A B C D E G H I M N P R S T V W
addCensored | Add Censored ratetest to brownie object |
addChoose | Add choose command to a brownie object (or list of brownie objects) |
addcmd.binary | Adding to commands block |
addcmd.freq | Adding to commands block |
addcmd.literal | Adding to commands block |
addcmd.model.continuous | Adding to commands block |
addcmd.model.discrete | Adding to commands block |
addcmd.states | Adding to commands block |
addcmd.taxaset | Adding to commands block |
addcmd.tvtype | Adding to commands block |
addDiscrete | Add Discrete character models and reconstructions to brownie object |
addEndLog | Add log stop command to brownie object |
addHS | Add Heuristic search command to brownie object |
addLiteral | Add command string to brownie object |
addModel | Add model selection command to brownie object |
addNonCensored | Add Noncensored rate test command to brownie object |
addNumopt | Add numerical optimization command to brownie object |
addOpt | Add Noncensored rate test command to brownie object |
addStartLog | Add log start command to brownie object |
addSubNode | Add subnode to phylo4d_ext object |
addTipvariance | Add tipvariance command |
areTaxaMono | Do taxa form a monophyletic clade |
areTaxaMutex | Are taxasets mutually exclusive |
areTaxaPara | Do taxa form a paraphyletic clade |
as.contData | Convert to continuous data |
as.discData | Convert to discrete data |
brownie | Class "brownie" |
brownie-class | Class "brownie" |
brownie-method | Methods for generic brownie constructor function |
brownie-methods | Methods for generic brownie constructor function |
brownie.datatypes | List datatypes |
brownie.freqs | List frequencies |
brownie.models.continuous | List valid continuous models |
brownie.models.discrete | List valid discrete models |
brownie.tvtypes | List tipvariance types |
Censored Ratetest | Add and Run Censored ratetest command to brownie object |
check.empty | Check character vectors |
check.freq | Check frequency |
check.statevector | Check statevector |
checkBrownie | Check if brownie object is valid. |
checkCommands | Check commands in a brownie object |
checkDataTypes | Check datatypes |
checkMono | Check for monophyly |
checkPara | Check for paraphyly |
checkval.dummy | Check value |
checkval.integer | Check value |
checkval.model.continuous | Check value |
checkval.model.discrete | Check value |
checkval.ratemat | Check value |
checkval.yesno | Check value |
clearCommands | Clear commands |
clearCommands-method | Clear commands |
clearCommands-methods | Clear commands |
collapse.singletons | Collapse singleton nodes |
collapse.subnodes | Collapse subnodes into singletons |
collapse.to.singles | Collapse zero-length branches |
commands | Class "brownie" |
commands-method | Class "brownie" |
commands<- | Class "brownie" |
commands<--method | Class "brownie" |
contData | Return datatype string representing the continuous datatype |
datatypes | Class "brownie" |
datatypes-method | Class "brownie" |
datatypes<- | Class "brownie" |
datatypes<--method | Class "brownie" |
deep.phy.copy | Copy a tree object slot by slot |
discData | Return datatype string representing the discrete datatype |
execute.brownie | Execute a brownie-formatted nexus file |
expand.singles | Expand singletons |
genericData | Return datatype string representing the generic datatype |
geospiza_ext | Data from Darwin's finches |
get.left.right | Get right and left tokens |
get.nexus.comments | Get comments from nexus text |
get.nodenames | Read node names from newick text |
get.tree.weights | Get tree weights |
getEmptyDataFrame | Get empty data.frame |
getSubNodeData | Return subnode data |
getSubNodeEdgeInds | Return subnode edge indices |
getSubNodePosish | Return the subnode position |
has.block | Check for nexus block |
has.characters2 | Check for CHARACTERS2 block |
has.weights | Check for tree weights |
haschar | Does character exist |
hasCommands | Check for commands |
hasData | Methods for Function hasData in Package 'RBrownie' |
hasData-method | Methods for Function hasData in Package 'RBrownie' |
hasData-methods | Methods for Function hasData in Package 'RBrownie' |
hasDataColumn | Does a tree object contain a specific data column |
hasDataColumn-method | Does a tree object contain a specific data column |
hasDataColumn-methods | Does a tree object contain a specific data column |
hasSubNodes | Does an object contain subnodes? |
hasSubNodes-method | Does an object contain subnodes? |
hasSubNodes-methods | Does an object contain subnodes? |
hasTaxasets | Check if there are taxasets |
hasTaxasets-method | Check if there are taxasets |
hasTaxasets-methods | Check if there are taxasets |
hasWeight | Class "phylo4d_ext" |
hasWeight-method | Class "phylo4d_ext" |
is.binary | Is data binary |
is.contData | Is data continuous |
is.discData | Is data discrete |
