-45: Dropping empty section \seealso prepare_Rd: summaryDiscrete.Rd:14-16: Dropping empty section \details prepare_Rd: summaryDiscrete.Rd:17-23: Dropping empty section \value prepare_Rd: summaryDiscrete.Rd:30-32: Dropping empty section \note prepare_Rd: summaryDiscrete.Rd:24-26: Dropping empty section \references prepare_Rd: summaryDiscrete.Rd:36-38: Dropping empty section \seealso prepare_Rd: summaryDiscrete.Rd:39-41: Dropping empty section \examples prepare_Rd: summaryRatetest.Rd:37-39: Dropping empty section \note prepare_Rd: summaryRatetest.Rd:31-33: Dropping empty section \references prepare_Rd: summaryRatetest.Rd:43-45: Dropping empty section \seealso prepare_Rd: taxData.Rd:14-16: Dropping empty section \details prepare_Rd: taxData.Rd:17-23: Dropping empty section \value prepare_Rd: taxData.Rd:30-32: Dropping empty section \note prepare_Rd: taxData.Rd:24-26: Dropping empty section \references prepare_Rd: taxData.Rd:36-38: Dropping empty section \seealso prepare_Rd: taxData.Rd:39-41: Dropping empty section \examples prepare_Rd: taxa.charvect.Rd:37-39: Dropping empty section \note prepare_Rd: taxa.charvect.Rd:31-33: Dropping empty section \references prepare_Rd: taxa.charvect.Rd:43-45: Dropping empty section \seealso prepare_Rd: taxa.mono.Rd:22-24: Dropping empty section \details prepare_Rd: taxa.mono.Rd:25-31: Dropping empty section \value prepare_Rd: taxa.mono.Rd:38-40: Dropping empty section \note prepare_Rd: taxa.mono.Rd:32-34: Dropping empty section \references prepare_Rd: taxa.mono.Rd:44-46: Dropping empty section \seealso prepare_Rd: taxa.mono.Rd:47-49: Dropping empty section \examples prepare_Rd: taxaname.to.taxind.Rd:22-24: Dropping empty section \details prepare_Rd: taxaname.to.taxind.Rd:25-31: Dropping empty section \value prepare_Rd: taxaname.to.taxind.Rd:38-40: Dropping empty section \note prepare_Rd: taxaname.to.taxind.Rd:32-34: Dropping empty section \references prepare_Rd: taxaname.to.taxind.Rd:44-46: Dropping empty section \seealso prepare_Rd: taxaname.to.taxind.Rd:47-49: Dropping empty section \examples prepare_Rd: taxaset.names.Rd:19-21: Dropping empty section \details prepare_Rd: taxaset.names.Rd:31-33: Dropping empty section \note prepare_Rd: taxaset.names.Rd:25-27: Dropping empty section \references prepare_Rd: taxaset.names.Rd:37-39: Dropping empty section \seealso prepare_Rd: taxaset.rename.Rd:19-21: Dropping empty section \details prepare_Rd: taxaset.rename.Rd:22-28: Dropping empty section \value prepare_Rd: taxaset.rename.Rd:35-37: Dropping empty section \note prepare_Rd: taxaset.rename.Rd:29-31: Dropping empty section \references prepare_Rd: taxaset.rename.Rd:41-43: Dropping empty section \seealso prepare_Rd: taxaset.rename.Rd:44-46: Dropping empty section \examples prepare_Rd: taxind.to.dataind.Rd:22-24: Dropping empty section \details prepare_Rd: taxind.to.dataind.Rd:34-36: Dropping empty section \note prepare_Rd: taxind.to.dataind.Rd:28-30: Dropping empty section \references prepare_Rd: taxind.to.dataind.Rd:40-42: Dropping empty section \seealso prepare_Rd: taxind.to.dataind.Rd:43-45: Dropping empty section \examples prepare_Rd: validPhylo4d_ext.Rd:19-21: Dropping empty section \details prepare_Rd: validPhylo4d_ext.Rd:31-33: Dropping empty section \note prepare_Rd: validPhylo4d_ext.Rd:25-27: Dropping empty section \references prepare_Rd: validPhylo4d_ext.Rd:37-39: Dropping empty section \seealso prepare_Rd: validPhylo4d_ext.Rd:40-42: Dropping empty section \examples prepare_Rd: which.mono.Rd:34-36: Dropping empty section \note prepare_Rd: which.mono.Rd:28-30: Dropping empty section \references prepare_Rd: which.para.Rd:34-36: Dropping empty section \note prepare_Rd: which.para.Rd:28-30: Dropping empty section \references prepare_Rd: write.brownie.matrix.Rd:19-21: Dropping empty section \details prepare_Rd: write.brownie.matrix.Rd:22-28: Dropping empty section \value prepare_Rd: write.brownie.matrix.Rd:35-37: Dropping empty section \note prepare_Rd: write.brownie.matrix.Rd:29-31: Dropping empty section \references prepare_Rd: write.brownie.string.Rd:22-24: Dropping empty section \details prepare_Rd: write.brownie.string.Rd:25-31: Dropping empty section \value prepare_Rd: write.brownie.string.Rd:38-40: Dropping empty section \note prepare_Rd: write.brownie.string.Rd:32-34: Dropping empty section \references prepare_Rd: write.brownie.string.Rd:44-46: Dropping empty section \seealso prepare_Rd: write.brownie.string.Rd:47-48: Dropping empty section \examples prepare_Rd: write.brownie.vector.Rd:22-24: Dropping empty section \details prepare_Rd: write.brownie.vector.Rd:34-36: Dropping empty section \note prepare_Rd: write.brownie.vector.Rd:28-30: Dropping empty section \references prepare_Rd: write.nexus.simmap.Rd:42-44: Dropping empty section \note prepare_Rd: write.nexus.simmap.Rd:36-38: Dropping empty section \references prepare_Rd: write.simmap.Rd:31-33: Dropping empty section \details prepare_Rd: write.simmap.Rd:43-45: Dropping empty section \note prepare_Rd: write.simmap.Rd:37-39: Dropping empty section \references * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking data for non-ASCII characters ... OK * checking line endings in C/C++/Fortran sources/headers ... OK * checking line endings in Makefiles ... OK * checking for portable compilation flags in Makevars ... OK * checking for portable use of $BLAS_LIBS ... OK * checking examples ... OK * checking package vignettes in 'inst/doc' ... NOTE LIB: Generator type: mt19937 LIB: Seed = 1302727440 LIB: First value = 2088592780 RCPP: 'd:/temp/RtmpwX9NTh/file56e51e51' Piping commands to brownie objectLIB: preprocessing command: execute 'd:/temp/RtmpwX9NTh/file56e51e51' .. conditioned command is: ;execute 'd:/temp/RtmpwX9NTh/file56e51e51';end; LIB: handle cmd ';execute 'd:/temp/RtmpwX9NTh/file56e51e51';end;' Opening d:/temp/RtmpwX9NTh/file56e51e51... Starting to execute NEXUS file Entering TAXA block...done Entering TREES block...done Entering CHARACTERS block...done (Skipping assumptions block) (Skipping brownie block) Finished executing NEXUS file TREES block contains 10 trees 1 UNTITLED (rooted, weight = 1) 2 UNTITLED (rooted, weight = 1) 3 UNTITLED (rooted, weight = 1) 4 UNTITLED (rooted, weight = 1) 5 UNTITLED (rooted, weight = 1) 6 UNTITLED (rooted, weight = 1) 7 UNTITLED (rooted, weight = 1) 8 UNTITLED (rooted, weight = 1) 9 UNTITLED (rooted, weight = 1) 10 UNTITLED (rooted, weight = 1,default tree) Reading TAXA block... Reading TREES block... Reading CHARACTERS block... Reading ASSUMPTIONS block... Reading BROWNIE block... You have chosen a single rate Brownian motion model Now optimizing with taxset ALL LIB: Generator type: mt19937 LIB: Seed = 1302727441 LIB: First value = 2632907644 Progress: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% |********************************************************************************| Now optimizing with taxset ALL -lnL = 102.58253 AIC = 209.165059 AICc = 209.552156 Ancestral state = 0.0 Optimal rate = 553.175467 +/- 0.000034 Note that +/- reflects imprecision due to numerical optimization LIB: Generator type: mt19937 LIB: Seed = 1302727441 LIB: First value = 2632907644 Progress: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% |********************************************************************************| Now optimizing with taxset ALL -lnL = 102.58253 AIC = 209.165059 AICc = 209.552156 Ancestral state = 0.0 Optimal rate = 553.175467 +/- 0.000034 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409867 AIC = 188.819734 AICc = 189.206831 Ancestral state = 0.0 Optimal rate = 304.077719 +/- 0.000007 Note that +/- reflects imprecision due to numerical optimization LIB: Generator type: mt19937 LIB: Seed = 1302727442 LIB: First value = 3067815321 Progress: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% |********************************************************************************| Now optimizing with taxset ALL -lnL = 102.58253 AIC = 209.165059 AICc = 209.552156 Ancestral state = 0.0 Optimal rate = 553.175467 +/- 0.000034 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409867 AIC = 188.819734 AICc = 189.206831 Ancestral state = 0.0 Optimal rate = 304.077719 +/- 0.000007 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.58259 AIC = 209.165181 AICc = 209.552277 Ancestral state = -0.0 Optimal rate = 407.442934 +/- 0.000026 Note that +/- reflects imprecision due to numerical optimization LIB: Generator type: mt19937 LIB: Seed = 1302727443 LIB: First value = 610317763 Progress: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% |********************************************************************************| Now optimizing with taxset ALL -lnL = 102.58253 AIC = 209.165059 AICc = 209.552156 Ancestral state = 0.0 Optimal rate = 553.175467 +/- 0.000034 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409867 AIC = 188.819734 AICc = 189.206831 Ancestral state = 0.0 Optimal rate = 304.077719 +/- 0.000007 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.58259 AIC = 209.165181 AICc = 209.552277 Ancestral state = -0.0 Optimal rate = 407.442934 +/- 0.000026 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.40986 AIC = 188.81972 AICc = 189.206817 Ancestral state = 0.0 Optimal rate = 223.968413 +/- 0.000006 Note that +/- reflects imprecision due to numerical optimization LIB: Generator type: mt19937 LIB: Seed = 1302727444 LIB: First value = 424910164 Progress: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% |********************************************************************************| Now optimizing with taxset ALL -lnL = 102.58253 AIC = 209.165059 AICc = 209.552156 Ancestral state = 0.0 Optimal rate = 553.175467 +/- 0.000034 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409867 AIC = 188.819734 AICc = 189.206831 Ancestral state = 0.0 Optimal rate = 304.077719 +/- 0.000007 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.58259 AIC = 209.165181 AICc = 209.552277 Ancestral state = -0.0 Optimal rate = 407.442934 +/- 0.000026 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.40986 AIC = 188.81972 AICc = 189.206817 Ancestral state = 0.0 Optimal rate = 223.968413 +/- 0.000006 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582641 AIC = 209.165282 AICc = 209.552379 Ancestral state = -0.0 Optimal rate = 512.373283 +/- 0.000029 Note that +/- reflects imprecision due to numerical optimization LIB: Generator type: mt19937 LIB: Seed = 1302727444 LIB: First value = 424910164 Progress: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% |********************************************************************************| Now optimizing with taxset ALL -lnL = 102.58253 AIC = 209.165059 AICc = 209.552156 Ancestral state = 0.0 Optimal rate = 553.175467 +/- 0.000034 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409867 AIC = 188.819734 AICc = 189.206831 Ancestral state = 0.0 Optimal rate = 304.077719 +/- 0.000007 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.58259 AIC = 209.165181 AICc = 209.552277 Ancestral state = -0.0 Optimal rate = 407.442934 +/- 0.000026 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.40986 AIC = 188.81972 AICc = 189.206817 Ancestral state = 0.0 Optimal rate = 223.968413 +/- 0.000006 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582641 AIC = 209.165282 AICc = 209.552379 Ancestral state = -0.0 Optimal rate = 512.373283 +/- 0.000029 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409857 AIC = 188.819714 AICc = 189.206811 Ancestral state = 0.0 Optimal rate = 281.646941 +/- 0.000005 Note that +/- reflects imprecision due to numerical optimization LIB: Generator type: mt19937 LIB: Seed = 1302727446 LIB: First value = 4072837392 Progress: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% |********************************************************************************| Now optimizing with taxset ALL -lnL = 102.58253 AIC = 209.165059 AICc = 209.552156 Ancestral state = 0.0 Optimal rate = 553.175467 +/- 0.000034 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409867 AIC = 188.819734 AICc = 189.206831 Ancestral state = 0.0 Optimal rate = 304.077719 +/- 0.000007 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.58259 AIC = 209.165181 AICc = 209.552277 Ancestral state = -0.0 Optimal rate = 407.442934 +/- 0.000026 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.40986 AIC = 188.81972 AICc = 189.206817 Ancestral state = 0.0 Optimal rate = 223.968413 +/- 0.000006 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582641 AIC = 209.165282 AICc = 209.552379 Ancestral state = -0.0 Optimal rate = 512.373283 +/- 0.000029 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409857 AIC = 188.819714 AICc = 189.206811 Ancestral state = 0.0 Optimal rate = 281.646941 +/- 0.000005 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582653 AIC = 209.165305 AICc = 209.552402 Ancestral state = -0.0 Optimal rate = 1725.471357 +/- 0.00006 Note that +/- reflects imprecision due to numerical optimization LIB: Generator type: mt19937 LIB: Seed = 1302727446 LIB: First value = 4072837392 Progress: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% |********************************************************************************| Now optimizing with taxset ALL -lnL = 102.58253 AIC = 209.165059 AICc = 209.552156 Ancestral state = 0.0 Optimal rate = 553.175467 +/- 0.000034 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409867 AIC = 188.819734 AICc = 189.206831 Ancestral state = 0.0 Optimal rate = 304.077719 +/- 0.000007 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.58259 AIC = 209.165181 AICc = 209.552277 Ancestral state = -0.0 Optimal rate = 407.442934 +/- 0.000026 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.40986 AIC = 188.81972 AICc = 189.206817 Ancestral state = 0.0 Optimal rate = 223.968413 +/- 0.000006 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582641 AIC = 209.165282 AICc = 209.552379 Ancestral state = -0.0 Optimal rate = 512.373283 +/- 0.000029 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409857 AIC = 188.819714 AICc = 189.206811 Ancestral state = 0.0 Optimal rate = 281.646941 +/- 0.000005 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582653 AIC = 209.165305 AICc = 209.552402 Ancestral state = -0.0 Optimal rate = 1725.471357 +/- 0.00006 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409862 AIC = 188.819725 AICc = 189.206822 Ancestral state = 0.0 Optimal rate = 948.475637 +/- 0.000017 Note that +/- reflects imprecision due to numerical optimization LIB: Generator type: mt19937 LIB: Seed = 1302727448 LIB: First value = 1404234004 Progress: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% |********************************************************************************| Now optimizing with taxset ALL -lnL = 102.58253 AIC = 209.165059 AICc = 209.552156 Ancestral state = 0.0 Optimal rate = 553.175467 +/- 0.000034 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409867 AIC = 188.819734 AICc = 189.206831 Ancestral state = 0.0 Optimal rate = 304.077719 +/- 0.000007 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.58259 AIC = 209.165181 AICc = 209.552277 Ancestral state = -0.0 Optimal rate = 407.442934 +/- 0.000026 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.40986 AIC = 188.81972 AICc = 189.206817 Ancestral state = 0.0 Optimal rate = 223.968413 +/- 0.000006 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582641 AIC = 209.165282 AICc = 209.552379 Ancestral state = -0.0 Optimal rate = 512.373283 +/- 0.000029 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409857 AIC = 188.819714 AICc = 189.206811 Ancestral state = 0.0 Optimal rate = 281.646941 +/- 0.000005 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582653 AIC = 209.165305 AICc = 209.552402 Ancestral state = -0.0 Optimal rate = 1725.471357 +/- 0.00006 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409862 AIC = 188.819725 AICc = 189.206822 Ancestral state = 0.0 Optimal rate = 948.475637 +/- 0.000017 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582565 AIC = 209.16513 AICc = 209.552227 Ancestral state = -0.0 Optimal rate = 365.943009 +/- 0.000018 Note that +/- reflects imprecision due to numerical optimization LIB: Generator type: mt19937 LIB: Seed = 1302727449 LIB: First value = 3084626600 Progress: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% |********************************************************************************| Now optimizing with taxset ALL -lnL = 102.58253 AIC = 209.165059 AICc = 209.552156 Ancestral state = 0.0 Optimal rate = 553.175467 +/- 0.000034 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409867 AIC = 188.819734 AICc = 189.206831 Ancestral state = 0.0 Optimal rate = 304.077719 +/- 0.000007 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.58259 AIC = 209.165181 AICc = 209.552277 Ancestral state = -0.0 Optimal rate = 407.442934 +/- 0.000026 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.40986 AIC = 188.81972 AICc = 189.206817 Ancestral state = 0.0 Optimal rate = 223.968413 +/- 0.000006 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582641 AIC = 209.165282 AICc = 209.552379 Ancestral state = -0.0 Optimal rate = 512.373283 +/- 0.000029 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409857 AIC = 188.819714 AICc = 189.206811 Ancestral state = 0.0 Optimal rate = 281.646941 +/- 0.000005 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582653 AIC = 209.165305 AICc = 209.552402 Ancestral state = -0.0 Optimal rate = 1725.471357 +/- 0.00006 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409862 AIC = 188.819725 AICc = 189.206822 Ancestral state = 0.0 Optimal rate = 948.475637 +/- 0.000017 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582565 AIC = 209.16513 AICc = 209.552227 Ancestral state = -0.0 Optimal rate = 365.943009 +/- 0.000018 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409854 AIC = 188.819707 AICc = 189.206804 Ancestral state = -0.0 Optimal rate = 201.156416 +/- 0.000004 Note that +/- reflects imprecision due to numerical optimization LIB: Generator type: mt19937 LIB: Seed = 1302727450 LIB: First value = 2540321655 Progress: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% |********************************************************************************| Now optimizing with taxset ALL -lnL = 102.58253 AIC = 209.165059 AICc = 209.552156 Ancestral state = 0.0 Optimal rate = 553.175467 +/- 0.000034 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409867 AIC = 188.819734 AICc = 189.206831 Ancestral state = 0.0 Optimal rate = 304.077719 +/- 0.000007 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.58259 AIC = 209.165181 AICc = 209.552277 Ancestral state = -0.0 Optimal rate = 407.442934 +/- 0.000026 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.40986 AIC = 188.81972 AICc = 189.206817 Ancestral state = 0.0 Optimal rate = 223.968413 +/- 0.000006 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582641 AIC = 209.165282 AICc = 209.552379 Ancestral state = -0.0 Optimal rate = 512.373283 +/- 0.000029 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409857 AIC = 188.819714 AICc = 189.206811 Ancestral state = 0.0 Optimal rate = 281.646941 +/- 0.000005 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582653 AIC = 209.165305 AICc = 209.552402 Ancestral state = -0.0 Optimal rate = 1725.471357 +/- 0.00006 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409862 AIC = 188.819725 AICc = 189.206822 Ancestral state = 0.0 Optimal rate = 948.475637 +/- 0.000017 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582565 AIC = 209.16513 AICc = 209.552227 Ancestral state = -0.0 Optimal rate = 365.943009 +/- 0.000018 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409854 AIC = 188.819707 AICc = 189.206804 Ancestral state = -0.0 Optimal rate = 201.156416 +/- 0.000004 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582495 AIC = 209.164991 AICc = 209.552087 Ancestral state = 0.0 Optimal rate = 1274.401489 +/- 0.000065 Note that +/- reflects imprecision due to numerical optimization LIB: Generator type: mt19937 LIB: Seed = 1302727450 LIB: First value = 2540321655 Progress: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% |********************************************************************************| Now optimizing with taxset ALL -lnL = 102.58253 AIC = 209.165059 AICc = 209.552156 Ancestral state = 0.0 Optimal rate = 553.175467 +/- 0.000034 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409867 AIC = 188.819734 AICc = 189.206831 Ancestral state = 0.0 Optimal rate = 304.077719 +/- 0.000007 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.58259 AIC = 209.165181 AICc = 209.552277 Ancestral state = -0.0 Optimal rate = 407.442934 +/- 0.000026 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.40986 AIC = 188.81972 AICc = 189.206817 Ancestral state = 0.0 Optimal rate = 223.968413 +/- 0.000006 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582641 AIC = 209.165282 AICc = 209.552379 Ancestral state = -0.0 Optimal rate = 512.373283 +/- 0.000029 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409857 AIC = 188.819714 AICc = 189.206811 Ancestral state = 0.0 Optimal rate = 281.646941 +/- 0.000005 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582653 AIC = 209.165305 AICc = 209.552402 Ancestral state = -0.0 Optimal rate = 1725.471357 +/- 0.00006 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409862 AIC = 188.819725 AICc = 189.206822 Ancestral state = 0.0 Optimal rate = 948.475637 +/- 0.000017 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582565 AIC = 