Continuous and discrete ancestral character reconstruction and evolutionary rate tests.


[Up] [Top]

Documentation for package ‘RBrownie’ version 0.1.1

Help Pages

A B C D E G H I M N P R S T V W

-- A --

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

-- B --

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

-- C --

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

-- D --

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

-- E --

execute.brownie Execute a brownie-formatted nexus file
expand.singles Expand singletons

-- G --

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

-- H --

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"

-- I --

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

-- M --

match.order Matching orders

-- N --

newlabels.v15 Generate simmap v1.5 labels
newlabels.v1x Generate simmap v1.0 or v1.1 labels
nSubNodes Get number of subnodes

-- P --

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

-- R --

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

-- S --

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.

-- T --

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

-- V --

validPhylo4d_ext Validate a phylo4d_ext object

-- W --

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"