is.simmap | Check SIMMAP v1.0 |
is.taxaname.internal | Check for internal taxanames |
isback | isback |
is_valid_datatype | Check for valid datatype |
is_valid_datatype_bound | Check for valid datatype limits |
is_valid_datatype_prob | Check for valid datatype probability |
match.order | Matching orders |
newlabels.v15 | Generate simmap v1.5 labels |
newlabels.v1x | Generate simmap v1.0 or v1.1 labels |
nSubNodes | Get number of subnodes |
parrot | Parrotfish data |
phyext | A function which returns a phylo4d_ext object |
phyext-method | A function which returns a phylo4d_ext object |
phyext-methods | A function which returns a phylo4d_ext object |
phyextPlot | Plot phylo4d_ext object |
phylo4d_ext-class | Class "phylo4d_ext" |
plot-method | Class "phylo4d_ext" |
plot.censored | Plot a censored tree |
plot.taxaset | Plot a taxaset |
RBrownie | Continuous and discrete ancestral character reconstruction and evolutionary rate tests. |
rcpp_hello_world | Test function |
read.analysis.output | Read brownie output to data.frame |
read.brownie.string | Read brownie command string into a list |
read.characters2 | Read CHARACTERS2 block |
read.continuous.output | Read brownie output from Noncensored analysis |
read.discrete.output | Read brownie output from discrete analysis |
read.nexus.block | Find a block in a nexus file |
read.nexus.simmap | Read a nexus file with SIMMAP-formatted trees (v1.0) |
read.ratetest.output | Read brownie output from Censored ratetest analysis |
read.simmap | Read simmap-formatted newick strings (version 1.0) |
read.simmap.new | Read simmap-formatted newick strings (version 1.5) |
readBrownie | Read in a brownie formatted nexus file |
removeCommands | Class "brownie" |
removeCommands-method | Class "brownie" |
removeTaxasets | Remove taxasets from a brownie object |
removeTaxasets-method | Remove taxasets from a brownie object |
removeTaxasets-methods | Remove taxasets from a brownie object |
rm.ending | Remove semi-colon from end of a string |
rmdata | rmdata from a tree object |
rmdata-method | Class "brownie" |
rmdata-method | rmdata from a tree object |
rmdata-methods | rmdata from a tree object |
run.analysis | Execute a brownie-formatted nexus file |
run.asis | Execute a brownie object |
runCensored | Add and Run Censored ratetest command to brownie object |
runDiscrete | Add and Run a discrete command to brownie object |
runNonCensored | Add and Run NonCensored ratetest command to brownie object |
scan.textout | Scan raw brownie analysis text |
scan.treesout | Scan raw brownie tree text |
showBrownie | Show brownie command functions |
showSubNodes | Display subnodes |
snbranch | Class "phylo4d_ext" |
snbranch-method | Class "phylo4d_ext" |
sndata | Class "phylo4d_ext" |
sndata-method | Class "phylo4d_ext" |
sndata<- | Class "phylo4d_ext" |
sndata<--method | Class "phylo4d_ext" |
snid | Class "phylo4d_ext" |
snid-method | Class "phylo4d_ext" |
snposition | Class "phylo4d_ext" |
snposition-method | Class "phylo4d_ext" |
strip | Strip whitespace |
summaryCont | Summarize the results of a Non-censored rate test. |
summaryDiscrete | Summarize the results of a discrete character evolution analysis. |
summaryRatetest | Summarize the results of a Censored rate test. |
taxa.charvect | Return a character vector of taxa |
taxa.mono | Are taxa monophyletic |
taxaname.to.taxind | Taxaset index to taxaset name |
taxaset.names | Get names of the taxasets |
taxaset.rename | Format a taxaset name for use internally |
taxasets | Class "brownie" |
taxasets-method | Class "brownie" |
taxasets<- | Class "brownie" |
taxasets<--method | Class "brownie" |
taxData | Return datatype string representing the taxaset datatype |
taxind.to.dataind | Convert taxaset column index to data slot column index |
tipdate.ci | Get coalescent intervals for a tip-dated tree |
treeHeight | Get the height (depth) of a tree |
treeHeight-method | Get the height (depth) of a tree |
treeHeight-methods | Get the height (depth) of a tree |
validPhylo4d_ext | Validate a phylo4d_ext object |
weight | Class "phylo4d_ext" |
weight-method | Class "phylo4d_ext" |
weight<- | Class "phylo4d_ext" |
weight<--method | Class "phylo4d_ext" |
which.mono | Find trees in a list which contain a monophyly for a certain taxaset |
which.para | Find trees in a list which contain a paraphyly for a certain taxaset |
write.brownie.matrix | Return a matrix formatted for the brownie core |
write.brownie.string | Convert commands list to commands string |
write.brownie.vector | Return a vector formatted for the brownie core |
write.nexus.simmap | Write phylo4d_ext object or list to a nexus file |
write.simmap | Write phylo4d_ext tree to newick string |
write.simmap.new | Wrapper for write.simmap |
write.simmap.old | Wrapper for write.simmap |
writeBrownie | Class "brownie" |
writeBrownie-method | Class "brownie" |