209.16513 AICc = 209.552227 Ancestral state = -0.0 Optimal rate = 365.943009 +/- 0.000018 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409854 AIC = 188.819707 AICc = 189.206804 Ancestral state = -0.0 Optimal rate = 201.156416 +/- 0.000004 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582495 AIC = 209.164991 AICc = 209.552087 Ancestral state = 0.0 Optimal rate = 1274.401489 +/- 0.000065 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409865 AIC = 188.819729 AICc = 189.206826 Ancestral state = 0.0 Optimal rate = 700.533329 +/- 0.000012 Note that +/- reflects imprecision due to numerical optimization LIB: Generator type: mt19937 LIB: Seed = 1302727452 LIB: First value = 971513941 Progress: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% |********************************************************************************| Now optimizing with taxset ALL -lnL = 102.58253 AIC = 209.165059 AICc = 209.552156 Ancestral state = 0.0 Optimal rate = 553.175467 +/- 0.000034 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409867 AIC = 188.819734 AICc = 189.206831 Ancestral state = 0.0 Optimal rate = 304.077719 +/- 0.000007 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.58259 AIC = 209.165181 AICc = 209.552277 Ancestral state = -0.0 Optimal rate = 407.442934 +/- 0.000026 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.40986 AIC = 188.81972 AICc = 189.206817 Ancestral state = 0.0 Optimal rate = 223.968413 +/- 0.000006 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582641 AIC = 209.165282 AICc = 209.552379 Ancestral state = -0.0 Optimal rate = 512.373283 +/- 0.000029 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409857 AIC = 188.819714 AICc = 189.206811 Ancestral state = 0.0 Optimal rate = 281.646941 +/- 0.000005 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582653 AIC = 209.165305 AICc = 209.552402 Ancestral state = -0.0 Optimal rate = 1725.471357 +/- 0.00006 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409862 AIC = 188.819725 AICc = 189.206822 Ancestral state = 0.0 Optimal rate = 948.475637 +/- 0.000017 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582565 AIC = 209.16513 AICc = 209.552227 Ancestral state = -0.0 Optimal rate = 365.943009 +/- 0.000018 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409854 AIC = 188.819707 AICc = 189.206804 Ancestral state = -0.0 Optimal rate = 201.156416 +/- 0.000004 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582495 AIC = 209.164991 AICc = 209.552087 Ancestral state = 0.0 Optimal rate = 1274.401489 +/- 0.000065 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409865 AIC = 188.819729 AICc = 189.206826 Ancestral state = 0.0 Optimal rate = 700.533329 +/- 0.000012 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582564 AIC = 209.165128 AICc = 209.552224 Ancestral state = -0.0 Optimal rate = 596.175574 +/- 0.000024 Note that +/- reflects imprecision due to numerical optimization LIB: Generator type: mt19937 LIB: Seed = 1302727453 LIB: First value = 3232019104 Progress: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% |********************************************************************************| Now optimizing with taxset ALL -lnL = 102.58253 AIC = 209.165059 AICc = 209.552156 Ancestral state = 0.0 Optimal rate = 553.175467 +/- 0.000034 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409867 AIC = 188.819734 AICc = 189.206831 Ancestral state = 0.0 Optimal rate = 304.077719 +/- 0.000007 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.58259 AIC = 209.165181 AICc = 209.552277 Ancestral state = -0.0 Optimal rate = 407.442934 +/- 0.000026 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.40986 AIC = 188.81972 AICc = 189.206817 Ancestral state = 0.0 Optimal rate = 223.968413 +/- 0.000006 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582641 AIC = 209.165282 AICc = 209.552379 Ancestral state = -0.0 Optimal rate = 512.373283 +/- 0.000029 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409857 AIC = 188.819714 AICc = 189.206811 Ancestral state = 0.0 Optimal rate = 281.646941 +/- 0.000005 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582653 AIC = 209.165305 AICc = 209.552402 Ancestral state = -0.0 Optimal rate = 1725.471357 +/- 0.00006 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409862 AIC = 188.819725 AICc = 189.206822 Ancestral state = 0.0 Optimal rate = 948.475637 +/- 0.000017 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582565 AIC = 209.16513 AICc = 209.552227 Ancestral state = -0.0 Optimal rate = 365.943009 +/- 0.000018 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409854 AIC = 188.819707 AICc = 189.206804 Ancestral state = -0.0 Optimal rate = 201.156416 +/- 0.000004 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582495 AIC = 209.164991 AICc = 209.552087 Ancestral state = 0.0 Optimal rate = 1274.401489 +/- 0.000065 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409865 AIC = 188.819729 AICc = 189.206826 Ancestral state = 0.0 Optimal rate = 700.533329 +/- 0.000012 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582564 AIC = 209.165128 AICc = 209.552224 Ancestral state = -0.0 Optimal rate = 596.175574 +/- 0.000024 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409859 AIC = 188.819718 AICc = 189.206814 Ancestral state = 0.0 Optimal rate = 327.71383 +/- 0.000006 Note that +/- reflects imprecision due to numerical optimization LIB: Generator type: mt19937 LIB: Seed = 1302727454 LIB: First value = 3054148760 Progress: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% |********************************************************************************| Now optimizing with taxset ALL -lnL = 102.58253 AIC = 209.165059 AICc = 209.552156 Ancestral state = 0.0 Optimal rate = 553.175467 +/- 0.000034 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409867 AIC = 188.819734 AICc = 189.206831 Ancestral state = 0.0 Optimal rate = 304.077719 +/- 0.000007 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.58259 AIC = 209.165181 AICc = 209.552277 Ancestral state = -0.0 Optimal rate = 407.442934 +/- 0.000026 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.40986 AIC = 188.81972 AICc = 189.206817 Ancestral state = 0.0 Optimal rate = 223.968413 +/- 0.000006 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582641 AIC = 209.165282 AICc = 209.552379 Ancestral state = -0.0 Optimal rate = 512.373283 +/- 0.000029 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409857 AIC = 188.819714 AICc = 189.206811 Ancestral state = 0.0 Optimal rate = 281.646941 +/- 0.000005 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582653 AIC = 209.165305 AICc = 209.552402 Ancestral state = -0.0 Optimal rate = 1725.471357 +/- 0.00006 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409862 AIC = 188.819725 AICc = 189.206822 Ancestral state = 0.0 Optimal rate = 948.475637 +/- 0.000017 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582565 AIC = 209.16513 AICc = 209.552227 Ancestral state = -0.0 Optimal rate = 365.943009 +/- 0.000018 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409854 AIC = 188.819707 AICc = 189.206804 Ancestral state = -0.0 Optimal rate = 201.156416 +/- 0.000004 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582495 AIC = 209.164991 AICc = 209.552087 Ancestral state = 0.0 Optimal rate = 1274.401489 +/- 0.000065 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409865 AIC = 188.819729 AICc = 189.206826 Ancestral state = 0.0 Optimal rate = 700.533329 +/- 0.000012 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582564 AIC = 209.165128 AICc = 209.552224 Ancestral state = -0.0 Optimal rate = 596.175574 +/- 0.000024 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409859 AIC = 188.819718 AICc = 189.206814 Ancestral state = 0.0 Optimal rate = 327.71383 +/- 0.000006 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582526 AIC = 209.165052 AICc = 209.552149 Ancestral state = -0.0 Optimal rate = 858.666895 +/- 0.000048 Note that +/- reflects imprecision due to numerical optimization LIB: Generator type: mt19937 LIB: Seed = 1302727454 LIB: First value = 3054148760 Progress: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% |********************************************************************************| Now optimizing with taxset ALL -lnL = 102.58253 AIC = 209.165059 AICc = 209.552156 Ancestral state = 0.0 Optimal rate = 553.175467 +/- 0.000034 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409867 AIC = 188.819734 AICc = 189.206831 Ancestral state = 0.0 Optimal rate = 304.077719 +/- 0.000007 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.58259 AIC = 209.165181 AICc = 209.552277 Ancestral state = -0.0 Optimal rate = 407.442934 +/- 0.000026 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.40986 AIC = 188.81972 AICc = 189.206817 Ancestral state = 0.0 Optimal rate = 223.968413 +/- 0.000006 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582641 AIC = 209.165282 AICc = 209.552379 Ancestral state = -0.0 Optimal rate = 512.373283 +/- 0.000029 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409857 AIC = 188.819714 AICc = 189.206811 Ancestral state = 0.0 Optimal rate = 281.646941 +/- 0.000005 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582653 AIC = 209.165305 AICc = 209.552402 Ancestral state = -0.0 Optimal rate = 1725.471357 +/- 0.00006 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409862 AIC = 188.819725 AICc = 189.206822 Ancestral state = 0.0 Optimal rate = 948.475637 +/- 0.000017 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582565 AIC = 209.16513 AICc = 209.552227 Ancestral state = -0.0 Optimal rate = 365.943009 +/- 0.000018 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409854 AIC = 188.819707 AICc = 189.206804 Ancestral state = -0.0 Optimal rate = 201.156416 +/- 0.000004 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582495 AIC = 209.164991 AICc = 209.552087 Ancestral state = 0.0 Optimal rate = 1274.401489 +/- 0.000065 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409865 AIC = 188.819729 AICc = 189.206826 Ancestral state = 0.0 Optimal rate = 700.533329 +/- 0.000012 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582564 AIC = 209.165128 AICc = 209.552224 Ancestral state = -0.0 Optimal rate = 596.175574 +/- 0.000024 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409859 AIC = 188.819718 AICc = 189.206814 Ancestral state = 0.0 Optimal rate = 327.71383 +/- 0.000006 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582526 AIC = 209.165052 AICc = 209.552149 Ancestral state = -0.0 Optimal rate = 858.666895 +/- 0.000048 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409861 AIC = 188.819722 AICc = 189.206819 Ancestral state = 0.0 Optimal rate = 472.004733 +/- 0.000013 Note that +/- reflects imprecision due to numerical optimization LIB: Generator type: mt19937 LIB: Seed = 1302727456 LIB: First value = 3899633531 Progress: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% |********************************************************************************| Now optimizing with taxset ALL -lnL = 102.58253 AIC = 209.165059 AICc = 209.552156 Ancestral state = 0.0 Optimal rate = 553.175467 +/- 0.000034 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409867 AIC = 188.819734 AICc = 189.206831 Ancestral state = 0.0 Optimal rate = 304.077719 +/- 0.000007 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.58259 AIC = 209.165181 AICc = 209.552277 Ancestral state = -0.0 Optimal rate = 407.442934 +/- 0.000026 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.40986 AIC = 188.81972 AICc = 189.206817 Ancestral state = 0.0 Optimal rate = 223.968413 +/- 0.000006 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582641 AIC = 209.165282 AICc = 209.552379 Ancestral state = -0.0 Optimal rate = 512.373283 +/- 0.000029 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409857 AIC = 188.819714 AICc = 189.206811 Ancestral state = 0.0 Optimal rate = 281.646941 +/- 0.000005 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582653 AIC = 209.165305 AICc = 209.552402 Ancestral state = -0.0 Optimal rate = 1725.471357 +/- 0.00006 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409862 AIC = 188.819725 AICc = 189.206822 Ancestral state = 0.0 Optimal rate = 948.475637 +/- 0.000017 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582565 AIC = 209.16513 AICc = 209.552227 Ancestral state = -0.0 Optimal rate = 365.943009 +/- 0.000018 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409854 AIC = 188.819707 AICc = 189.206804 Ancestral state = -0.0 Optimal rate = 201.156416 +/- 0.000004 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582495 AIC = 209.164991 AICc = 209.552087 Ancestral state = 0.0 Optimal rate = 1274.401489 +/- 0.000065 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409865 AIC = 188.819729 AICc = 189.206826 Ancestral state = 0.0 Optimal rate = 700.533329 +/- 0.000012 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582564 AIC = 209.165128 AICc = 209.552224 Ancestral state = -0.0 Optimal rate = 596.175574 +/- 0.000024 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409859 AIC = 188.819718 AICc = 189.206814 Ancestral state = 0.0 Optimal rate = 327.71383 +/- 0.000006 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582526 AIC = 209.165052 AICc = 209.552149 Ancestral state = -0.0 Optimal rate = 858.666895 +/- 0.000048 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409861 AIC = 188.819722 AICc = 189.206819 Ancestral state = 0.0 Optimal rate = 472.004733 +/- 0.000013 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582562 AIC = 209.165124 AICc = 209.552221 Ancestral state = 0.0 Optimal rate = 539.373286 +/- 0.000024 Note that +/- reflects imprecision due to numerical optimization LIB: Generator type: mt19937 LIB: Seed = 1302727457 LIB: First value = 1517420483 Progress: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% |********************************************************************************| Now optimizing with taxset ALL -lnL = 102.58253 AIC = 209.165059 AICc = 209.552156 Ancestral state = 0.0 Optimal rate = 553.175467 +/- 0.000034 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409867 AIC = 188.819734 AICc = 189.206831 Ancestral state = 0.0 Optimal rate = 304.077719 +/- 0.000007 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.58259 AIC = 209.165181 AICc = 209.552277 Ancestral state = -0.0 Optimal rate = 407.442934 +/- 0.000026 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.40986 AIC = 188.81972 AICc = 189.206817 Ancestral state = 0.0 Optimal rate = 223.968413 +/- 0.000006 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582641 AIC = 209.165282 AICc = 209.552379 Ancestral state = -0.0 Optimal rate = 512.373283 +/- 0.000029 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409857 AIC = 188.819714 AICc = 189.206811 Ancestral state = 0.0 Optimal rate = 281.646941 +/- 0.000005 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582653 AIC = 209.165305 AICc = 209.552402 Ancestral state = -0.0 Optimal rate = 1725.471357 +/- 0.00006 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409862 AIC = 188.819725 AICc = 189.206822 Ancestral state = 0.0 Optimal rate = 948.475637 +/- 0.000017 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582565 AIC = 209.16513 AICc = 209.552227 Ancestral state = -0.0 Optimal rate = 365.943009 +/- 0.000018 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409854 AIC = 188.819707 AICc = 189.206804 Ancestral state = -0.0 Optimal rate = 201.156416 +/- 0.000004 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582495 AIC = 209.164991 AICc = 209.552087 Ancestral state = 0.0 Optimal rate = 1274.401489 +/- 0.000065 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409865 AIC = 188.819729 AICc = 189.206826 Ancestral state = 0.0 Optimal rate = 700.533329 +/- 0.000012 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582564 AIC = 209.165128 AICc = 209.552224 Ancestral state = -0.0 Optimal rate = 596.175574 +/- 0.000024 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409859 AIC = 188.819718 AICc = 189.206814 Ancestral state = 0.0 Optimal rate = 327.71383 +/- 0.000006 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582526 AIC = 209.165052 AICc = 209.552149 Ancestral state = -0.0 Optimal rate = 858.666895 +/- 0.000048 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409861 AIC = 188.819722 AICc = 189.206819 Ancestral state = 0.0 Optimal rate = 472.004733 +/- 0.000013 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582562 AIC = 209.165124 AICc = 209.552221 Ancestral state = 0.0 Optimal rate = 539.373286 +/- 0.000024 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409855 AIC = 188.81971 AICc = 189.206807 Ancestral state = 0.0 Optimal rate = 296.489959 +/- 0.000009 Note that +/- reflects imprecision due to numerical optimization LIB: Generator type: mt19937 LIB: Seed = 1302727458 LIB: First value = 2546716026 Progress: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% |********************************************************************************| Now optimizing with taxset ALL -lnL = 102.58253 AIC = 209.165059 AICc = 209.552156 Ancestral state = 0.0 Optimal rate = 553.175467 +/- 0.000034 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409867 AIC = 188.819734 AICc = 189.206831 Ancestral state = 0.0 Optimal rate = 304.077719 +/- 0.000007 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.58259 AIC = 209.165181 AICc = 209.552277 Ancestral state = -0.0 Optimal rate = 407.442934 +/- 0.000026 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.40986 AIC = 188.81972 AICc = 189.206817 Ancestral state = 0.0 Optimal rate = 223.968413 +/- 0.000006 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582641 AIC = 209.165282 AICc = 209.552379 Ancestral state = -0.0 Optimal rate = 512.373283 +/- 0.000029 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409857 AIC = 188.819714 AICc = 189.206811 Ancestral state = 0.0 Optimal rate = 281.646941 +/- 0.000005 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582653 AIC = 209.165305 AICc = 209.552402 Ancestral state = -0.0 Optimal rate = 1725.471357 +/- 0.00006 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409862 AIC = 188.819725 AICc = 189.206822 Ancestral state = 0.0 Optimal rate = 948.475637 +/- 0.000017 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582565 AIC = 209.16513 AICc = 209.552227 Ancestral state = -0.0 Optimal rate = 365.943009 +/- 0.000018 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409854 AIC = 188.819707 AICc = 189.206804 Ancestral state = -0.0 Optimal rate = 201.156416 +/- 0.000004 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582495 AIC = 209.164991 AICc = 209.552087 Ancestral state = 0.0 Optimal rate = 1274.401489 +/- 0.000065 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409865 AIC = 188.819729 AICc = 189.206826 Ancestral state = 0.0 Optimal rate = 700.533329 +/- 0.000012 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582564 AIC = 209.165128 AICc = 209.552224 Ancestral state = -0.0 Optimal rate = 596.175574 +/- 0.000024 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409859 AIC = 188.819718 AICc = 189.206814 Ancestral state = 0.0 Optimal rate = 327.71383 +/- 0.000006 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582526 AIC = 209.165052 AICc = 209.552149 Ancestral state = -0.0 Optimal rate = 858.666895 +/- 0.000048 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409861 AIC = 188.819722 AICc = 189.206819 Ancestral state = 0.0 Optimal rate = 472.004733 +/- 0.000013 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582562 AIC = 209.165124 AICc = 209.552221 Ancestral state = 0.0 Optimal rate = 539.373286 +/- 0.000024 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409855 AIC = 188.81971 AICc = 189.206807 Ancestral state = 0.0 Optimal rate = 296.489959 +/- 0.000009 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582569 AIC = 209.165138 AICc = 209.552235 Ancestral state = -0.0 Optimal rate = 1120.318891 +/- 0.000039 Note that +/- reflects imprecision due to numerical optimization LIB: Generator type: mt19937 LIB: Seed = 1302727458 LIB: First value = 2546716026 Progress: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% |********************************************************************************| Now optimizing with taxset ALL -lnL = 102.58253 AIC = 209.165059 AICc = 209.552156 Ancestral state = 0.0 Optimal rate = 553.175467 +/- 0.000034 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409867 AIC = 188.819734 AICc = 189.206831 Ancestral state = 0.0 Optimal rate = 304.077719 +/- 0.000007 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.58259 AIC = 209.165181 AICc = 209.552277 Ancestral state = -0.0 Optimal rate = 407.442934 +/- 0.000026 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.40986 AIC = 188.81972 AICc = 189.206817 Ancestral state = 0.0 Optimal rate = 223.968413 +/- 0.000006 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582641 AIC = 209.165282 AICc = 209.552379 Ancestral state = -0.0 Optimal rate = 512.373283 +/- 0.000029 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409857 AIC = 188.819714 AICc = 189.206811 Ancestral state = 0.0 Optimal rate = 281.646941 +/- 0.000005 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582653 AIC = 209.165305 AICc = 209.552402 Ancestral state = -0.0 Optimal rate = 1725.471357 +/- 0.00006 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409862 AIC = 188.819725 AICc = 189.206822 Ancestral state = 0.0 Optimal rate = 948.475637 +/- 0.000017 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582565 AIC = 209.16513 AICc = 209.552227 Ancestral state = -0.0 Optimal rate = 365.943009 +/- 0.000018 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409854 AIC = 188.819707 AICc = 189.206804 Ancestral state = -0.0 Optimal rate = 201.156416 +/- 0.000004 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582495 AIC = 209.164991 AICc = 209.552087 Ancestral state = 0.0 Optimal rate = 1274.401489 +/- 0.000065 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409865 AIC = 188.819729 AICc = 189.206826 Ancestral state = 0.0 Optimal rate = 700.533329 +/- 0.000012 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582564 AIC = 209.165128 AICc = 209.552224 Ancestral state = -0.0 Optimal rate = 596.175574 +/- 0.000024 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409859 AIC = 188.819718 AICc = 189.206814 Ancestral state = 0.0 Optimal rate = 327.71383 +/- 0.000006 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582526 AIC = 209.165052 AICc = 209.552149 Ancestral state = -0.0 Optimal rate = 858.666895 +/- 0.000048 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409861 AIC = 188.819722 AICc = 189.206819 Ancestral state = 0.0 Optimal rate = 472.004733 +/- 0.000013 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582562 AIC = 209.165124 AICc = 209.552221 Ancestral state = 0.0 Optimal rate = 539.373286 +/- 0.000024 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409855 AIC = 188.81971 AICc = 189.206807 Ancestral state = 0.0 Optimal rate = 296.489959 +/- 0.000009 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582569 AIC = 209.165138 AICc = 209.552235 Ancestral state = -0.0 Optimal rate = 1120.318891 +/- 0.000039 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.40986 AIC = 188.819721 AICc = 189.206817 Ancestral state = -0.0 Optimal rate = 615.831887 +/- 0.000009 Note that +/- reflects imprecision due to numerical optimization You have chosen Brownian motion with one rate parameter per state Now optimizing with taxset ALL LIB: Generator type: mt19937 LIB: Seed = 1302727461 LIB: First value = 2903988330 Progress: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% |********************************************************************************| -lnL = 102.50545 AIC = 211.010899 AICc = 211.810899 Ancestral state = 0.16698 +/- 0.000001 Rate in state 0 = 464.475533 +/- 0.000045 Rate in state 1 = 579.916676 +/- 0.000035 LIB: Generator type: mt19937 LIB: Seed = 1302727463 LIB: First value = 3344018096 Progress: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% |********************************************************************************| -lnL = 89.254264 AIC = 184.508528 AICc = 185.308528 Ancestral state = 1.672717 +/- 0.0 Rate in state 0 = 48.509065 +/- 0.000003 Rate in state 1 = 389.34434 +/- 0.000011 LIB: Generator type: mt19937 LIB: Seed = 1302727466 LIB: First value = 1410584868 Progress: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% |********************************************************************************| -lnL = 102.419208 AIC = 210.838417 AICc = 211.638417 Ancestral state = 0.174772 +/- 0.000001 Rate in state 0 = 316.96875 +/- 0.000017 Rate in state 1 = 437.333142 +/- 0.000017 LIB: Generator type: mt19937 LIB: Seed = 1302727468 LIB: First value = 1433307345 Progress: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% |********************************************************************************| -lnL = 89.407904 AIC = 184.815808 AICc = 185.615808 Ancestral state = 1.805435 +/- 0.0 Rate in state 0 = 46.421966 +/- 0.000002 Rate in state 1 = 289.212085 +/- 0.000007 LIB: Generator type: mt19937 LIB: Seed = 1302727471 LIB: First value = 3466328654 Progress: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% |********************************************************************************| -lnL = 102.096225 AIC = 210.19245 AICc = 210.99245 Ancestral state = 0.339608 +/- 0.000001 Rate in state 0 = 345.323825 +/- 0.000025 Rate in state 1 = 583.688283 +/- 0.000019 LIB: Generator type: mt19937 LIB: Seed = 1302727474 LIB: First value = 494466172 Progress: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% |********************************************************************************| -lnL = 88.816161 AIC = 183.632321 AICc = 184.432321 Ancestral state = 2.018542 +/- 0.0 Rate in state 0 = 62.912363 +/- 0.000003 Rate in state 1 = 383.826341 +/- 0.000007 LIB: Generator type: mt19937 LIB: Seed = 1302727477 LIB: First value = 2797064562 Progress: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% |********************************************************************************| -lnL = 102.443898 AIC = 210.887796 AICc = 211.687796 Ancestral state = 0.174469 +/- 0.000001 Rate in state 0 = 1365.815895 +/- 0.000104 Rate in state 1 = 1840.154442 +/- 0.000092 LIB: Generator type: mt19937 LIB: Seed = 1302727479 LIB: First value = 2967194247 Progress: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% |********************************************************************************| -lnL = 89.378442 AIC = 184.756885 AICc = 185.556885 Ancestral state = 1.897972 +/- 0.0 Rate in state 0 = 192.521305 +/- 0.000009 Rate in state 1 = 1213.884622 +/- 0.000016 LIB: Generator type: mt19937 LIB: Seed = 1302727482 LIB: First value = 2318368694 Progress: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% |********************************************************************************| -lnL = 102.561873 AIC = 211.123746 AICc = 211.923746 Ancestral state = 0.091665 +/- 0.000001 Rate in state 0 = 333.333099 +/- 0.000022 Rate in state 1 = 374.619234 +/- 0.000015 LIB: Generator type: mt19937 LIB: Seed = 1302727484 LIB: First value = 3423587287 Progress: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% |********************************************************************************| -lnL = 89.341861 AIC = 184.683723 AICc = 185.483723 Ancestral state = 0.775709 +/- 0.0 Rate in state 0 = 32.408445 +/- 0.000002 Rate in state 1 = 242.161631 +/- 0.000004 LIB: Generator type: mt19937 LIB: Seed = 1302727487 LIB: First value = 3379164416 Progress: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% |********************************************************************************| -lnL = 102.212816 AIC = 210.425632 AICc = 211.225632 Ancestral state = 0.263325 +/- 0.000001 Rate in state 0 = 891.261852 +/- 0.000083 Rate in state 1 = 1427.791161 +/- 0.000053 LIB: Generator type: mt19937 LIB: Seed = 1302727489 LIB: First value = 1883118147 Progress: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% |********************************************************************************| ---------------------------------------------------------------------------- WARNING: Out of 15 optimization starts, 15 were stopped by hitting the maximum # of iterations. This means that those replicates may not even have hit the local maximum. You can increase the maximum number of iterations or decrease the precision with the NumOpt command. You could also consider increasing the number of random starts using that same command. If this happened on a small proportion of replicates, though, or if the precision (below) is good enough, don't worry about it. ---------------------------------------------------------------------------- -lnL = 89.226381 AIC = 184.452762 AICc = 185.252762 Ancestral state = 1.717434 +/- 0.0 Rate in state 0 = 171.94297 +/- 0.000008 Rate in state 1 = 932.902619 +/- 0.000014 LIB: Generator type: mt19937 LIB: Seed = 1302727492 LIB: First value = 1540126853 Progress: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% |********************************************************************************| -lnL = 102.386965 AIC = 210.77393 AICc = 211.57393 Ancestral state = 0.132403 +/- 0.0 Rate in state 0 = 455.284916 +/- 0.000031 Rate in state 1 = 643.934334 +/- 0.000026 LIB: Generator type: mt19937 LIB: Seed = 1302727494 LIB: First value = 2033371763 Progress: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% |********************************************************************************| ---------------------------------------------------------------------------- WARNING: Out of 15 optimization starts, 15 were stopped by hitting the maximum # of iterations. This means that those replicates may not even have hit the local maximum. You can increase the maximum number of iterations or decrease the precision with the NumOpt command. You could also consider increasing the number of random starts using that same command. If this happened on a small proportion of replicates, though, or if the precision (below) is good enough, don't worry about it. ---------------------------------------------------------------------------- -lnL = 89.443934 AIC = 184.887868 AICc = 185.687868 Ancestral state = 1.598443 +/- 0.0 Rate in state 0 = 70.025334 +/- 0.000004 Rate in state 1 = 424.579028 +/- 0.000011 LIB: Generator type: mt19937 LIB: Seed = 1302727498 LIB: First value = 3469342264 Progress: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% |********************************************************************************| -lnL = 102.456304 AIC = 210.912609 AICc = 211.712609 Ancestral state = 0.191219 +/- 0.0 Rate in state 0 = 687.330963 +/- 0.000044 Rate in state 1 = 912.949162 +/- 0.000025 LIB: Generator type: mt19937 LIB: Seed = 1302727500 LIB: First value = 2818527318 Progress: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% |********************************************************************************| ---------------------------------------------------------------------------- WARNING: Out of 15 optimization starts, 15 were stopped by hitting the maximum # of iterations. This means that those replicates may not even have hit the local maximum. You can increase the maximum number of iterations or decrease the precision with the NumOpt command. You could also consider increasing the number of random starts using that same command. If this happened on a small proportion of replicates, though, or if the precision (below) is good enough, don't worry about it. ---------------------------------------------------------------------------- -lnL = 89.434966 AIC = 184.869932 AICc = 185.669932 Ancestral state = 1.890061 +/- 0.0 Rate in state 0 = 95.620084 +/- 0.000006 Rate in state 1 = 599.007667 +/- 0.000014 LIB: Generator type: mt19937 LIB: Seed = 1302727503 LIB: First value = 728061371 Progress: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% |********************************************************************************| -lnL = 102.461326 AIC = 210.922652 AICc = 211.722652 Ancestral state = 0.140938 +/- 0.000001 Rate in state 0 = 432.723484 +/- 0.000038 Rate in state 1 = 572.399179 +/- 0.000025 LIB: Generator type: mt19937 LIB: Seed = 1302727505 LIB: First value = 3883961944 Progress: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% |********************************************************************************| -lnL = 89.510107 AIC = 185.020214 AICc = 185.820214 Ancestral state = 1.828222 +/- 0.0 Rate in state 0 = 61.010673 +/- 0.000002 Rate in state 1 = 377.431718 +/- 0.000011 LIB: Generator type: mt19937 LIB: Seed = 1302727508 LIB: First value = 1152422121 Progress: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% |********************************************************************************| -lnL = 102.43169 AIC = 210.86338 AICc = 211.66338 Ancestral state = 0.236904 +/- 0.000001 Rate in state 0 = 877.956543 +/- 0.00007 Rate in state 1 = 1199.851036 +/- 0.000038 LIB: Generator type: mt19937 LIB: Seed = 1302727510 LIB: First value = 2476311302 Progress: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% |********************************************************************************| -lnL = 89.229662 AIC = 184.459323 AICc = 185.259323 Ancestral state = 2.148045 +/- 0.0 Rate in state 0 = 122.388928 +/- 0.000006 Rate in state 1 = 793.281976 +/- 0.000023 LIB: Generator type: mt19937 LIB: Seed = 1302727515 LIB: First value = 2645052777 RCPP: 'd:/temp/RtmpwX9NTh/file10e16159' Piping commands to brownie objectLIB: preprocessing command: execute 'd:/temp/RtmpwX9NTh/file10e16159' .. conditioned command is: ;execute 'd:/temp/RtmpwX9NTh/file10e16159';end; LIB: handle cmd ';execute 'd:/temp/RtmpwX9NTh/file10e16159';end;' Opening d:/temp/RtmpwX9NTh/file10e16159... Starting to execute NEXUS file Entering TAXA block...done Entering TREES block...done Entering CHARACTERS block...done (Skipping assumptions block) (Skipping brownie block) Finished executing NEXUS file TREES block contains 10 trees 1 UNTITLED (rooted, weight = 1) 2 UNTITLED (rooted, weight = 1) 3 UNTITLED (rooted, weight = 1) 4 UNTITLED (rooted, weight = 1) 5 UNTITLED (rooted, weight = 1) 6 UNTITLED (rooted, weight = 1) 7 UNTITLED (rooted, weight = 1) 8 UNTITLED (rooted, weight = 1) 9 UNTITLED (rooted, weight = 1) 10 UNTITLED (rooted, weight = 1,default tree) Reading TAXA block... Reading TREES block... Reading CHARACTERS block... Reading ASSUMPTIONS block... Reading BROWNIE block... You have chosen a single rate Brownian motion model Now optimizing with taxset ALL LIB: Generator type: mt19937 LIB: Seed = 1302727515 LIB: First value = 2645052777 Progress: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% |********************************************************************************| Now optimizing with taxset ALL -lnL = 102.58253 AIC = 209.165059 AICc = 209.552156 Ancestral state = 0.0 Optimal rate = 553.175459 +/- 0.000029 Note that +/- reflects imprecision due to numerical optimization LIB: Generator type: mt19937 LIB: Seed = 1302727515 LIB: First value = 2645052777 Progress: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% |********************************************************************************| Now optimizing with taxset ALL -lnL = 102.58253 AIC = 209.165059 AICc = 209.552156 Ancestral state = 0.0 Optimal rate = 553.175459 +/- 0.000029 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409867 AIC = 188.819734 AICc = 189.206831 Ancestral state = 0.0 Optimal rate = 304.077719 +/- 0.000005 Note that +/- reflects imprecision due to numerical optimization LIB: Generator type: mt19937 LIB: Seed = 1302727518 LIB: First value = 2848801299 Progress: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% |********************************************************************************| Now optimizing with taxset ALL -lnL = 102.58253 AIC = 209.165059 AICc = 209.552156 Ancestral state = 0.0 Optimal rate = 553.175459 +/- 0.000029 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409867 AIC = 188.819734 AICc = 189.206831 Ancestral state = 0.0 Optimal rate = 304.077719 +/- 0.000005 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.58259 AIC = 209.165181 AICc = 209.552277 Ancestral state = -0.0 Optimal rate = 407.442947 +/- 0.000029 Note that +/- reflects imprecision due to numerical optimization LIB: Generator type: mt19937 LIB: Seed = 1302727518 LIB: First value = 2848801299 Progress: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% |********************************************************************************| Now optimizing with taxset ALL -lnL = 102.58253 AIC = 209.165059 AICc = 209.552156 Ancestral state = 0.0 Optimal rate = 553.175459 +/- 0.000029 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409867 AIC = 188.819734 AICc = 189.206831 Ancestral state = 0.0 Optimal rate = 304.077719 +/- 0.000005 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.58259 AIC = 209.165181 AICc = 209.552277 Ancestral state = -0.0 Optimal rate = 407.442947 +/- 0.000029 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.40986 AIC = 188.81972 AICc = 189.206817 Ancestral state = 0.0 Optimal rate = 223.968401 +/- 0.000006 Note that +/- reflects imprecision due to numerical optimization LIB: Generator type: mt19937 LIB: Seed = 1302727519 LIB: First value = 4086003447 Progress: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% |********************************************************************************| Now optimizing with taxset ALL -lnL = 102.58253 AIC = 209.165059 AICc = 209.552156 Ancestral state = 0.0 Optimal rate = 553.175459 +/- 0.000029 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409867 AIC = 188.819734 AICc = 189.206831 Ancestral state = 0.0 Optimal rate = 304.077719 +/- 0.000005 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.58259 AIC = 209.165181 AICc = 209.552277 Ancestral state = -0.0 Optimal rate = 407.442947 +/- 0.000029 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.40986 AIC = 188.81972 AICc = 189.206817 Ancestral state = 0.0 Optimal rate = 223.968401 +/- 0.000006 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582641 AIC = 209.165282 AICc = 209.552379 Ancestral state = -0.0 Optimal rate = 512.373252 +/- 0.000029 Note that +/- reflects imprecision due to numerical optimization LIB: Generator type: mt19937 LIB: Seed = 1302727520 LIB: First value = 3591016437 Progress: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% |********************************************************************************| Now optimizing with taxset ALL -lnL = 102.58253 AIC = 209.165059 AICc = 209.552156 Ancestral state = 0.0 Optimal rate = 553.175459 +/- 0.000029 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409867 AIC = 188.819734 AICc = 189.206831 Ancestral state = 0.0 Optimal rate = 304.077719 +/- 0.000005 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.58259 AIC = 209.165181 AICc = 209.552277 Ancestral state = -0.0 Optimal rate = 407.442947 +/- 0.000029 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.40986 AIC = 188.81972 AICc = 189.206817 Ancestral state = 0.0 Optimal rate = 223.968401 +/- 0.000006 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582641 AIC = 209.165282 AICc = 209.552379 Ancestral state = -0.0 Optimal rate = 512.373252 +/- 0.000029 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409857 AIC = 188.819714 AICc = 189.206811 Ancestral state = 0.0 Optimal rate = 281.646938 +/- 0.000007 Note that +/- reflects imprecision due to numerical optimization LIB: Generator type: mt19937 LIB: Seed = 1302727521 LIB: First value = 883552649 Progress: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% |********************************************************************************| Now optimizing with taxset ALL -lnL = 102.58253 AIC = 209.165059 AICc = 209.552156 Ancestral state = 0.0 Optimal rate = 553.175459 +/- 0.000029 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409867 AIC = 188.819734 AICc = 189.206831 Ancestral state = 0.0 Optimal rate = 304.077719 +/- 0.000005 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.58259 AIC = 209.165181 AICc = 209.552277 Ancestral state = -0.0 Optimal rate = 407.442947 +/- 0.000029 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.40986 AIC = 188.81972 AICc = 189.206817 Ancestral state = 0.0 Optimal rate = 223.968401 +/- 0.000006 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582641 AIC = 209.165282 AICc = 209.552379 Ancestral state = -0.0 Optimal rate = 512.373252 +/- 0.000029 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409857 AIC = 188.819714 AICc = 189.206811 Ancestral state = 0.0 Optimal rate = 281.646938 +/- 0.000007 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582653 AIC = 209.165305 AICc = 209.552402 Ancestral state = -0.0 Optimal rate = 1725.471372 +/- 0.000098 Note that +/- reflects imprecision due to numerical optimization LIB: Generator type: mt19937 LIB: Seed = 1302727522 LIB: First value = 2249609173 Progress: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% |********************************************************************************| Now optimizing with taxset ALL -lnL = 102.58253 AIC = 209.165059 AICc = 209.552156 Ancestral state = 0.0 Optimal rate = 553.175459 +/- 0.000029 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409867 AIC = 188.819734 AICc = 189.206831 Ancestral state = 0.0 Optimal rate = 304.077719 +/- 0.000005 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.58259 AIC = 209.165181 AICc = 209.552277 Ancestral state = -0.0 Optimal rate = 407.442947 +/- 0.000029 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.40986 AIC = 188.81972 AICc = 189.206817 Ancestral state = 0.0 Optimal rate = 223.968401 +/- 0.000006 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582641 AIC = 209.165282 AICc = 209.552379 Ancestral state = -0.0 Optimal rate = 512.373252 +/- 0.000029 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409857 AIC = 188.819714 AICc = 189.206811 Ancestral state = 0.0 Optimal rate = 281.646938 +/- 0.000007 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582653 AIC = 209.165305 AICc = 209.552402 Ancestral state = -0.0 Optimal rate = 1725.471372 +/- 0.000098 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409862 AIC = 188.819725 AICc = 189.206822 Ancestral state = 0.0 Optimal rate = 948.475659 +/- 0.000016 Note that +/- reflects imprecision due to numerical optimization LIB: Generator type: mt19937 LIB: Seed = 1302727524 LIB: First value = 994475436 Progress: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% |********************************************************************************| Now optimizing with taxset ALL -lnL = 102.58253 AIC = 209.165059 AICc = 209.552156 Ancestral state = 0.0 Optimal rate = 553.175459 +/- 0.000029 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409867 AIC = 188.819734 AICc = 189.206831 Ancestral state = 0.0 Optimal rate = 304.077719 +/- 0.000005 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.58259 AIC = 209.165181 AICc = 209.552277 Ancestral state = -0.0 Optimal rate = 407.442947 +/- 0.000029 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.40986 AIC = 188.81972 AICc = 189.206817 Ancestral state = 0.0 Optimal rate = 223.968401 +/- 0.000006 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582641 AIC = 209.165282 AICc = 209.552379 Ancestral state = -0.0 Optimal rate = 512.373252 +/- 0.000029 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409857 AIC = 188.819714 AICc = 189.206811 Ancestral state = 0.0 Optimal rate = 281.646938 +/- 0.000007 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582653 AIC = 209.165305 AICc = 209.552402 Ancestral state = -0.0 Optimal rate = 1725.471372 +/- 0.000098 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409862 AIC = 188.819725 AICc = 189.206822 Ancestral state = 0.0 Optimal rate = 948.475659 +/- 0.000016 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582565 AIC = 209.16513 AICc = 209.552227 Ancestral state = -0.0 Optimal rate = 365.942973 +/- 0.000021 Note that +/- reflects imprecision due to numerical optimization LIB: Generator type: mt19937 LIB: Seed = 1302727525 LIB: First value = 3454557464 Progress: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% |********************************************************************************| Now optimizing with taxset ALL -lnL = 102.58253 AIC = 209.165059 AICc = 209.552156 Ancestral state = 0.0 Optimal rate = 553.175459 +/- 0.000029 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409867 AIC = 188.819734 AICc = 189.206831 Ancestral state = 0.0 Optimal rate = 304.077719 +/- 0.000005 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.58259 AIC = 209.165181 AICc = 209.552277 Ancestral state = -0.0 Optimal rate = 407.442947 +/- 0.000029 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.40986 AIC = 188.81972 AICc = 189.206817 Ancestral state = 0.0 Optimal rate = 223.968401 +/- 0.000006 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582641 AIC = 209.165282 AICc = 209.552379 Ancestral state = -0.0 Optimal rate = 512.373252 +/- 0.000029 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409857 AIC = 188.819714 AICc = 189.206811 Ancestral state = 0.0 Optimal rate = 281.646938 +/- 0.000007 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582653 AIC = 209.165305 AICc = 209.552402 Ancestral state = -0.0 Optimal rate = 1725.471372 +/- 0.000098 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409862 AIC = 188.819725 AICc = 189.206822 Ancestral state = 0.0 Optimal rate = 948.475659 +/- 0.000016 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582565 AIC = 209.16513 AICc = 209.552227 Ancestral state = -0.0 Optimal rate = 365.942973 +/- 0.000021 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409854 AIC = 188.819707 AICc = 189.206804 Ancestral state = -0.0 Optimal rate = 201.156412 +/- 0.000004 Note that +/- reflects imprecision due to numerical optimization LIB: Generator type: mt19937 LIB: Seed = 1302727526 LIB: First value = 3213900068 Progress: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% |********************************************************************************| Now optimizing with taxset ALL -lnL = 102.58253 AIC = 209.165059 AICc = 209.552156 Ancestral state = 0.0 Optimal rate = 553.175459 +/- 0.000029 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409867 AIC = 188.819734 AICc = 189.206831 Ancestral state = 0.0 Optimal rate = 304.077719 +/- 0.000005 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.58259 AIC = 209.165181 AICc = 209.552277 Ancestral state = -0.0 Optimal rate = 407.442947 +/- 0.000029 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.40986 AIC = 188.81972 AICc = 189.206817 Ancestral state = 0.0 Optimal rate = 223.968401 +/- 0.000006 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582641 AIC = 209.165282 AICc = 209.552379 Ancestral state = -0.0 Optimal rate = 512.373252 +/- 0.000029 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409857 AIC = 188.819714 AICc = 189.206811 Ancestral state = 0.0 Optimal rate = 281.646938 +/- 0.000007 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582653 AIC = 209.165305 AICc = 209.552402 Ancestral state = -0.0 Optimal rate = 1725.471372 +/- 0.000098 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409862 AIC = 188.819725 AICc = 189.206822 Ancestral state = 0.0 Optimal rate = 948.475659 +/- 0.000016 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582565 AIC = 209.16513 AICc = 209.552227 Ancestral state = -0.0 Optimal rate = 365.942973 +/- 0.000021 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409854 AIC = 188.819707 AICc = 189.206804 Ancestral state = -0.0 Optimal rate = 201.156412 +/- 0.000004 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582495 AIC = 209.164991 AICc = 209.552087 Ancestral state = 0.0 Optimal rate = 1274.401442 +/- 0.000087 Note that +/- reflects imprecision due to numerical optimization LIB: Generator type: mt19937 LIB: Seed = 1302727526 LIB: First value = 3213900068 Progress: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% |********************************************************************************| Now optimizing with taxset ALL -lnL = 102.58253 AIC = 209.165059 AICc = 209.552156 Ancestral state = 0.0 Optimal rate = 553.175459 +/- 0.000029 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409867 AIC = 188.819734 AICc = 189.206831 Ancestral state = 0.0 Optimal rate = 304.077719 +/- 0.000005 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.58259 AIC = 209.165181 AICc = 209.552277 Ancestral state = -0.0 Optimal rate = 407.442947 +/- 0.000029 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.40986 AIC = 188.81972 AICc = 189.206817 Ancestral state = 0.0 Optimal rate = 223.968401 +/- 0.000006 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582641 AIC = 209.165282 AICc = 209.552379 Ancestral state = -0.0 Optimal rate = 512.373252 +/- 0.000029 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409857 AIC = 188.819714 AICc = 189.206811 Ancestral state = 0.0 Optimal rate = 281.646938 +/- 0.000007 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582653 AIC = 209.165305 AICc = 209.552402 Ancestral state = -0.0 Optimal rate = 1725.471372 +/- 0.000098 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409862 AIC = 188.819725 AICc = 189.206822 Ancestral state = 0.0 Optimal rate = 948.475659 +/- 0.000016 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582565 AIC = 209.16513 AICc = 209.552227 Ancestral state = -0.0 Optimal rate = 365.942973 +/- 0.000021 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409854 AIC = 188.819707 AICc = 189.206804 Ancestral state = -0.0 Optimal rate = 201.156412 +/- 0.000004 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582495 AIC = 209.164991 AICc = 209.552087 Ancestral state = 0.0 Optimal rate = 1274.401442 +/- 0.000087 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409865 AIC = 188.819729 AICc = 189.206826 Ancestral state = 0.0 Optimal rate = 700.533344 +/- 0.000018 Note that +/- reflects imprecision due to numerical optimization LIB: Generator type: mt19937 LIB: Seed = 1302727528 LIB: First value = 1188576384 Progress: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% |********************************************************************************| Now optimizing with taxset ALL -lnL = 102.58253 AIC = 209.165059 AICc = 209.552156 Ancestral state = 0.0 Optimal rate = 553.175459 +/- 0.000029 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409867 AIC = 188.819734 AICc = 189.206831 Ancestral state = 0.0 Optimal rate = 304.077719 +/- 0.000005 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.58259 AIC = 209.165181 AICc = 209.552277 Ancestral state = -0.0 Optimal rate = 407.442947 +/- 0.000029 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.40986 AIC = 188.81972 AICc = 189.206817 Ancestral state = 0.0 Optimal rate = 223.968401 +/- 0.000006 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582641 AIC = 209.165282 AICc = 209.552379 Ancestral state = -0.0 Optimal rate = 512.373252 +/- 0.000029 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409857 AIC = 188.819714 AICc = 189.206811 Ancestral state = 0.0 Optimal rate = 281.646938 +/- 0.000007 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582653 AIC = 209.165305 AICc = 209.552402 Ancestral state = -0.0 Optimal rate = 1725.471372 +/- 0.000098 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409862 AIC = 188.819725 AICc = 189.206822 Ancestral state = 0.0 Optimal rate = 948.475659 +/- 0.000016 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582565 AIC = 209.16513 AICc = 209.552227 Ancestral state = -0.0 Optimal rate = 365.942973 +/- 0.000021 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409854 AIC = 188.819707 AICc = 189.206804 Ancestral state = -0.0 Optimal rate = 201.156412 +/- 0.000004 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582495 AIC = 209.164991 AICc = 209.552087 Ancestral state = 0.0 Optimal rate = 1274.401442 +/- 0.000087 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409865 AIC = 188.819729 AICc = 189.206826 Ancestral state = 0.0 Optimal rate = 700.533344 +/- 0.000018 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582564 AIC = 209.165128 AICc = 209.552224 Ancestral state = -0.0 Optimal rate = 596.175554 +/- 0.000031 Note that +/- reflects imprecision due to numerical optimization LIB: Generator type: mt19937 LIB: Seed = 1302727529 LIB: First value = 1366723555 Progress: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% |********************************************************************************| Now optimizing with taxset ALL -lnL = 102.58253 AIC = 209.165059 AICc = 209.552156 Ancestral state = 0.0 Optimal rate = 553.175459 +/- 0.000029 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409867 AIC = 188.819734 AICc = 189.206831 Ancestral state = 0.0 Optimal rate = 304.077719 +/- 0.000005 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.58259 AIC = 209.165181 AICc = 209.552277 Ancestral state = -0.0 Optimal rate = 407.442947 +/- 0.000029 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.40986 AIC = 188.81972 AICc = 189.206817 Ancestral state = 0.0 Optimal rate = 223.968401 +/- 0.000006 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582641 AIC = 209.165282 AICc = 209.552379 Ancestral state = -0.0 Optimal rate = 512.373252 +/- 0.000029 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409857 AIC = 188.819714 AICc = 189.206811 Ancestral state = 0.0 Optimal rate = 281.646938 +/- 0.000007 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582653 AIC = 209.165305 AICc = 209.552402 Ancestral state = -0.0 Optimal rate = 1725.471372 +/- 0.000098 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409862 AIC = 188.819725 AICc = 189.206822 Ancestral state = 0.0 Optimal rate = 948.475659 +/- 0.000016 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582565 AIC = 209.16513 AICc = 209.552227 Ancestral state = -0.0 Optimal rate = 365.942973 +/- 0.000021 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409854 AIC = 188.819707 AICc = 189.206804 Ancestral state = -0.0 Optimal rate = 201.156412 +/- 0.000004 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582495 AIC = 209.164991 AICc = 209.552087 Ancestral state = 0.0 Optimal rate = 1274.401442 +/- 0.000087 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409865 AIC = 188.819729 AICc = 189.206826 Ancestral state = 0.0 Optimal rate = 700.533344 +/- 0.000018 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582564 AIC = 209.165128 AICc = 209.552224 Ancestral state = -0.0 Optimal rate = 596.175554 +/- 0.000031 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409859 AIC = 188.819718 AICc = 189.206814 Ancestral state = 0.0 Optimal rate = 327.713843 +/- 0.000007 Note that +/- reflects imprecision due to numerical optimization LIB: Generator type: mt19937 LIB: Seed = 1302727530 LIB: First value = 2771362649 Progress: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% |********************************************************************************| Now optimizing with taxset ALL -lnL = 102.58253 AIC = 209.165059 AICc = 209.552156 Ancestral state = 0.0 Optimal rate = 553.175459 +/- 0.000029 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409867 AIC = 188.819734 AICc = 189.206831 Ancestral state = 0.0 Optimal rate = 304.077719 +/- 0.000005 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.58259 AIC = 209.165181 AICc = 209.552277 Ancestral state = -0.0 Optimal rate = 407.442947 +/- 0.000029 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.40986 AIC = 188.81972 AICc = 189.206817 Ancestral state = 0.0 Optimal rate = 223.968401 +/- 0.000006 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582641 AIC = 209.165282 AICc = 209.552379 Ancestral state = -0.0 Optimal rate = 512.373252 +/- 0.000029 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409857 AIC = 188.819714 AICc = 189.206811 Ancestral state = 0.0 Optimal rate = 281.646938 +/- 0.000007 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582653 AIC = 209.165305 AICc = 209.552402 Ancestral state = -0.0 Optimal rate = 1725.471372 +/- 0.000098 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409862 AIC = 188.819725 AICc = 189.206822 Ancestral state = 0.0 Optimal rate = 948.475659 +/- 0.000016 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582565 AIC = 209.16513 AICc = 209.552227 Ancestral state = -0.0 Optimal rate = 365.942973 +/- 0.000021 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409854 AIC = 188.819707 AICc = 189.206804 Ancestral state = -0.0 Optimal rate = 201.156412 +/- 0.000004 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582495 AIC = 209.164991 AICc = 209.552087 Ancestral state = 0.0 Optimal rate = 1274.401442 +/- 0.000087 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409865 AIC = 188.819729 AICc = 189.206826 Ancestral state = 0.0 Optimal rate = 700.533344 +/- 0.000018 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582564 AIC = 209.165128 AICc = 209.552224 Ancestral state = -0.0 Optimal rate = 596.175554 +/- 0.000031 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409859 AIC = 188.819718 AICc = 189.206814 Ancestral state = 0.0 Optimal rate = 327.713843 +/- 0.000007 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582526 AIC = 209.165052 AICc = 209.552149 Ancestral state = -0.0 Optimal rate = 858.66687 +/- 0.00005 Note that +/- reflects imprecision due to numerical optimization LIB: Generator type: mt19937 LIB: Seed = 1302727530 LIB: First value = 2771362649 Progress: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% |********************************************************************************| Now optimizing with taxset ALL -lnL = 102.58253 AIC = 209.165059 AICc = 209.552156 Ancestral state = 0.0 Optimal rate = 553.175459 +/- 0.000029 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409867 AIC = 188.819734 AICc = 189.206831 Ancestral state = 0.0 Optimal rate = 304.077719 +/- 0.000005 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.58259 AIC = 209.165181 AICc = 209.552277 Ancestral state = -0.0 Optimal rate = 407.442947 +/- 0.000029 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.40986 AIC = 188.81972 AICc = 189.206817 Ancestral state = 0.0 Optimal rate = 223.968401 +/- 0.000006 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582641 AIC = 209.165282 AICc = 209.552379 Ancestral state = -0.0 Optimal rate = 512.373252 +/- 0.000029 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409857 AIC = 188.819714 AICc = 189.206811 Ancestral state = 0.0 Optimal rate = 281.646938 +/- 0.000007 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582653 AIC = 209.165305 AICc = 209.552402 Ancestral state = -0.0 Optimal rate = 1725.471372 +/- 0.000098 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409862 AIC = 188.819725 AICc = 189.206822 Ancestral state = 0.0 Optimal rate = 948.475659 +/- 0.000016 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582565 AIC = 209.16513 AICc = 209.552227 Ancestral state = -0.0 Optimal rate = 365.942973 +/- 0.000021 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409854 AIC = 188.819707 AICc = 189.206804 Ancestral state = -0.0 Optimal rate = 201.156412 +/- 0.000004 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582495 AIC = 209.164991 AICc = 209.552087 Ancestral state = 0.0 Optimal rate = 1274.401442 +/- 0.000087 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409865 AIC = 188.819729 AICc = 189.206826 Ancestral state = 0.0 Optimal rate = 700.533344 +/- 0.000018 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582564 AIC = 209.165128 AICc = 209.552224 Ancestral state = -0.0 Optimal rate = 596.175554 +/- 0.000031 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409859 AIC = 188.819718 AICc = 189.206814 Ancestral state = 0.0 Optimal rate = 327.713843 +/- 0.000007 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582526 AIC = 209.165052 AICc = 209.552149 Ancestral state = -0.0 Optimal rate = 858.66687 +/- 0.00005 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409861 AIC = 188.819722 AICc = 189.206819 Ancestral state = 0.0 Optimal rate = 472.004726 +/- 0.000008 Note that +/- reflects imprecision due to numerical optimization LIB: Generator type: mt19937 LIB: Seed = 1302727532 LIB: First value = 3959481164 Progress: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% |********************************************************************************| Now optimizing with taxset ALL -lnL = 102.58253 AIC = 209.165059 AICc = 209.552156 Ancestral state = 0.0 Optimal rate = 553.175459 +/- 0.000029 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409867 AIC = 188.819734 AICc = 189.206831 Ancestral state = 0.0 Optimal rate = 304.077719 +/- 0.000005 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.58259 AIC = 209.165181 AICc = 209.552277 Ancestral state = -0.0 Optimal rate = 407.442947 +/- 0.000029 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.40986 AIC = 188.81972 AICc = 189.206817 Ancestral state = 0.0 Optimal rate = 223.968401 +/- 0.000006 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582641 AIC = 209.165282 AICc = 209.552379 Ancestral state = -0.0 Optimal rate = 512.373252 +/- 0.000029 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409857 AIC = 188.819714 AICc = 189.206811 Ancestral state = 0.0 Optimal rate = 281.646938 +/- 0.000007 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582653 AIC = 209.165305 AICc = 209.552402 Ancestral state = -0.0 Optimal rate = 1725.471372 +/- 0.000098 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409862 AIC = 188.819725 AICc = 189.206822 Ancestral state = 0.0 Optimal rate = 948.475659 +/- 0.000016 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582565 AIC = 209.16513 AICc = 209.552227 Ancestral state = -0.0 Optimal rate = 365.942973 +/- 0.000021 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409854 AIC = 188.819707 AICc = 189.206804 Ancestral state = -0.0 Optimal rate = 201.156412 +/- 0.000004 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582495 AIC = 209.164991 AICc = 209.552087 Ancestral state = 0.0 Optimal rate = 1274.401442 +/- 0.000087 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409865 AIC = 188.819729 AICc = 189.206826 Ancestral state = 0.0 Optimal rate = 700.533344 +/- 0.000018 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582564 AIC = 209.165128 AICc = 209.552224 Ancestral state = -0.0 Optimal rate = 596.175554 +/- 0.000031 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409859 AIC = 188.819718 AICc = 189.206814 Ancestral state = 0.0 Optimal rate = 327.713843 +/- 0.000007 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582526 AIC = 209.165052 AICc = 209.552149 Ancestral state = -0.0 Optimal rate = 858.66687 +/- 0.00005 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409861 AIC = 188.819722 AICc = 189.206819 Ancestral state = 0.0 Optimal rate = 472.004726 +/- 0.000008 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582562 AIC = 209.165124 AICc = 209.552221 Ancestral state = 0.0 Optimal rate = 539.373257 +/- 0.000039 Note that +/- reflects imprecision due to numerical optimization LIB: Generator type: mt19937 LIB: Seed = 1302727532 LIB: First value = 3959481164 Progress: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% |********************************************************************************| Now optimizing with taxset ALL -lnL = 102.58253 AIC = 209.165059 AICc = 209.552156 Ancestral state = 0.0 Optimal rate = 553.175459 +/- 0.000029 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409867 AIC = 188.819734 AICc = 189.206831 Ancestral state = 0.0 Optimal rate = 304.077719 +/- 0.000005 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.58259 AIC = 209.165181 AICc = 209.552277 Ancestral state = -0.0 Optimal rate = 407.442947 +/- 0.000029 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.40986 AIC = 188.81972 AICc = 189.206817 Ancestral state = 0.0 Optimal rate = 223.968401 +/- 0.000006 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582641 AIC = 209.165282 AICc = 209.552379 Ancestral state = -0.0 Optimal rate = 512.373252 +/- 0.000029 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409857 AIC = 188.819714 AICc = 189.206811 Ancestral state = 0.0 Optimal rate = 281.646938 +/- 0.000007 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582653 AIC = 209.165305 AICc = 209.552402 Ancestral state = -0.0 Optimal rate = 1725.471372 +/- 0.000098 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409862 AIC = 188.819725 AICc = 189.206822 Ancestral state = 0.0 Optimal rate = 948.475659 +/- 0.000016 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582565 AIC = 209.16513 AICc = 209.552227 Ancestral state = -0.0 Optimal rate = 365.942973 +/- 0.000021 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409854 AIC = 188.819707 AICc = 189.206804 Ancestral state = -0.0 Optimal rate = 201.156412 +/- 0.000004 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582495 AIC = 209.164991 AICc = 209.552087 Ancestral state = 0.0 Optimal rate = 1274.401442 +/- 0.000087 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409865 AIC = 188.819729 AICc = 189.206826 Ancestral state = 0.0 Optimal rate = 700.533344 +/- 0.000018 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582564 AIC = 209.165128 AICc = 209.552224 Ancestral state = -0.0 Optimal rate = 596.175554 +/- 0.000031 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409859 AIC = 188.819718 AICc = 189.206814 Ancestral state = 0.0 Optimal rate = 327.713843 +/- 0.000007 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582526 AIC = 209.165052 AICc = 209.552149 Ancestral state = -0.0 Optimal rate = 858.66687 +/- 0.00005 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409861 AIC = 188.819722 AICc = 189.206819 Ancestral state = 0.0 Optimal rate = 472.004726 +/- 0.000008 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582562 AIC = 209.165124 AICc = 209.552221 Ancestral state = 0.0 Optimal rate = 539.373257 +/- 0.000039 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409855 AIC = 188.81971 AICc = 189.206807 Ancestral state = 0.0 Optimal rate = 296.48995 +/- 0.000008 Note that +/- reflects imprecision due to numerical optimization LIB: Generator type: mt19937 LIB: Seed = 1302727533 LIB: First value = 1384920002 Progress: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% |********************************************************************************| Now optimizing with taxset ALL -lnL = 102.58253 AIC = 209.165059 AICc = 209.552156 Ancestral state = 0.0 Optimal rate = 553.175459 +/- 0.000029 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409867 AIC = 188.819734 AICc = 189.206831 Ancestral state = 0.0 Optimal rate = 304.077719 +/- 0.000005 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.58259 AIC = 209.165181 AICc = 209.552277 Ancestral state = -0.0 Optimal rate = 407.442947 +/- 0.000029 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.40986 AIC = 188.81972 AICc = 189.206817 Ancestral state = 0.0 Optimal rate = 223.968401 +/- 0.000006 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582641 AIC = 209.165282 AICc = 209.552379 Ancestral state = -0.0 Optimal rate = 512.373252 +/- 0.000029 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409857 AIC = 188.819714 AICc = 189.206811 Ancestral state = 0.0 Optimal rate = 281.646938 +/- 0.000007 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582653 AIC = 209.165305 AICc = 209.552402 Ancestral state = -0.0 Optimal rate = 1725.471372 +/- 0.000098 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409862 AIC = 188.819725 AICc = 189.206822 Ancestral state = 0.0 Optimal rate = 948.475659 +/- 0.000016 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582565 AIC = 209.16513 AICc = 209.552227 Ancestral state = -0.0 Optimal rate = 365.942973 +/- 0.000021 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409854 AIC = 188.819707 AICc = 189.206804 Ancestral state = -0.0 Optimal rate = 201.156412 +/- 0.000004 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582495 AIC = 209.164991 AICc = 209.552087 Ancestral state = 0.0 Optimal rate = 1274.401442 +/- 0.000087 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409865 AIC = 188.819729 AICc = 189.206826 Ancestral state = 0.0 Optimal rate = 700.533344 +/- 0.000018 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582564 AIC = 209.165128 AICc = 209.552224 Ancestral state = -0.0 Optimal rate = 596.175554 +/- 0.000031 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409859 AIC = 188.819718 AICc = 189.206814 Ancestral state = 0.0 Optimal rate = 327.713843 +/- 0.000007 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582526 AIC = 209.165052 AICc = 209.552149 Ancestral state = -0.0 Optimal rate = 858.66687 +/- 0.00005 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409861 AIC = 188.819722 AICc = 189.206819 Ancestral state = 0.0 Optimal rate = 472.004726 +/- 0.000008 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582562 AIC = 209.165124 AICc = 209.552221 Ancestral state = 0.0 Optimal rate = 539.373257 +/- 0.000039 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409855 AIC = 188.81971 AICc = 189.206807 Ancestral state = 0.0 Optimal rate = 296.48995 +/- 0.000008 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582569 AIC = 209.165138 AICc = 209.552235 Ancestral state = -0.0 Optimal rate = 1120.318849 +/- 0.000065 Note that +/- reflects imprecision due to numerical optimization LIB: Generator type: mt19937 LIB: Seed = 1302727534 LIB: First value = 1281193530 Progress: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% |********************************************************************************| Now optimizing with taxset ALL -lnL = 102.58253 AIC = 209.165059 AICc = 209.552156 Ancestral state = 0.0 Optimal rate = 553.175459 +/- 0.000029 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409867 AIC = 188.819734 AICc = 189.206831 Ancestral state = 0.0 Optimal rate = 304.077719 +/- 0.000005 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.58259 AIC = 209.165181 AICc = 209.552277 Ancestral state = -0.0 Optimal rate = 407.442947 +/- 0.000029 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.40986 AIC = 188.81972 AICc = 189.206817 Ancestral state = 0.0 Optimal rate = 223.968401 +/- 0.000006 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582641 AIC = 209.165282 AICc = 209.552379 Ancestral state = -0.0 Optimal rate = 512.373252 +/- 0.000029 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409857 AIC = 188.819714 AICc = 189.206811 Ancestral state = 0.0 Optimal rate = 281.646938 +/- 0.000007 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582653 AIC = 209.165305 AICc = 209.552402 Ancestral state = -0.0 Optimal rate = 1725.471372 +/- 0.000098 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409862 AIC = 188.819725 AICc = 189.206822 Ancestral state = 0.0 Optimal rate = 948.475659 +/- 0.000016 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582565 AIC = 209.16513 AICc = 209.552227 Ancestral state = -0.0 Optimal rate = 365.942973 +/- 0.000021 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409854 AIC = 188.819707 AICc = 189.206804 Ancestral state = -0.0 Optimal rate = 201.156412 +/- 0.000004 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582495 AIC = 209.164991 AICc = 209.552087 Ancestral state = 0.0 Optimal rate = 1274.401442 +/- 0.000087 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409865 AIC = 188.819729 AICc = 189.206826 Ancestral state = 0.0 Optimal rate = 700.533344 +/- 0.000018 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582564 AIC = 209.165128 AICc = 209.552224 Ancestral state = -0.0 Optimal rate = 596.175554 +/- 0.000031 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409859 AIC = 188.819718 AICc = 189.206814 Ancestral state = 0.0 Optimal rate = 327.713843 +/- 0.000007 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582526 AIC = 209.165052 AICc = 209.552149 Ancestral state = -0.0 Optimal rate = 858.66687 +/- 0.00005 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409861 AIC = 188.819722 AICc = 189.206819 Ancestral state = 0.0 Optimal rate = 472.004726 +/- 0.000008 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582562 AIC = 209.165124 AICc = 209.552221 Ancestral state = 0.0 Optimal rate = 539.373257 +/- 0.000039 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409855 AIC = 188.81971 AICc = 189.206807 Ancestral state = 0.0 Optimal rate = 296.48995 +/- 0.000008 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582569 AIC = 209.165138 AICc = 209.552235 Ancestral state = -0.0 Optimal rate = 1120.318849 +/- 0.000065 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.40986 AIC = 188.819721 AICc = 189.206817 Ancestral state = -0.0 Optimal rate = 615.831899 +/- 0.00001 Note that +/- reflects imprecision due to numerical optimization You have chosen Brownian motion with one rate parameter per state Now optimizing with taxset ALL LIB: Generator type: mt19937 LIB: Seed = 1302727535 LIB: First value = 2968608221 Progress: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% |********************************************************************************| -lnL = 102.50545 AIC = 211.010899 AICc = 211.810899 Ancestral state = 0.166981 +/- 0.000001 Rate in state 0 = 464.475553 +/- 0.000031 Rate in state 1 = 579.916691 +/- 0.000028 LIB: Generator type: mt19937 LIB: Seed = 1302727537 LIB: First value = 1108462641 Progress: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% |********************************************************************************| ---------------------------------------------------------------------------- WARNING: Out of 15 optimization starts, 15 were stopped by hitting the maximum # of iterations. This means that those replicates may not even have hit the local maximum. You can increase the maximum number of iterations or decrease the precision with the NumOpt command. You could also consider increasing the number of random starts using that same command. If this happened on a small proportion of replicates, though, or if the precision (below) is good enough, don't worry about it. ---------------------------------------------------------------------------- -lnL = 89.254264 AIC = 184.508528 AICc = 185.308528 Ancestral state = 1.672717 +/- 0.0 Rate in state 0 = 48.509067 +/- 0.000003 Rate in state 1 = 389.344333 +/- 0.000008 LIB: Generator type: mt19937 LIB: Seed = 1302727541 LIB: First value = 2013379606 Progress: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% |********************************************************************************| -lnL = 102.419208 AIC = 210.838417 AICc = 211.638417 Ancestral state = 0.174772 +/- 0.000001 Rate in state 0 = 316.968765 +/- 0.000028 Rate in state 1 = 437.333142 +/- 0.00002 LIB: Generator type: mt19937 LIB: Seed = 1302727543 LIB: First value = 1719332486 Progress: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% |********************************************************************************| -lnL = 89.407904 AIC = 184.815808 AICc = 185.615808 Ancestral state = 1.805435 +/- 0.0 Rate in state 0 = 46.421967 +/- 0.000003 Rate in state 1 = 289.212087 +/- 0.000005 LIB: Generator type: mt19937 LIB: Seed = 1302727546 LIB: First value = 804140161 Progress: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% |********************************************************************************| -lnL = 102.096225 AIC = 210.19245 AICc = 210.99245 Ancestral state = 0.339607 +/- 0.0 Rate in state 0 = 345.323809 +/- 0.000018 Rate in state 1 = 583.688317 +/- 0.000018 LIB: Generator type: mt19937 LIB: Seed = 1302727548 LIB: First value = 2161192413 Progress: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% |********************************************************************************| ---------------------------------------------------------------------------- WARNING: Out of 15 optimization starts, 15 were stopped by hitting the maximum # of iterations. This means that those replicates may not even have hit the local maximum. You can increase the maximum number of iterations or decrease the precision with the NumOpt command. You could also consider increasing the number of random starts using that same command. If this happened on a small proportion of replicates, though, or if the precision (below) is good enough, don't worry about it. ---------------------------------------------------------------------------- -lnL = 88.816161 AIC = 183.632321 AICc = 184.432321 Ancestral state = 2.018542 +/- 0.0 Rate in state 0 = 62.912362 +/- 0.000002 Rate in state 1 = 383.826347 +/- 0.000007 LIB: Generator type: mt19937 LIB: Seed = 1302727552 LIB: First value = 127440128 Progress: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% |********************************************************************************| -lnL = 102.443898 AIC = 210.887796 AICc = 211.687796 Ancestral state = 0.174469 +/- 0.000001 Rate in state 0 = 1365.815936 +/- 0.000103 Rate in state 1 = 1840.154542 +/- 0.000088 LIB: Generator type: mt19937 LIB: Seed = 1302727554 LIB: First value = 2072378342 Progress: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% |********************************************************************************| -lnL = 89.378442 AIC = 184.756885 AICc = 185.556885 Ancestral state = 1.897972 +/- 0.0 Rate in state 0 = 192.5213 +/- 0.00001 Rate in state 1 = 1213.884592 +/- 0.000019 LIB: Generator type: mt19937 LIB: Seed = 1302727557 LIB: First value = 704880477 Progress: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% |********************************************************************************| -lnL = 102.561873 AIC = 211.123746 AICc = 211.923746 Ancestral state = 0.091664 +/- 0.000001 Rate in state 0 = 333.33312 +/- 0.000034 Rate in state 1 = 374.619226 +/- 0.000015 LIB: Generator type: mt19937 LIB: Seed = 1302727560 LIB: First value = 1685295529 Progress: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% |********************************************************************************| -lnL = 89.341861 AIC = 184.683723 AICc = 185.483723 Ancestral state = 0.775709 +/- 0.0 Rate in state 0 = 32.408443 +/- 0.000002 Rate in state 1 = 242.161624 +/- 0.000007 LIB: Generator type: mt19937 LIB: Seed = 1302727563 LIB: First value = 170968775 Progress: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% |********************************************************************************| -lnL = 102.212816 AIC = 210.425632 AICc = 211.225632 Ancestral state = 0.263325 +/- 0.0 Rate in state 0 = 891.261859 +/- 0.000049 Rate in state 1 = 1427.791236 +/- 0.000063 LIB: Generator type: mt19937 LIB: Seed = 1302727565 LIB: First value = 2304400551 Progress: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% |********************************************************************************| ---------------------------------------------------------------------------- WARNING: Out of 15 optimization starts, 15 were stopped by hitting the maximum # of iterations. This means that those replicates may not even have hit the local maximum. You can increase the maximum number of iterations or decrease the precision with the NumOpt command. You could also consider increasing the number of random starts using that same command. If this happened on a small proportion of replicates, though, or if the precision (below) is good enough, don't worry about it. ---------------------------------------------------------------------------- -lnL = 89.226381 AIC = 184.452762 AICc = 185.252762 Ancestral state = 1.717434 +/- 0.0 Rate in state 0 = 171.942968 +/- 0.000008 Rate in state 1 = 932.902616 +/- 0.000021 LIB: Generator type: mt19937 LIB: Seed = 1302727568 LIB: First value = 3245976897 Progress: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% |********************************************************************************| -lnL = 102.386965 AIC = 210.77393 AICc = 211.57393 Ancestral state = 0.132403 +/- 0.0 Rate in state 0 = 455.284921 +/- 0.000036 Rate in state 1 = 643.934317 +/- 0.000022 LIB: Generator type: mt19937 LIB: Seed = 1302727571 LIB: First value = 4029788160 Progress: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% |********************************************************************************| -lnL = 89.443934 AIC = 184.887868 AICc = 185.687868 Ancestral state = 1.598443 +/- 0.0 Rate in state 0 = 70.025337 +/- 0.000004 Rate in state 1 = 424.57902 +/- 0.000014 LIB: Generator type: mt19937 LIB: Seed = 1302727574 LIB: First value = 3516222328 Progress: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% |********************************************************************************| -lnL = 102.456304 AIC = 210.912609 AICc = 211.712609 Ancestral state = 0.191219 +/- 0.000001 Rate in state 0 = 687.33086 +/- 0.000044 Rate in state 1 = 912.949138 +/- 0.00003 LIB: Generator type: mt19937 LIB: Seed = 1302727576 LIB: First value = 2575371681 Progress: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% |********************************************************************************| ---------------------------------------------------------------------------- WARNING: Out of 15 optimization starts, 15 were stopped by hitting the maximum # of iterations. This means that those replicates may not even have hit the local maximum. You can increase the maximum number of iterations or decrease the precision with the NumOpt command. You could also consider increasing the number of random starts using that same command. If this happened on a small proportion of replicates, though, or if the precision (below) is good enough, don't worry about it. ---------------------------------------------------------------------------- -lnL = 89.434966 AIC = 184.869932 AICc = 185.669932 Ancestral state = 1.890061 +/- 0.0 Rate in state 0 = 95.620084 +/- 0.000005 Rate in state 1 = 599.007666 +/- 0.000014 LIB: Generator type: mt19937 LIB: Seed = 1302727580 LIB: First value = 2812866238 Progress: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% |********************************************************************************| -lnL = 102.461326 AIC = 210.922652 AICc = 211.722652 Ancestral state = 0.140937 +/- 0.000001 Rate in state 0 = 432.723476 +/- 0.000034 Rate in state 1 = 572.399137 +/- 0.000019 LIB: Generator type: mt19937 LIB: Seed = 1302727582 LIB: First value = 1602509530 Progress: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% |********************************************************************************| ---------------------------------------------------------------------------- WARNING: Out of 15 optimization starts, 15 were stopped by hitting the maximum # of iterations. This means that those replicates may not even have hit the local maximum. You can increase the maximum number of iterations or decrease the precision with the NumOpt command. You could also consider increasing the number of random starts using that same command. If this happened on a small proportion of replicates, though, or if the precision (below) is good enough, don't worry about it. ---------------------------------------------------------------------------- -lnL = 89.510107 AIC = 185.020214 AICc = 185.820214 Ancestral state = 1.828222 +/- 0.0 Rate in state 0 = 61.010675 +/- 0.000003 Rate in state 1 = 377.431708 +/- 0.000008 LIB: Generator type: mt19937 LIB: Seed = 1302727585 LIB: First value = 2735043952 Progress: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% |********************************************************************************| -lnL = 102.43169 AIC = 210.86338 AICc = 211.66338 Ancestral state = 0.236904 +/- 0.000001 Rate in state 0 = 877.956597 +/- 0.000084 Rate in state 1 = 1199.850973 +/- 0.000056 LIB: Generator type: mt19937 LIB: Seed = 1302727588 LIB: First value = 623674096 Progress: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% |********************************************************************************| ---------------------------------------------------------------------------- WARNING: Out of 15 optimization starts, 15 were stopped by hitting the maximum # of iterations. This means that those replicates may not even have hit the local maximum. You can increase the maximum number of iterations or decrease the precision with the NumOpt command. You could also consider increasing the number of random starts using that same command. If this happened on a small proportion of replicates, though, or if the precision (below) is good enough, don't worry about it. ---------------------------------------------------------------------------- -lnL = 89.229662 AIC = 184.459323 AICc = 185.259323 Ancestral state = 2.148044 +/- 0.0 Rate in state 0 = 122.388928 +/- 0.000004 Rate in state 1 = 793.282 +/- 0.000016 LIB: Generator type: mt19937 LIB: Seed = 1302727592 LIB: First value = 2611683002 RCPP: 'd:/temp/RtmpwX9NTh/file10263eaf' Piping commands to brownie objectLIB: preprocessing command: execute 'd:/temp/RtmpwX9NTh/file10263eaf' .. conditioned command is: ;execute 'd:/temp/RtmpwX9NTh/file10263eaf';end; LIB: handle cmd ';execute 'd:/temp/RtmpwX9NTh/file10263eaf';end;' Opening d:/temp/RtmpwX9NTh/file10263eaf... Starting to execute NEXUS file Entering TAXA block...done Entering TREES block...done Entering CHARACTERS block...done (Skipping assumptions block) (Skipping brownie block) Finished executing NEXUS file TREES block contains 10 trees 1 UNTITLED (rooted, weight = 1) 2 UNTITLED (rooted, weight = 1) 3 UNTITLED (rooted, weight = 1) 4 UNTITLED (rooted, weight = 1) 5 UNTITLED (rooted, weight = 1) 6 UNTITLED (rooted, weight = 1) 7 UNTITLED (rooted, weight = 1) 8 UNTITLED (rooted, weight = 1) 9 UNTITLED (rooted, weight = 1) 10 UNTITLED (rooted, weight = 1,default tree) Reading TAXA block... Reading TREES block... Reading CHARACTERS block... Reading ASSUMPTIONS block... Reading BROWNIE block... You have chosen a single rate Brownian motion model Now optimizing with taxset ALL LIB: Generator type: mt19937 LIB: Seed = 1302727593 LIB: First value = 1144209741 Progress: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% |********************************************************************************| Now optimizing with taxset ALL -lnL = 102.58253 AIC = 209.165059 AICc = 209.552156 Ancestral state = 0.0 Optimal rate = 553.175444 +/- 0.000025 Note that +/- reflects imprecision due to numerical optimization LIB: Generator type: mt19937 LIB: Seed = 1302727593 LIB: First value = 1144209741 Progress: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% |********************************************************************************| Now optimizing with taxset ALL -lnL = 102.58253 AIC = 209.165059 AICc = 209.552156 Ancestral state = 0.0 Optimal rate = 553.175444 +/- 0.000025 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409867 AIC = 188.819734 AICc = 189.206831 Ancestral state = 0.0 Optimal rate = 304.077721 +/- 0.000006 Note that +/- reflects imprecision due to numerical optimization LIB: Generator type: mt19937 LIB: Seed = 1302727595 LIB: First value = 2088695621 Progress: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% |********************************************************************************| Now optimizing with taxset ALL -lnL = 102.58253 AIC = 209.165059 AICc = 209.552156 Ancestral state = 0.0 Optimal rate = 553.175444 +/- 0.000025 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409867 AIC = 188.819734 AICc = 189.206831 Ancestral state = 0.0 Optimal rate = 304.077721 +/- 0.000006 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.58259 AIC = 209.165181 AICc = 209.552277 Ancestral state = -0.0 Optimal rate = 407.442903 +/- 0.000024 Note that +/- reflects imprecision due to numerical optimization LIB: Generator type: mt19937 LIB: Seed = 1302727595 LIB: First value = 2088695621 Progress: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% |********************************************************************************| Now optimizing with taxset ALL -lnL = 102.58253 AIC = 209.165059 AICc = 209.552156 Ancestral state = 0.0 Optimal rate = 553.175444 +/- 0.000025 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409867 AIC = 188.819734 AICc = 189.206831 Ancestral state = 0.0 Optimal rate = 304.077721 +/- 0.000006 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.58259 AIC = 209.165181 AICc = 209.552277 Ancestral state = -0.0 Optimal rate = 407.442903 +/- 0.000024 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.40986 AIC = 188.81972 AICc = 189.206817 Ancestral state = 0.0 Optimal rate = 223.968404 +/- 0.000004 Note that +/- reflects imprecision due to numerical optimization LIB: Generator type: mt19937 LIB: Seed = 1302727596 LIB: First value = 3613616874 Progress: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% |********************************************************************************| Now optimizing with taxset ALL -lnL = 102.58253 AIC = 209.165059 AICc = 209.552156 Ancestral state = 0.0 Optimal rate = 553.175444 +/- 0.000025 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409867 AIC = 188.819734 AICc = 189.206831 Ancestral state = 0.0 Optimal rate = 304.077721 +/- 0.000006 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.58259 AIC = 209.165181 AICc = 209.552277 Ancestral state = -0.0 Optimal rate = 407.442903 +/- 0.000024 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.40986 AIC = 188.81972 AICc = 189.206817 Ancestral state = 0.0 Optimal rate = 223.968404 +/- 0.000004 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582641 AIC = 209.165282 AICc = 209.552379 Ancestral state = -0.0 Optimal rate = 512.373249 +/- 0.00003 Note that +/- reflects imprecision due to numerical optimization LIB: Generator type: mt19937 LIB: Seed = 1302727596 LIB: First value = 3613616874 Progress: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% |********************************************************************************| Now optimizing with taxset ALL -lnL = 102.58253 AIC = 209.165059 AICc = 209.552156 Ancestral state = 0.0 Optimal rate = 553.175444 +/- 0.000025 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409867 AIC = 188.819734 AICc = 189.206831 Ancestral state = 0.0 Optimal rate = 304.077721 +/- 0.000006 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.58259 AIC = 209.165181 AICc = 209.552277 Ancestral state = -0.0 Optimal rate = 407.442903 +/- 0.000024 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.40986 AIC = 188.81972 AICc = 189.206817 Ancestral state = 0.0 Optimal rate = 223.968404 +/- 0.000004 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582641 AIC = 209.165282 AICc = 209.552379 Ancestral state = -0.0 Optimal rate = 512.373249 +/- 0.00003 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409857 AIC = 188.819714 AICc = 189.206811 Ancestral state = 0.0 Optimal rate = 281.646938 +/- 0.000006 Note that +/- reflects imprecision due to numerical optimization LIB: Generator type: mt19937 LIB: Seed = 1302727597 LIB: First value = 3866927231 Progress: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% |********************************************************************************| Now optimizing with taxset ALL -lnL = 102.58253 AIC = 209.165059 AICc = 209.552156 Ancestral state = 0.0 Optimal rate = 553.175444 +/- 0.000025 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409867 AIC = 188.819734 AICc = 189.206831 Ancestral state = 0.0 Optimal rate = 304.077721 +/- 0.000006 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.58259 AIC = 209.165181 AICc = 209.552277 Ancestral state = -0.0 Optimal rate = 407.442903 +/- 0.000024 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.40986 AIC = 188.81972 AICc = 189.206817 Ancestral state = 0.0 Optimal rate = 223.968404 +/- 0.000004 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582641 AIC = 209.165282 AICc = 209.552379 Ancestral state = -0.0 Optimal rate = 512.373249 +/- 0.00003 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409857 AIC = 188.819714 AICc = 189.206811 Ancestral state = 0.0 Optimal rate = 281.646938 +/- 0.000006 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582653 AIC = 209.165305 AICc = 209.552402 Ancestral state = -0.0 Optimal rate = 1725.471354 +/- 0.000091 Note that +/- reflects imprecision due to numerical optimization LIB: Generator type: mt19937 LIB: Seed = 1302727598 LIB: First value = 3428687226 Progress: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% |********************************************************************************| Now optimizing with taxset ALL -lnL = 102.58253 AIC = 209.165059 AICc = 209.552156 Ancestral state = 0.0 Optimal rate = 553.175444 +/- 0.000025 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409867 AIC = 188.819734 AICc = 189.206831 Ancestral state = 0.0 Optimal rate = 304.077721 +/- 0.000006 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.58259 AIC = 209.165181 AICc = 209.552277 Ancestral state = -0.0 Optimal rate = 407.442903 +/- 0.000024 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.40986 AIC = 188.81972 AICc = 189.206817 Ancestral state = 0.0 Optimal rate = 223.968404 +/- 0.000004 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582641 AIC = 209.165282 AICc = 209.552379 Ancestral state = -0.0 Optimal rate = 512.373249 +/- 0.00003 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409857 AIC = 188.819714 AICc = 189.206811 Ancestral state = 0.0 Optimal rate = 281.646938 +/- 0.000006 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582653 AIC = 209.165305 AICc = 209.552402 Ancestral state = -0.0 Optimal rate = 1725.471354 +/- 0.000091 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409862 AIC = 188.819725 AICc = 189.206822 Ancestral state = 0.0 Optimal rate = 948.475661 +/- 0.000016 Note that +/- reflects imprecision due to numerical optimization LIB: Generator type: mt19937 LIB: Seed = 1302727600 LIB: First value = 2685631630 Progress: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% |********************************************************************************| Now optimizing with taxset ALL -lnL = 102.58253 AIC = 209.165059 AICc = 209.552156 Ancestral state = 0.0 Optimal rate = 553.175444 +/- 0.000025 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409867 AIC = 188.819734 AICc = 189.206831 Ancestral state = 0.0 Optimal rate = 304.077721 +/- 0.000006 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.58259 AIC = 209.165181 AICc = 209.552277 Ancestral state = -0.0 Optimal rate = 407.442903 +/- 0.000024 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.40986 AIC = 188.81972 AICc = 189.206817 Ancestral state = 0.0 Optimal rate = 223.968404 +/- 0.000004 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582641 AIC = 209.165282 AICc = 209.552379 Ancestral state = -0.0 Optimal rate = 512.373249 +/- 0.00003 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409857 AIC = 188.819714 AICc = 189.206811 Ancestral state = 0.0 Optimal rate = 281.646938 +/- 0.000006 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582653 AIC = 209.165305 AICc = 209.552402 Ancestral state = -0.0 Optimal rate = 1725.471354 +/- 0.000091 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409862 AIC = 188.819725 AICc = 189.206822 Ancestral state = 0.0 Optimal rate = 948.475661 +/- 0.000016 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582565 AIC = 209.16513 AICc = 209.552227 Ancestral state = -0.0 Optimal rate = 365.943014 +/- 0.000018 Note that +/- reflects imprecision due to numerical optimization LIB: Generator type: mt19937 LIB: Seed = 1302727601 LIB: First value = 2837375310 Progress: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% |********************************************************************************| Now optimizing with taxset ALL -lnL = 102.58253 AIC = 209.165059 AICc = 209.552156 Ancestral state = 0.0 Optimal rate = 553.175444 +/- 0.000025 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409867 AIC = 188.819734 AICc = 189.206831 Ancestral state = 0.0 Optimal rate = 304.077721 +/- 0.000006 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.58259 AIC = 209.165181 AICc = 209.552277 Ancestral state = -0.0 Optimal rate = 407.442903 +/- 0.000024 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.40986 AIC = 188.81972 AICc = 189.206817 Ancestral state = 0.0 Optimal rate = 223.968404 +/- 0.000004 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582641 AIC = 209.165282 AICc = 209.552379 Ancestral state = -0.0 Optimal rate = 512.373249 +/- 0.00003 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409857 AIC = 188.819714 AICc = 189.206811 Ancestral state = 0.0 Optimal rate = 281.646938 +/- 0.000006 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582653 AIC = 209.165305 AICc = 209.552402 Ancestral state = -0.0 Optimal rate = 1725.471354 +/- 0.000091 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409862 AIC = 188.819725 AICc = 189.206822 Ancestral state = 0.0 Optimal rate = 948.475661 +/- 0.000016 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582565 AIC = 209.16513 AICc = 209.552227 Ancestral state = -0.0 Optimal rate = 365.943014 +/- 0.000018 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409854 AIC = 188.819707 AICc = 189.206804 Ancestral state = -0.0 Optimal rate = 201.156418 +/- 0.000005 Note that +/- reflects imprecision due to numerical optimization LIB: Generator type: mt19937 LIB: Seed = 1302727603 LIB: First value = 1401083107 Progress: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% |********************************************************************************| Now optimizing with taxset ALL -lnL = 102.58253 AIC = 209.165059 AICc = 209.552156 Ancestral state = 0.0 Optimal rate = 553.175444 +/- 0.000025 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409867 AIC = 188.819734 AICc = 189.206831 Ancestral state = 0.0 Optimal rate = 304.077721 +/- 0.000006 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.58259 AIC = 209.165181 AICc = 209.552277 Ancestral state = -0.0 Optimal rate = 407.442903 +/- 0.000024 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.40986 AIC = 188.81972 AICc = 189.206817 Ancestral state = 0.0 Optimal rate = 223.968404 +/- 0.000004 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582641 AIC = 209.165282 AICc = 209.552379 Ancestral state = -0.0 Optimal rate = 512.373249 +/- 0.00003 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409857 AIC = 188.819714 AICc = 189.206811 Ancestral state = 0.0 Optimal rate = 281.646938 +/- 0.000006 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582653 AIC = 209.165305 AICc = 209.552402 Ancestral state = -0.0 Optimal rate = 1725.471354 +/- 0.000091 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409862 AIC = 188.819725 AICc = 189.206822 Ancestral state = 0.0 Optimal rate = 948.475661 +/- 0.000016 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582565 AIC = 209.16513 AICc = 209.552227 Ancestral state = -0.0 Optimal rate = 365.943014 +/- 0.000018 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409854 AIC = 188.819707 AICc = 189.206804 Ancestral state = -0.0 Optimal rate = 201.156418 +/- 0.000005 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582495 AIC = 209.164991 AICc = 209.552087 Ancestral state = 0.0 Optimal rate = 1274.401497 +/- 0.000076 Note that +/- reflects imprecision due to numerical optimization LIB: Generator type: mt19937 LIB: Seed = 1302727603 LIB: First value = 1401083107 Progress: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% |********************************************************************************| Now optimizing with taxset ALL -lnL = 102.58253 AIC = 209.165059 AICc = 209.552156 Ancestral state = 0.0 Optimal rate = 553.175444 +/- 0.000025 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409867 AIC = 188.819734 AICc = 189.206831 Ancestral state = 0.0 Optimal rate = 304.077721 +/- 0.000006 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.58259 AIC = 209.165181 AICc = 209.552277 Ancestral state = -0.0 Optimal rate = 407.442903 +/- 0.000024 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.40986 AIC = 188.81972 AICc = 189.206817 Ancestral state = 0.0 Optimal rate = 223.968404 +/- 0.000004 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582641 AIC = 209.165282 AICc = 209.552379 Ancestral state = -0.0 Optimal rate = 512.373249 +/- 0.00003 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409857 AIC = 188.819714 AICc = 189.206811 Ancestral state = 0.0 Optimal rate = 281.646938 +/- 0.000006 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582653 AIC = 209.165305 AICc = 209.552402 Ancestral state = -0.0 Optimal rate = 1725.471354 +/- 0.000091 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409862 AIC = 188.819725 AICc = 189.206822 Ancestral state = 0.0 Optimal rate = 948.475661 +/- 0.000016 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582565 AIC = 209.16513 AICc = 209.552227 Ancestral state = -0.0 Optimal rate = 365.943014 +/- 0.000018 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409854 AIC = 188.819707 AICc = 189.206804 Ancestral state = -0.0 Optimal rate = 201.156418 +/- 0.000005 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582495 AIC = 209.164991 AICc = 209.552087 Ancestral state = 0.0 Optimal rate = 1274.401497 +/- 0.000076 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409865 AIC = 188.819729 AICc = 189.206826 Ancestral state = 0.0 Optimal rate = 700.533322 +/- 0.000014 Note that +/- reflects imprecision due to numerical optimization LIB: Generator type: mt19937 LIB: Seed = 1302727606 LIB: First value = 2556898150 Progress: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% |********************************************************************************| Now optimizing with taxset ALL -lnL = 102.58253 AIC = 209.165059 AICc = 209.552156 Ancestral state = 0.0 Optimal rate = 553.175444 +/- 0.000025 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409867 AIC = 188.819734 AICc = 189.206831 Ancestral state = 0.0 Optimal rate = 304.077721 +/- 0.000006 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.58259 AIC = 209.165181 AICc = 209.552277 Ancestral state = -0.0 Optimal rate = 407.442903 +/- 0.000024 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.40986 AIC = 188.81972 AICc = 189.206817 Ancestral state = 0.0 Optimal rate = 223.968404 +/- 0.000004 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582641 AIC = 209.165282 AICc = 209.552379 Ancestral state = -0.0 Optimal rate = 512.373249 +/- 0.00003 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409857 AIC = 188.819714 AICc = 189.206811 Ancestral state = 0.0 Optimal rate = 281.646938 +/- 0.000006 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582653 AIC = 209.165305 AICc = 209.552402 Ancestral state = -0.0 Optimal rate = 1725.471354 +/- 0.000091 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409862 AIC = 188.819725 AICc = 189.206822 Ancestral state = 0.0 Optimal rate = 948.475661 +/- 0.000016 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582565 AIC = 209.16513 AICc = 209.552227 Ancestral state = -0.0 Optimal rate = 365.943014 +/- 0.000018 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409854 AIC = 188.819707 AICc = 189.206804 Ancestral state = -0.0 Optimal rate = 201.156418 +/- 0.000005 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582495 AIC = 209.164991 AICc = 209.552087 Ancestral state = 0.0 Optimal rate = 1274.401497 +/- 0.000076 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409865 AIC = 188.819729 AICc = 189.206826 Ancestral state = 0.0 Optimal rate = 700.533322 +/- 0.000014 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582564 AIC = 209.165128 AICc = 209.552224 Ancestral state = -0.0 Optimal rate = 596.175545 +/- 0.000029 Note that +/- reflects imprecision due to numerical optimization LIB: Generator type: mt19937 LIB: Seed = 1302727606 LIB: First value = 2556898150 Progress: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% |********************************************************************************| Now optimizing with taxset ALL -lnL = 102.58253 AIC = 209.165059 AICc = 209.552156 Ancestral state = 0.0 Optimal rate = 553.175444 +/- 0.000025 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409867 AIC = 188.819734 AICc = 189.206831 Ancestral state = 0.0 Optimal rate = 304.077721 +/- 0.000006 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.58259 AIC = 209.165181 AICc = 209.552277 Ancestral state = -0.0 Optimal rate = 407.442903 +/- 0.000024 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.40986 AIC = 188.81972 AICc = 189.206817 Ancestral state = 0.0 Optimal rate = 223.968404 +/- 0.000004 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582641 AIC = 209.165282 AICc = 209.552379 Ancestral state = -0.0 Optimal rate = 512.373249 +/- 0.00003 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409857 AIC = 188.819714 AICc = 189.206811 Ancestral state = 0.0 Optimal rate = 281.646938 +/- 0.000006 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582653 AIC = 209.165305 AICc = 209.552402 Ancestral state = -0.0 Optimal rate = 1725.471354 +/- 0.000091 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409862 AIC = 188.819725 AICc = 189.206822 Ancestral state = 0.0 Optimal rate = 948.475661 +/- 0.000016 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582565 AIC = 209.16513 AICc = 209.552227 Ancestral state = -0.0 Optimal rate = 365.943014 +/- 0.000018 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409854 AIC = 188.819707 AICc = 189.206804 Ancestral state = -0.0 Optimal rate = 201.156418 +/- 0.000005 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582495 AIC = 209.164991 AICc = 209.552087 Ancestral state = 0.0 Optimal rate = 1274.401497 +/- 0.000076 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409865 AIC = 188.819729 AICc = 189.206826 Ancestral state = 0.0 Optimal rate = 700.533322 +/- 0.000014 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582564 AIC = 209.165128 AICc = 209.552224 Ancestral state = -0.0 Optimal rate = 596.175545 +/- 0.000029 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409859 AIC = 188.819718 AICc = 189.206814 Ancestral state = 0.0 Optimal rate = 327.713832 +/- 0.000007 Note that +/- reflects imprecision due to numerical optimization LIB: Generator type: mt19937 LIB: Seed = 1302727607 LIB: First value = 2270895862 Progress: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% |********************************************************************************| Now optimizing with taxset ALL -lnL = 102.58253 AIC = 209.165059 AICc = 209.552156 Ancestral state = 0.0 Optimal rate = 553.175444 +/- 0.000025 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409867 AIC = 188.819734 AICc = 189.206831 Ancestral state = 0.0 Optimal rate = 304.077721 +/- 0.000006 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.58259 AIC = 209.165181 AICc = 209.552277 Ancestral state = -0.0 Optimal rate = 407.442903 +/- 0.000024 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.40986 AIC = 188.81972 AICc = 189.206817 Ancestral state = 0.0 Optimal rate = 223.968404 +/- 0.000004 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582641 AIC = 209.165282 AICc = 209.552379 Ancestral state = -0.0 Optimal rate = 512.373249 +/- 0.00003 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409857 AIC = 188.819714 AICc = 189.206811 Ancestral state = 0.0 Optimal rate = 281.646938 +/- 0.000006 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582653 AIC = 209.165305 AICc = 209.552402 Ancestral state = -0.0 Optimal rate = 1725.471354 +/- 0.000091 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409862 AIC = 188.819725 AICc = 189.206822 Ancestral state = 0.0 Optimal rate = 948.475661 +/- 0.000016 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582565 AIC = 209.16513 AICc = 209.552227 Ancestral state = -0.0 Optimal rate = 365.943014 +/- 0.000018 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409854 AIC = 188.819707 AICc = 189.206804 Ancestral state = -0.0 Optimal rate = 201.156418 +/- 0.000005 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582495 AIC = 209.164991 AICc = 209.552087 Ancestral state = 0.0 Optimal rate = 1274.401497 +/- 0.000076 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409865 AIC = 188.819729 AICc = 189.206826 Ancestral state = 0.0 Optimal rate = 700.533322 +/- 0.000014 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582564 AIC = 209.165128 AICc = 209.552224 Ancestral state = -0.0 Optimal rate = 596.175545 +/- 0.000029 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409859 AIC = 188.819718 AICc = 189.206814 Ancestral state = 0.0 Optimal rate = 327.713832 +/- 0.000007 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582526 AIC = 209.165052 AICc = 209.552149 Ancestral state = -0.0 Optimal rate = 858.666867 +/- 0.000042 Note that +/- reflects imprecision due to numerical optimization LIB: Generator type: mt19937 LIB: Seed = 1302727609 LIB: First value = 260994250 Progress: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% |********************************************************************************| Now optimizing with taxset ALL -lnL = 102.58253 AIC = 209.165059 AICc = 209.552156 Ancestral state = 0.0 Optimal rate = 553.175444 +/- 0.000025 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409867 AIC = 188.819734 AICc = 189.206831 Ancestral state = 0.0 Optimal rate = 304.077721 +/- 0.000006 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.58259 AIC = 209.165181 AICc = 209.552277 Ancestral state = -0.0 Optimal rate = 407.442903 +/- 0.000024 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.40986 AIC = 188.81972 AICc = 189.206817 Ancestral state = 0.0 Optimal rate = 223.968404 +/- 0.000004 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582641 AIC = 209.165282 AICc = 209.552379 Ancestral state = -0.0 Optimal rate = 512.373249 +/- 0.00003 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409857 AIC = 188.819714 AICc = 189.206811 Ancestral state = 0.0 Optimal rate = 281.646938 +/- 0.000006 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582653 AIC = 209.165305 AICc = 209.552402 Ancestral state = -0.0 Optimal rate = 1725.471354 +/- 0.000091 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409862 AIC = 188.819725 AICc = 189.206822 Ancestral state = 0.0 Optimal rate = 948.475661 +/- 0.000016 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582565 AIC = 209.16513 AICc = 209.552227 Ancestral state = -0.0 Optimal rate = 365.943014 +/- 0.000018 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409854 AIC = 188.819707 AICc = 189.206804 Ancestral state = -0.0 Optimal rate = 201.156418 +/- 0.000005 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582495 AIC = 209.164991 AICc = 209.552087 Ancestral state = 0.0 Optimal rate = 1274.401497 +/- 0.000076 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409865 AIC = 188.819729 AICc = 189.206826 Ancestral state = 0.0 Optimal rate = 700.533322 +/- 0.000014 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582564 AIC = 209.165128 AICc = 209.552224 Ancestral state = -0.0 Optimal rate = 596.175545 +/- 0.000029 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409859 AIC = 188.819718 AICc = 189.206814 Ancestral state = 0.0 Optimal rate = 327.713832 +/- 0.000007 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582526 AIC = 209.165052 AICc = 209.552149 Ancestral state = -0.0 Optimal rate = 858.666867 +/- 0.000042 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409861 AIC = 188.819722 AICc = 189.206819 Ancestral state = 0.0 Optimal rate = 472.004734 +/- 0.00001 Note that +/- reflects imprecision due to numerical optimization LIB: Generator type: mt19937 LIB: Seed = 1302727609 LIB: First value = 260994250 Progress: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% |********************************************************************************| Now optimizing with taxset ALL -lnL = 102.58253 AIC = 209.165059 AICc = 209.552156 Ancestral state = 0.0 Optimal rate = 553.175444 +/- 0.000025 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409867 AIC = 188.819734 AICc = 189.206831 Ancestral state = 0.0 Optimal rate = 304.077721 +/- 0.000006 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.58259 AIC = 209.165181 AICc = 209.552277 Ancestral state = -0.0 Optimal rate = 407.442903 +/- 0.000024 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.40986 AIC = 188.81972 AICc = 189.206817 Ancestral state = 0.0 Optimal rate = 223.968404 +/- 0.000004 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582641 AIC = 209.165282 AICc = 209.552379 Ancestral state = -0.0 Optimal rate = 512.373249 +/- 0.00003 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409857 AIC = 188.819714 AICc = 189.206811 Ancestral state = 0.0 Optimal rate = 281.646938 +/- 0.000006 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582653 AIC = 209.165305 AICc = 209.552402 Ancestral state = -0.0 Optimal rate = 1725.471354 +/- 0.000091 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409862 AIC = 188.819725 AICc = 189.206822 Ancestral state = 0.0 Optimal rate = 948.475661 +/- 0.000016 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582565 AIC = 209.16513 AICc = 209.552227 Ancestral state = -0.0 Optimal rate = 365.943014 +/- 0.000018 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409854 AIC = 188.819707 AICc = 189.206804 Ancestral state = -0.0 Optimal rate = 201.156418 +/- 0.000005 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582495 AIC = 209.164991 AICc = 209.552087 Ancestral state = 0.0 Optimal rate = 1274.401497 +/- 0.000076 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409865 AIC = 188.819729 AICc = 189.206826 Ancestral state = 0.0 Optimal rate = 700.533322 +/- 0.000014 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582564 AIC = 209.165128 AICc = 209.552224 Ancestral state = -0.0 Optimal rate = 596.175545 +/- 0.000029 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409859 AIC = 188.819718 AICc = 189.206814 Ancestral state = 0.0 Optimal rate = 327.713832 +/- 0.000007 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582526 AIC = 209.165052 AICc = 209.552149 Ancestral state = -0.0 Optimal rate = 858.666867 +/- 0.000042 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409861 AIC = 188.819722 AICc = 189.206819 Ancestral state = 0.0 Optimal rate = 472.004734 +/- 0.00001 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582562 AIC = 209.165124 AICc = 209.552221 Ancestral state = 0.0 Optimal rate = 539.373263 +/- 0.000032 Note that +/- reflects imprecision due to numerical optimization LIB: Generator type: mt19937 LIB: Seed = 1302727610 LIB: First value = 2386457453 Progress: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% |********************************************************************************| Now optimizing with taxset ALL -lnL = 102.58253 AIC = 209.165059 AICc = 209.552156 Ancestral state = 0.0 Optimal rate = 553.175444 +/- 0.000025 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409867 AIC = 188.819734 AICc = 189.206831 Ancestral state = 0.0 Optimal rate = 304.077721 +/- 0.000006 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.58259 AIC = 209.165181 AICc = 209.552277 Ancestral state = -0.0 Optimal rate = 407.442903 +/- 0.000024 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.40986 AIC = 188.81972 AICc = 189.206817 Ancestral state = 0.0 Optimal rate = 223.968404 +/- 0.000004 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582641 AIC = 209.165282 AICc = 209.552379 Ancestral state = -0.0 Optimal rate = 512.373249 +/- 0.00003 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409857 AIC = 188.819714 AICc = 189.206811 Ancestral state = 0.0 Optimal rate = 281.646938 +/- 0.000006 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582653 AIC = 209.165305 AICc = 209.552402 Ancestral state = -0.0 Optimal rate = 1725.471354 +/- 0.000091 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409862 AIC = 188.819725 AICc = 189.206822 Ancestral state = 0.0 Optimal rate = 948.475661 +/- 0.000016 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582565 AIC = 209.16513 AICc = 209.552227 Ancestral state = -0.0 Optimal rate = 365.943014 +/- 0.000018 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409854 AIC = 188.819707 AICc = 189.206804 Ancestral state = -0.0 Optimal rate = 201.156418 +/- 0.000005 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582495 AIC = 209.164991 AICc = 209.552087 Ancestral state = 0.0 Optimal rate = 1274.401497 +/- 0.000076 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409865 AIC = 188.819729 AICc = 189.206826 Ancestral state = 0.0 Optimal rate = 700.533322 +/- 0.000014 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582564 AIC = 209.165128 AICc = 209.552224 Ancestral state = -0.0 Optimal rate = 596.175545 +/- 0.000029 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409859 AIC = 188.819718 AICc = 189.206814 Ancestral state = 0.0 Optimal rate = 327.713832 +/- 0.000007 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582526 AIC = 209.165052 AICc = 209.552149 Ancestral state = -0.0 Optimal rate = 858.666867 +/- 0.000042 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409861 AIC = 188.819722 AICc = 189.206819 Ancestral state = 0.0 Optimal rate = 472.004734 +/- 0.00001 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582562 AIC = 209.165124 AICc = 209.552221 Ancestral state = 0.0 Optimal rate = 539.373263 +/- 0.000032 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409855 AIC = 188.81971 AICc = 189.206807 Ancestral state = 0.0 Optimal rate = 296.489945 +/- 0.000007 Note that +/- reflects imprecision due to numerical optimization LIB: Generator type: mt19937 LIB: Seed = 1302727611 LIB: First value = 3442876234 Progress: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% |********************************************************************************| Now optimizing with taxset ALL -lnL = 102.58253 AIC = 209.165059 AICc = 209.552156 Ancestral state = 0.0 Optimal rate = 553.175444 +/- 0.000025 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409867 AIC = 188.819734 AICc = 189.206831 Ancestral state = 0.0 Optimal rate = 304.077721 +/- 0.000006 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.58259 AIC = 209.165181 AICc = 209.552277 Ancestral state = -0.0 Optimal rate = 407.442903 +/- 0.000024 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.40986 AIC = 188.81972 AICc = 189.206817 Ancestral state = 0.0 Optimal rate = 223.968404 +/- 0.000004 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582641 AIC = 209.165282 AICc = 209.552379 Ancestral state = -0.0 Optimal rate = 512.373249 +/- 0.00003 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409857 AIC = 188.819714 AICc = 189.206811 Ancestral state = 0.0 Optimal rate = 281.646938 +/- 0.000006 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582653 AIC = 209.165305 AICc = 209.552402 Ancestral state = -0.0 Optimal rate = 1725.471354 +/- 0.000091 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409862 AIC = 188.819725 AICc = 189.206822 Ancestral state = 0.0 Optimal rate = 948.475661 +/- 0.000016 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582565 AIC = 209.16513 AICc = 209.552227 Ancestral state = -0.0 Optimal rate = 365.943014 +/- 0.000018 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409854 AIC = 188.819707 AICc = 189.206804 Ancestral state = -0.0 Optimal rate = 201.156418 +/- 0.000005 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582495 AIC = 209.164991 AICc = 209.552087 Ancestral state = 0.0 Optimal rate = 1274.401497 +/- 0.000076 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409865 AIC = 188.819729 AICc = 189.206826 Ancestral state = 0.0 Optimal rate = 700.533322 +/- 0.000014 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582564 AIC = 209.165128 AICc = 209.552224 Ancestral state = -0.0 Optimal rate = 596.175545 +/- 0.000029 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409859 AIC = 188.819718 AICc = 189.206814 Ancestral state = 0.0 Optimal rate = 327.713832 +/- 0.000007 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582526 AIC = 209.165052 AICc = 209.552149 Ancestral state = -0.0 Optimal rate = 858.666867 +/- 0.000042 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409861 AIC = 188.819722 AICc = 189.206819 Ancestral state = 0.0 Optimal rate = 472.004734 +/- 0.00001 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582562 AIC = 209.165124 AICc = 209.552221 Ancestral state = 0.0 Optimal rate = 539.373263 +/- 0.000032 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409855 AIC = 188.81971 AICc = 189.206807 Ancestral state = 0.0 Optimal rate = 296.489945 +/- 0.000007 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582569 AIC = 209.165138 AICc = 209.552235 Ancestral state = -0.0 Optimal rate = 1120.318889 +/- 0.000046 Note that +/- reflects imprecision due to numerical optimization LIB: Generator type: mt19937 LIB: Seed = 1302727612 LIB: First value = 3364798794 Progress: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% |********************************************************************************| Now optimizing with taxset ALL -lnL = 102.58253 AIC = 209.165059 AICc = 209.552156 Ancestral state = 0.0 Optimal rate = 553.175444 +/- 0.000025 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409867 AIC = 188.819734 AICc = 189.206831 Ancestral state = 0.0 Optimal rate = 304.077721 +/- 0.000006 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.58259 AIC = 209.165181 AICc = 209.552277 Ancestral state = -0.0 Optimal rate = 407.442903 +/- 0.000024 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.40986 AIC = 188.81972 AICc = 189.206817 Ancestral state = 0.0 Optimal rate = 223.968404 +/- 0.000004 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582641 AIC = 209.165282 AICc = 209.552379 Ancestral state = -0.0 Optimal rate = 512.373249 +/- 0.00003 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409857 AIC = 188.819714 AICc = 189.206811 Ancestral state = 0.0 Optimal rate = 281.646938 +/- 0.000006 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582653 AIC = 209.165305 AICc = 209.552402 Ancestral state = -0.0 Optimal rate = 1725.471354 +/- 0.000091 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409862 AIC = 188.819725 AICc = 189.206822 Ancestral state = 0.0 Optimal rate = 948.475661 +/- 0.000016 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582565 AIC = 209.16513 AICc = 209.552227 Ancestral state = -0.0 Optimal rate = 365.943014 +/- 0.000018 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409854 AIC = 188.819707 AICc = 189.206804 Ancestral state = -0.0 Optimal rate = 201.156418 +/- 0.000005 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582495 AIC = 209.164991 AICc = 209.552087 Ancestral state = 0.0 Optimal rate = 1274.401497 +/- 0.000076 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409865 AIC = 188.819729 AICc = 189.206826 Ancestral state = 0.0 Optimal rate = 700.533322 +/- 0.000014 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582564 AIC = 209.165128 AICc = 209.552224 Ancestral state = -0.0 Optimal rate = 596.175545 +/- 0.000029 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409859 AIC = 188.819718 AICc = 189.206814 Ancestral state = 0.0 Optimal rate = 327.713832 +/- 0.000007 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582526 AIC = 209.165052 AICc = 209.552149 Ancestral state = -0.0 Optimal rate = 858.666867 +/- 0.000042 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409861 AIC = 188.819722 AICc = 189.206819 Ancestral state = 0.0 Optimal rate = 472.004734 +/- 0.00001 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582562 AIC = 209.165124 AICc = 209.552221 Ancestral state = 0.0 Optimal rate = 539.373263 +/- 0.000032 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.409855 AIC = 188.81971 AICc = 189.206807 Ancestral state = 0.0 Optimal rate = 296.489945 +/- 0.000007 Note that +/- reflects imprecision due to numerical optimization -lnL = 102.582569 AIC = 209.165138 AICc = 209.552235 Ancestral state = -0.0 Optimal rate = 1120.318889 +/- 0.000046 Note that +/- reflects imprecision due to numerical optimization -lnL = 92.40986 AIC = 188.819721 AICc = 189.206817 Ancestral state = -0.0 Optimal rate = 615.831884 +/- 0.000018 Note that +/- reflects imprecision due to numerical optimization You have chosen Brownian motion with one rate parameter per state Now optimizing with taxset ALL LIB: Generator type: mt19937 LIB: Seed = 1302727613 LIB: First value = 584949607 Progress: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% |********************************************************************************| -lnL = 102.50545 AIC = 211.010899 AICc = 211.810899 Ancestral state = 0.166982 +/- 0.0 Rate in state 0 = 464.475508 +/- 0.000022 Rate in state 1 = 579.916677 +/- 0.000025 LIB: Generator type: mt19937 LIB: Seed = 1302727615 LIB: First value = 1261007019 Progress: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% |********************************************************************************| -lnL = 89.254264 AIC = 184.508528 AICc = 185.308528 Ancestral state = 1.672717 +/- 0.0 Rate in state 0 = 48.509069 +/- 0.000003 Rate in state 1 = 389.344332 +/- 0.000007 LIB: Generator type: mt19937 LIB: Seed = 1302727618 LIB: First value = 1742015646 Progress: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% |********************************************************************************| -lnL = 102.419208 AIC = 210.838417 AICc = 211.638417 Ancestral state = 0.174773 +/- 0.000001 Rate in state 0 = 316.968765 +/- 0.000018 Rate in state 1 = 437.333154 +/- 0.000014 LIB: Generator type: mt19937 LIB: Seed = 1302727620 LIB: First value = 1277249478 Progress: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% |********************************************************************************| -lnL = 89.407904 AIC = 184.815808 AICc = 185.615808 Ancestral state = 1.805435 +/- 0.0 Rate in state 0 = 46.421965 +/- 0.000002 Rate in state 1 = 289.212085 +/- 0.000007 LIB: Generator type: mt19937 LIB: Seed = 1302727623 LIB: First value = 956999990 Progress: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% |********************************************************************************| -lnL = 102.096225 AIC = 210.19245 AICc = 210.99245 Ancestral state = 0.339607 +/- 0.0 Rate in state 0 = 345.32383 +/- 0.000022 Rate in state 1 = 583.688279 +/- 0.000032 LIB: Generator type: mt19937 LIB: Seed = 1302727625 LIB: First value = 3594869176 Progress: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% |********************************************************************************| -lnL = 88.816161 AIC = 183.632321 AICc = 184.432321 Ancestral state = 2.018542 +/- 0.0 Rate in state 0 = 62.912362 +/- 0.000002 Rate in state 1 = 383.826342 +/- 0.000009 LIB: Generator type: mt19937 LIB: Seed = 1302727629 LIB: First value = 191978224 Progress: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% |********************************************************************************| -lnL = 102.443898 AIC = 210.887796 AICc = 211.687796 Ancestral state = 0.174468 +/- 0.000001 Rate in state 0 = 1365.815697 +/- 0.000114 Rate in state 1 = 1840.154464 +/- 0.000077 LIB: Generator type: mt19937 LIB: Seed = 1302727631 LIB: First value = 2768440757 Progress: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% |********************************************************************************| -lnL = 89.378442 AIC = 184.756885 AICc = 185.556885 Ancestral state = 1.897972 +/- 0.0 Rate in state 0 = 192.521295 +/- 0.000009 Rate in state 1 = 1213.884642 +/- 0.000024 LIB: Generator type: mt19937 LIB: Seed = 1302727634 LIB: First value = 726981980 Progress: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% |********************************************************************************| -lnL = 102.561873 AIC = 211.123746 AICc = 211.923746 Ancestral state = 0.091664 +/- 0.000001 Rate in state 0 = 333.333132 +/- 0.000029 Rate in state 1 = 374.619225 +/- 0.000016 LIB: Generator type: mt19937 LIB: Seed = 1302727636 LIB: First value = 4018168641 Progress: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% |********************************************************************************| -lnL = 89.341861 AIC = 184.683723 AICc = 185.483723 Ancestral state = 0.775709 +/- 0.0 Rate in state 0 = 32.408443 +/- 0.000001 Rate in state 1 = 242.161629 +/- 0.000005 LIB: Generator type: mt19937 LIB: Seed = 1302727640 LIB: First value = 821474179 Progress: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% |********************************************************************************| -lnL = 102.212816 AIC = 210.425632 AICc = 211.225632 Ancestral state = 0.263324 +/- 0.0 Rate in state 0 = 891.261916 +/- 0.000059 Rate in state 1 = 1427.791203 +/- 0.000057 LIB: Generator type: mt19937 LIB: Seed = 1302727642 LIB: First value = 1636060086 Progress: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% |********************************************************************************| -lnL = 89.226381 AIC = 184.452762 AICc = 185.252762 Ancestral state = 1.717434 +/- 0.0 Rate in state 0 = 171.942948 +/- 0.000009 Rate in state 1 = 932.902619 +/- 0.000017 LIB: Generator type: mt19937 LIB: Seed = 1302727645 LIB: First value = 383827996 Progress: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% |********************************************************************************| -lnL = 102.386965 AIC = 210.77393 AICc = 211.57393 Ancestral state = 0.132402 +/- 0.0 Rate in state 0 = 455.28497 +/- 0.00003 Rate in state 1 = 643.934328 +/- 0.000024 LIB: Generator type: mt19937 LIB: Seed = 1302727648 LIB: First value = 1824695489 Progress: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% |********************************************************************************| -lnL = 89.443934 AIC = 184.887868 AICc = 185.687868 Ancestral state = 1.598443 +/- 0.0 Rate in state 0 = 70.025337 +/- 0.000004 Rate in state 1 = 424.579028 +/- 0.00001 LIB: Generator type: mt19937 LIB: Seed = 1302727651 LIB: First value = 268450339 Progress: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% |********************************************************************************| -lnL = 102.456304 AIC = 210.912609 AICc = 211.712609 Ancestral state = 0.191219 +/- 0.0 Rate in state 0 = 687.330893 +/- 0.000039 Rate in state 1 = 912.949181 +/- 0.000024 LIB: Generator type: mt19937 LIB: Seed = 1302727653 LIB: First value = 1145686196 Progress: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% |********************************************************************************| -lnL = 89.434966 AIC = 184.869932 AICc = 185.669932 Ancestral state = 1.890061 +/- 0.0 Rate in state 0 = 95.620086 +/- 0.000003 Rate in state 1 = 599.007677 +/- 0.000013 LIB: Generator type: mt19937 LIB: Seed = 1302727656 LIB: First value = 2154935793 Progress: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% |********************************************************************************| -lnL = 102.461326 AIC = 210.922652 AICc = 211.722652 Ancestral state = 0.140937 +/- 0.000001 Rate in state 0 = 432.723485 +/- 0.000035 Rate in state 1 = 572.399145 +/- 0.00002 LIB: Generator type: mt19937 LIB: Seed = 1302727658 LIB: First value = 3681056695 Progress: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% |********************************************************************************| -lnL = 89.510107 AIC = 185.020214 AICc = 185.820214 Ancestral state = 1.828222 +/- 0.0 Rate in state 0 = 61.010674 +/- 0.000004 Rate in state 1 = 377.431703 +/- 0.000012 LIB: Generator type: mt19937 LIB: Seed = 1302727662 LIB: First value = 711453016 Progress: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% |********************************************************************************| -lnL = 102.43169 AIC = 210.86338 AICc = 211.66338 Ancestral state = 0.236905 +/- 0.0 Rate in state 0 = 877.956583 +/- 0.000073 Rate in state 1 = 1199.851098 +/- 0.000064 LIB: Generator type: mt19937 LIB: Seed = 1302727664 LIB: First value = 2247657109 Progress: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% |********************************************************************************| -lnL = 89.229662 AIC = 184.459323 AICc = 185.259323 Ancestral state = 2.148044 +/- 0.0 Rate in state 0 = 122.38892 +/- 0.000005 Rate in state 1 = 793.282047 +/- 0.000021 LIB: Generator type: mt19937 LIB: Seed = 1302727668 LIB: First value = 3805842839 RCPP: 'd:/temp/RtmpwX9NTh/file69d7190b' Piping commands to brownie objectLIB: preprocessing command: execute 'd:/temp/RtmpwX9NTh/file69d7190b' .. conditioned command is: ;execute 'd:/temp/RtmpwX9NTh/file69d7190b';end; LIB: handle cmd ';execute 'd:/temp/RtmpwX9NTh/file69d7190b';end;' Opening d:/temp/RtmpwX9NTh/file69d7190b... Starting to execute NEXUS file Entering TAXA block...done Entering TREES block...done Entering CHARACTERS block...done (Skipping brownie block) Finished executing NEXUS file TREES block contains one tree 1 UNTITLED (rooted, weight = 1,default tree) Reading TAXA block... Reading TREES block... Reading CHARACTERS block... Reading BROWNIE block... You have chosen a non-time-reversible model: rates are free to vary You have chosen equal frequencies for all states WARNING: if some characters have fewer than 2 character states, the output in the output table will be wrong for those chars ------------------------------------------------------------------------------- WARNING: You are trying to estimate 2 parameters, but only have 13 taxa. Make sure to try some simpler models, and expect quite imprecise estimates. ------------------------------------------------------------------------------- Progress: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% |********************************************************************************| Tree = 1: UNTITLED -lnL = 6.043574 AIC = 16.087148 AICc = 17.287148 Rates: nonreversible q_0_1 = 1.652106 +/- 0.0 q_1_0 = 6.252674 +/- 0.0 Statefreqs: uniform P(0) = 0.5 P(1) = 0.5 tree input1 = (((((((((fuliginosa[&S 1:0.055]:0.055,fortis[&S 1:0.055]:0.055)'[&S 0:0.0275,1:0.0275]':0.055,magnirostris[&S 0:0.11]:0.11)'[&S 0:0.07333]':0.07333,conirostris[&S 0:0.18333]:0.18333)'[&S 0:0.00917]':0.00917,scandens[&S 0:0.1925]:0.1925)'[&S 0:0.0355]':0.0355,difficilis[&S 0:0.114,1:0.114]:0.228)'[&S 0:0.10346]':0.10346,(pallida[&S 0:0.08667]:0.08667,((parvulus[&S 0:0.02]:0.02,psittacula[&S 0:0.02]:0.02)'[&S 0:0.015]':0.015,pauper[&S 0:0.035]:0.035)'[&S 0:0.05167]':0.05167)'[&S 0:0.24479]':0.24479)'[&S 0:0.13404]':0.13404,Platyspiza[&S 0:0.4655]:0.4655)'[&S 0:0.06859]':0.06859,fusca[&S 0:0.53409]:0.53409)'[&S 0:0.04924]':0.04924,Pinaroloxias[&S 0:0.58333]:0.58333); tree input1 = (((((((((fuliginosa:{1,0.055},fortis:{1,0.055})':{0,0.0275:1,0.0275}',magnirostris:{0,0.11})':{0,0.07333}',conirostris:{0,0.18333})':{0,0.00917}',scandens:{0,0.1925})':{0,0.0355}',difficilis:{0,0.114:1,0.114})':{0,0.10346}',(pallida:{0,0.08667},((parvulus:{0,0.02},psittacula:{0,0.02})':{0,0.015}',pauper:{0,0.035})':{0,0.05167}')':{0,0.24479}')':{0,0.13404}',Platyspiza:{0,0.4655})':{0,0.06859}',fusca:{0,0.53409})':{0,0.04924}',Pinaroloxias:{0,0.58333}); ÚÄ fuliginosa:{1,0.055} Ú´:{0,0.0275:1,0.0275} ³ÀÄ fortis:{1,0.055} Ú´:{0,0.07333} ³ÀÄÄ magnirostris:{0,0.11} Ú´:{0,0.00917} ³ÀÄÄÄ conirostris:{0,0.18333} Ú´:{0,0.0355} ³ÀÄÄÄÄ scandens:{0,0.1925} ÚÄÄÄ´:{0,0.10346} ³ ÀÄÄÄÄÄ difficilis:{0,0.114:1,0.114} Ú´:{0,0.13404} ³³ ÚÄÄÄ pallida:{0,0.08667} ³ÀÄÄÄÄÄ´:{0,0.24479} ³ ³ ÚÄ parvulus:{0,0.02} ³ ³Ú´:{0,0.015} ³ ³³ÀÄ psittacula:{0,0.02} ³ À´:{0,0.05167} ³ ÀÄÄ pauper:{0,0.035} Ú´:{0,0.06859} ³ÀÄÄÄÄÄÄÄÄÄÄ Platyspiza:{0,0.4655} Ú´:{0,0.04924} ³ÀÄÄÄÄÄÄÄÄÄÄÄ fusca:{0,0.53409} ´ ÀÄÄÄÄÄÄÄÄÄÄÄÄ Pinaroloxias:{0,0.58333} You have chosen a non-time-reversible model: rates are free to vary You have chosen to use equilibrium state frequencies WARNING: if some characters have fewer than 2 character states, the output in the output table will be wrong for those chars ------------------------------------------------------------------------------- WARNING: You are trying to estimate 2 parameters, but only have 13 taxa. Make sure to try some simpler models, and expect quite imprecise estimates. ------------------------------------------------------------------------------- Progress: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% |********************************************************************************| Tree = 1: UNTITLED -lnL = 6.042915 AIC = 16.085830 AICc = 17.285830 Rates: nonreversible q_0_1 = 1.661837 +/- 0.000001 q_1_0 = 6.181369 +/- 0.000002 Statefreqs: equilibrium P(0) = 0.788118 P(1) = 0.211882 tree input1 = (((((((((fuliginosa[&S 1:0.055]:0.055,fortis[&S 1:0.055]:0.055)'[&S 0:0.0275,1:0.0275]':0.055,magnirostris[&S 0:0.11]:0.11)'[&S 0:0.07333]':0.07333,conirostris[&S 0:0.18333]:0.18333)'[&S 0:0.00917]':0.00917,scandens[&S 0:0.1925]:0.1925)'[&S 0:0.0355]':0.0355,difficilis[&S 0:0.114,1:0.114]:0.228)'[&S 0:0.10346]':0.10346,(pallida[&S 0:0.08667]:0.08667,((parvulus[&S 0:0.02]:0.02,psittacula[&S 0:0.02]:0.02)'[&S 0:0.015]':0.015,pauper[&S 0:0.035]:0.035)'[&S 0:0.05167]':0.05167)'[&S 0:0.24479]':0.24479)'[&S 0:0.13404]':0.13404,Platyspiza[&S 0:0.4655]:0.4655)'[&S 0:0.06859]':0.06859,fusca[&S 0:0.53409]:0.53409)'[&S 0:0.04924]':0.04924,Pinaroloxias[&S 0:0.58333]:0.58333); tree input1 = (((((((((fuliginosa:{1,0.055},fortis:{1,0.055})':{0,0.0275:1,0.0275}',magnirostris:{0,0.11})':{0,0.07333}',conirostris:{0,0.18333})':{0,0.00917}',scandens:{0,0.1925})':{0,0.0355}',difficilis:{0,0.114:1,0.114})':{0,0.10346}',(pallida:{0,0.08667},((parvulus:{0,0.02},psittacula:{0,0.02})':{0,0.015}',pauper:{0,0.035})':{0,0.05167}')':{0,0.24479}')':{0,0.13404}',Platyspiza:{0,0.4655})':{0,0.06859}',fusca:{0,0.53409})':{0,0.04924}',Pinaroloxias:{0,0.58333}); ÚÄ fuliginosa:{1,0.055} Ú´:{0,0.0275:1,0.0275} ³ÀÄ fortis:{1,0.055} Ú´:{0,0.07333} ³ÀÄÄ magnirostris:{0,0.11} Ú´:{0,0.00917} ³ÀÄÄÄ conirostris:{0,0.18333} Ú´:{0,0.0355} ³ÀÄÄÄÄ scandens:{0,0.1925} ÚÄÄÄ´:{0,0.10346} ³ ÀÄÄÄÄÄ difficilis:{0,0.114:1,0.114} Ú´:{0,0.13404} ³³ ÚÄÄÄ pallida:{0,0.08667} ³ÀÄÄÄÄÄ´:{0,0.24479} ³ ³ ÚÄ parvulus:{0,0.02} ³ ³Ú´:{0,0.015} ³ ³³ÀÄ psittacula:{0,0.02} ³ À´:{0,0.05167} ³ ÀÄÄ pauper:{0,0.035} Ú´:{0,0.06859} ³ÀÄÄÄÄÄÄÄÄÄÄ Platyspiza:{0,0.4655} Ú´:{0,0.04924} ³ÀÄÄÄÄÄÄÄÄÄÄÄ fusca:{0,0.53409} ´ ÀÄÄÄÄÄÄÄÄÄÄÄÄ Pinaroloxias:{0,0.58333} LIB: Generator type: mt19937 LIB: Seed = 1302727671 LIB: First value = 637677713 RCPP: 'd:/temp/RtmpwX9NTh/file21ed26b7' Piping commands to brownie objectLIB: preprocessing command: execute 'd:/temp/RtmpwX9NTh/file21ed26b7' .. conditioned command is: ;execute 'd:/temp/RtmpwX9NTh/file21ed26b7';end; LIB: handle cmd ';execute 'd:/temp/RtmpwX9NTh/file21ed26b7';end;' Opening d:/temp/RtmpwX9NTh/file21ed26b7... Starting to execute NEXUS file Entering TAXA block...done Entering TREES block...done Entering CHARACTERS block...done (Skipping brownie block) Finished executing NEXUS file TREES block contains one tree 1 UNTITLED (rooted, weight = 1,default tree) Reading TAXA block... Reading TREES block... Reading CHARACTERS block... Reading BROWNIE block... You have chosen a non-time-reversible model: rates are free to vary You have chosen equal frequencies for all states WARNING: if some characters have fewer than 2 character states, the output in the output table will be wrong for those chars ------------------------------------------------------------------------------- WARNING: You are trying to estimate 2 parameters, but only have 13 taxa. Make sure to try some simpler models, and expect quite imprecise estimates. ------------------------------------------------------------------------------- Progress: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% |********************************************************************************| Tree = 1: UNTITLED -lnL = 6.043574 AIC = 16.087148 AICc = 17.287148 Rates: nonreversible q_0_1 = 1.652106 +/- 0.0 q_1_0 = 6.252674 +/- 0.0 Statefreqs: uniform P(0) = 0.5 P(1) = 0.5 tree input1 = (((((((((fuliginosa[&S 1:0.055]:0.055,fortis[&S 1:0.055]:0.055)'[&S 0:0.0275,1:0.0275]':0.055,magnirostris[&S 0:0.11]:0.11)'[&S 0:0.07333]':0.07333,conirostris[&S 0:0.18333]:0.18333)'[&S 0:0.00917]':0.00917,scandens[&S 0:0.1925]:0.1925)'[&S 0:0.0355]':0.0355,difficilis[&S 0:0.114,1:0.114]:0.228)'[&S 0:0.10346]':0.10346,(pallida[&S 0:0.08667]:0.08667,((parvulus[&S 0:0.02]:0.02,psittacula[&S 0:0.02]:0.02)'[&S 0:0.015]':0.015,pauper[&S 0:0.035]:0.035)'[&S 0:0.05167]':0.05167)'[&S 0:0.24479]':0.24479)'[&S 0:0.13404]':0.13404,Platyspiza[&S 0:0.4655]:0.4655)'[&S 0:0.06859]':0.06859,fusca[&S 0:0.53409]:0.53409)'[&S 0:0.04924]':0.04924,Pinaroloxias[&S 0:0.58333]:0.58333); tree input1 = (((((((((fuliginosa:{1,0.055},fortis:{1,0.055})':{0,0.0275:1,0.0275}',magnirostris:{0,0.11})':{0,0.07333}',conirostris:{0,0.18333})':{0,0.00917}',scandens:{0,0.1925})':{0,0.0355}',difficilis:{0,0.114:1,0.114})':{0,0.10346}',(pallida:{0,0.08667},((parvulus:{0,0.02},psittacula:{0,0.02})':{0,0.015}',pauper:{0,0.035})':{0,0.05167}')':{0,0.24479}')':{0,0.13404}',Platyspiza:{0,0.4655})':{0,0.06859}',fusca:{0,0.53409})':{0,0.04924}',Pinaroloxias:{0,0.58333}); ÚÄ fuliginosa:{1,0.055} Ú´:{0,0.0275:1,0.0275} ³ÀÄ fortis:{1,0.055} Ú´:{0,0.07333} ³ÀÄÄ magnirostris:{0,0.11} Ú´:{0,0.00917} ³ÀÄÄÄ conirostris:{0,0.18333} Ú´:{0,0.0355} ³ÀÄÄÄÄ scandens:{0,0.1925} ÚÄÄÄ´:{0,0.10346} ³ ÀÄÄÄÄÄ difficilis:{0,0.114:1,0.114} Ú´:{0,0.13404} ³³ ÚÄÄÄ pallida:{0,0.08667} ³ÀÄÄÄÄÄ´:{0,0.24479} ³ ³ ÚÄ parvulus:{0,0.02} ³ ³Ú´:{0,0.015} ³ ³³ÀÄ psittacula:{0,0.02} ³ À´:{0,0.05167} ³ ÀÄÄ pauper:{0,0.035} Ú´:{0,0.06859} ³ÀÄÄÄÄÄÄÄÄÄÄ Platyspiza:{0,0.4655} Ú´:{0,0.04924} ³ÀÄÄÄÄÄÄÄÄÄÄÄ fusca:{0,0.53409} ´ ÀÄÄÄÄÄÄÄÄÄÄÄÄ Pinaroloxias:{0,0.58333} You have chosen a non-time-reversible model: rates are free to vary You have chosen to use equilibrium state frequencies WARNING: if some characters have fewer than 2 character states, the output in the output table will be wrong for those chars ------------------------------------------------------------------------------- WARNING: You are trying to estimate 2 parameters, but only have 13 taxa. Make sure to try some simpler models, and expect quite imprecise estimates. ------------------------------------------------------------------------------- Progress: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% |********************************************************************************| Tree = 1: UNTITLED -lnL = 6.042915 AIC = 16.085830 AICc = 17.285830 Rates: nonreversible q_0_1 = 1.661837 +/- 0.000001 q_1_0 = 6.181369 +/- 0.000002 Statefreqs: equilibrium P(0) = 0.788118 P(1) = 0.211882 tree input1 = (((((((((fuliginosa[&S 1:0.055]:0.055,fortis[&S 1:0.055]:0.055)'[&S 0:0.0275,1:0.0275]':0.055,magnirostris[&S 0:0.11]:0.11)'[&S 0:0.07333]':0.07333,conirostris[&S 0:0.18333]:0.18333)'[&S 0:0.00917]':0.00917,scandens[&S 0:0.1925]:0.1925)'[&S 0:0.0355]':0.0355,difficilis[&S 0:0.114,1:0.114]:0.228)'[&S 0:0.10346]':0.10346,(pallida[&S 0:0.08667]:0.08667,((parvulus[&S 0:0.02]:0.02,psittacula[&S 0:0.02]:0.02)'[&S 0:0.015]':0.015,pauper[&S 0:0.035]:0.035)'[&S 0:0.05167]':0.05167)'[&S 0:0.24479]':0.24479)'[&S 0:0.13404]':0.13404,Platyspiza[&S 0:0.4655]:0.4655)'[&S 0:0.06859]':0.06859,fusca[&S 0:0.53409]:0.53409)'[&S 0:0.04924]':0.04924,Pinaroloxias[&S 0:0.58333]:0.58333); tree input1 = (((((((((fuliginosa:{1,0.055},fortis:{1,0.055})':{0,0.0275:1,0.0275}',magnirostris:{0,0.11})':{0,0.07333}',conirostris:{0,0.18333})':{0,0.00917}',scandens:{0,0.1925})':{0,0.0355}',difficilis:{0,0.114:1,0.114})':{0,0.10346}',(pallida:{0,0.08667},((parvulus:{0,0.02},psittacula:{0,0.02})':{0,0.015}',pauper:{0,0.035})':{0,0.05167}')':{0,0.24479}')':{0,0.13404}',Platyspiza:{0,0.4655})':{0,0.06859}',fusca:{0,0.53409})':{0,0.04924}',Pinaroloxias:{0,0.58333}); ÚÄ fuliginosa:{1,0.055} Ú´:{0,0.0275:1,0.0275} ³ÀÄ fortis:{1,0.055} Ú´:{0,0.07333} ³ÀÄÄ magnirostris:{0,0.11} Ú´:{0,0.00917} ³ÀÄÄÄ conirostris:{0,0.18333} Ú´:{0,0.0355} ³ÀÄÄÄÄ scandens:{0,0.1925} ÚÄÄÄ´:{0,0.10346} ³ ÀÄÄÄÄÄ difficilis:{0,0.114:1,0.114} Ú´:{0,0.13404} ³³ ÚÄÄÄ pallida:{0,0.08667} ³ÀÄÄÄÄÄ´:{0,0.24479} ³ ³ ÚÄ parvulus:{0,0.02} ³ ³Ú´:{0,0.015} ³ ³³ÀÄ psittacula:{0,0.02} ³ À´:{0,0.05167} ³ ÀÄÄ pauper:{0,0.035} Ú´:{0,0.06859} ³ÀÄÄÄÄÄÄÄÄÄÄ Platyspiza:{0,0.4655} Ú´:{0,0.04924} ³ÀÄÄÄÄÄÄÄÄÄÄÄ fusca:{0,0.53409} ´ ÀÄÄÄÄÄÄÄÄÄÄÄÄ Pinaroloxias:{0,0.58333} LIB: Generator type: mt19937 LIB: Seed = 1302727675 LIB: First value = 2620911194 RCPP: 'd:/temp/RtmpwX9NTh/file6d3e6502' Piping commands to brownie objectLIB: preprocessing command: execute 'd:/temp/RtmpwX9NTh/file6d3e6502' .. conditioned command is: ;execute 'd:/temp/RtmpwX9NTh/file6d3e6502';end; LIB: handle cmd ';execute 'd:/temp/RtmpwX9NTh/file6d3e6502';end;' Opening d:/temp/RtmpwX9NTh/file6d3e6502... Starting to execute NEXUS file Entering TAXA block...done Entering TREES block...done Entering CHARACTERS block...done (Skipping brownie block) Finished executing NEXUS file TREES block contains one tree 1 UNTITLED (rooted, weight = 1,default tree) Reading TAXA block... Reading TREES block... Reading CHARACTERS block... Reading BROWNIE block... You have chosen a non-time-reversible model: rates are free to vary You have chosen equal frequencies for all states WARNING: if some characters have fewer than 2 character states, the output in the output table will be wrong for those chars ------------------------------------------------------------------------------- WARNING: You are trying to estimate 2 parameters, but only have 13 taxa. Make sure to try some simpler models, and expect quite imprecise estimates. ------------------------------------------------------------------------------- Progress: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% |********************************************************************************| Tree = 1: UNTITLED -lnL = 6.043574 AIC = 16.087148 AICc = 17.287148 Rates: nonreversible q_0_1 = 1.652106 +/- 0.0 q_1_0 = 6.252674 +/- 0.0 Statefreqs: uniform P(0) = 0.5 P(1) = 0.5 tree input1 = (((((((((fuliginosa[&S 1:0.055]:0.055,fortis[&S 1:0.055]:0.055)'[&S 0:0.0275,1:0.0275]':0.055,magnirostris[&S 0:0.11]:0.11)'[&S 0:0.07333]':0.07333,conirostris[&S 0:0.18333]:0.18333)'[&S 0:0.00917]':0.00917,scandens[&S 0:0.1925]:0.1925)'[&S 0:0.0355]':0.0355,difficilis[&S 0:0.114,1:0.114]:0.228)'[&S 0:0.10346]':0.10346,(pallida[&S 0:0.08667]:0.08667,((parvulus[&S 0:0.02]:0.02,psittacula[&S 0:0.02]:0.02)'[&S 0:0.015]':0.015,pauper[&S 0:0.035]:0.035)'[&S 0:0.05167]':0.05167)'[&S 0:0.24479]':0.24479)'[&S 0:0.13404]':0.13404,Platyspiza[&S 0:0.4655]:0.4655)'[&S 0:0.06859]':0.06859,fusca[&S 0:0.53409]:0.53409)'[&S 0:0.04924]':0.04924,Pinaroloxias[&S 0:0.58333]:0.58333); tree input1 = (((((((((fuliginosa:{1,0.055},fortis:{1,0.055})':{0,0.0275:1,0.0275}',magnirostris:{0,0.11})':{0,0.07333}',conirostris:{0,0.18333})':{0,0.00917}',scandens:{0,0.1925})':{0,0.0355}',difficilis:{0,0.114:1,0.114})':{0,0.10346}',(pallida:{0,0.08667},((parvulus:{0,0.02},psittacula:{0,0.02})':{0,0.015}',pauper:{0,0.035})':{0,0.05167}')':{0,0.24479}')':{0,0.13404}',Platyspiza:{0,0.4655})':{0,0.06859}',fusca:{0,0.53409})':{0,0.04924}',Pinaroloxias:{0,0.58333}); ÚÄ fuliginosa:{1,0.055} Ú´:{0,0.0275:1,0.0275} ³ÀÄ fortis:{1,0.055} Ú´:{0,0.07333} ³ÀÄÄ magnirostris:{0,0.11} Ú´:{0,0.00917} ³ÀÄÄÄ conirostris:{0,0.18333} Ú´:{0,0.0355} ³ÀÄÄÄÄ scandens:{0,0.1925} ÚÄÄÄ´:{0,0.10346} ³ ÀÄÄÄÄÄ difficilis:{0,0.114:1,0.114} Ú´:{0,0.13404} ³³ ÚÄÄÄ pallida:{0,0.08667} ³ÀÄÄÄÄÄ´:{0,0.24479} ³ ³ ÚÄ parvulus:{0,0.02} ³ ³Ú´:{0,0.015} ³ ³³ÀÄ psittacula:{0,0.02} ³ À´:{0,0.05167} ³ ÀÄÄ pauper:{0,0.035} Ú´:{0,0.06859} ³ÀÄÄÄÄÄÄÄÄÄÄ Platyspiza:{0,0.4655} Ú´:{0,0.04924} ³ÀÄÄÄÄÄÄÄÄÄÄÄ fusca:{0,0.53409} ´ ÀÄÄÄÄÄÄÄÄÄÄÄÄ Pinaroloxias:{0,0.58333} You have chosen a non-time-reversible model: rates are free to vary You have chosen to use equilibrium state frequencies WARNING: if some characters have fewer than 2 character states, the output in the output table will be wrong for those chars ------------------------------------------------------------------------------- WARNING: You are trying to estimate 2 parameters, but only have 13 taxa. Make sure to try some simpler models, and expect quite imprecise estimates. ------------------------------------------------------------------------------- Progress: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% |********************************************************************************| Tree = 1: UNTITLED -lnL = 6.042915 AIC = 16.085830 AICc = 17.285830 Rates: nonreversible q_0_1 = 1.661837 +/- 0.000001 q_1_0 = 6.181368 +/- 0.000002 Statefreqs: equilibrium P(0) = 0.788118 P(1) = 0.211882 tree input1 = (((((((((fuliginosa[&S 1:0.055]:0.055,fortis[&S 1:0.055]:0.055)'[&S 0:0.0275,1:0.0275]':0.055,magnirostris[&S 0:0.11]:0.11)'[&S 0:0.07333]':0.07333,conirostris[&S 0:0.18333]:0.18333)'[&S 0:0.00917]':0.00917,scandens[&S 0:0.1925]:0.1925)'[&S 0:0.0355]':0.0355,difficilis[&S 0:0.114,1:0.114]:0.228)'[&S 0:0.10346]':0.10346,(pallida[&S 0:0.08667]:0.08667,((parvulus[&S 0:0.02]:0.02,psittacula[&S 0:0.02]:0.02)'[&S 0:0.015]':0.015,pauper[&S 0:0.035]:0.035)'[&S 0:0.05167]':0.05167)'[&S 0:0.24479]':0.24479)'[&S 0:0.13404]':0.13404,Platyspiza[&S 0:0.4655]:0.4655)'[&S 0:0.06859]':0.06859,fusca[&S 0:0.53409]:0.53409)'[&S 0:0.04924]':0.04924,Pinaroloxias[&S 0:0.58333]:0.58333); tree input1 = (((((((((fuliginosa:{1,0.055},fortis:{1,0.055})':{0,0.0275:1,0.0275}',magnirostris:{0,0.11})':{0,0.07333}',conirostris:{0,0.18333})':{0,0.00917}',scandens:{0,0.1925})':{0,0.0355}',difficilis:{0,0.114:1,0.114})':{0,0.10346}',(pallida:{0,0.08667},((parvulus:{0,0.02},psittacula:{0,0.02})':{0,0.015}',pauper:{0,0.035})':{0,0.05167}')':{0,0.24479}')':{0,0.13404}',Platyspiza:{0,0.4655})':{0,0.06859}',fusca:{0,0.53409})':{0,0.04924}',Pinaroloxias:{0,0.58333}); ÚÄ fuliginosa:{1,0.055} Ú´:{0,0.0275:1,0.0275} ³ÀÄ fortis:{1,0.055} Ú´:{0,0.07333} ³ÀÄÄ magnirostris:{0,0.11} Ú´:{0,0.00917} ³ÀÄÄÄ conirostris:{0,0.18333} Ú´:{0,0.0355} ³ÀÄÄÄÄ scandens:{0,0.1925} ÚÄÄÄ´:{0,0.10346} ³ ÀÄÄÄÄÄ difficilis:{0,0.114:1,0.114} Ú´:{0,0.13404} ³³ ÚÄÄÄ pallida:{0,0.08667} ³ÀÄÄÄÄÄ´:{0,0.24479} ³ ³ ÚÄ parvulus:{0,0.02} ³ ³Ú´:{0,0.015} ³ ³³ÀÄ psittacula:{0,0.02} ³ À´:{0,0.05167} ³ ÀÄÄ pauper:{0,0.035} Ú´:{0,0.06859} ³ÀÄÄÄÄÄÄÄÄÄÄ Platyspiza:{0,0.4655} Ú´:{0,0.04924} ³ÀÄÄÄÄÄÄÄÄÄÄÄ fusca:{0,0.53409} ´ ÀÄÄÄÄÄÄÄÄÄÄÄÄ Pinaroloxias:{0,0.58333} * checking PDF version of manual ... OK