Title: Prepare MCMCtree Analyses and Plot Bayesian Divergence Time Analyses Estimates on Trees
Version: 1.1
Author: Mark Puttick [aut,cre], Pascal Title [ctb]
Maintainer: Mark Puttick <mark.puttick@bristol.ac.uk>
Description: Provides functions to prepare time priors for 'MCMCtree' analyses in the 'PAML' software from Yang (2007)<doi:10.1093/molbev/msm088> and plot time-scaled phylogenies from any Bayesian divergence time analysis. Most time-calibrated node prior distributions require user-specified parameters. The package provides functions to refine these parameters, so that the resulting prior distributions accurately reflect confidence in known, usually fossil, time information. These functions also enable users to visualise distributions and write 'MCMCtree' ready input files. Additionally, the package supplies flexible functions to visualise age uncertainty on a plotted tree with using node bars, using branch widths proportional to the age uncertainty, or by plotting the full posterior distributions on nodes. Time-scaled phylogenetic plots can be visualised with absolute and geological timescales . All plotting functions are applicable with output from any Bayesian software, not just 'MCMCtree'.
Depends: R (≥ 3.3), ape (≥ 3.0-7), sn, coda
Imports: methods, utils, stats, grDevices, graphics
License: GPL-2 | GPL-3 [expanded from: GPL (≥ 2)]
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.1.1
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2019-05-21 19:24:11 UTC; markputtick
Repository: CRAN
Date/Publication: 2019-05-21 22:20:31 UTC

Plot time-scaled phylogenies

Description

Plot time-scaled phylogenies with node uncertainty and timescale

Usage

MCMC.tree.plot(phy = NULL, analysis.type = "MCMCtree",
  MCMC.chain = NULL, node.ages = NULL, directory.files = NULL,
  plot.type = "phylogram", build.tree = FALSE, node.method = "bar",
  all.nodes = NULL, add.time.scale = TRUE, add.abs.time = TRUE,
  scale.res = "Epoch", label.timescale.names = FALSE,
  time.correction = 1, col.age = "blue", tip.lengths = FALSE,
  density.col = "#00000050", density.border.col = "#00000080",
  cex.tips = 1, show.tip.label = TRUE, col.tree = "black",
  tip.color = "black", lwd.bar = 1, grey.bars = TRUE, cex.age = 1,
  cex.labels = 1, cex.names = 1, relative.height = 0.08,
  tip.bar.col = "#ff000050", burn.in = 0.25,
  distribution.height = 0.8, abs.age.mgp = c(3, 0.35, 0),
  abs.age.lwd.ticks = 0.7, abs.age.lwd = 0, tck.abs.age = -0.01,
  abs.age.line = -0.4, pos.age = NULL, n.runs = 2,
  ladderize.tree = TRUE, ...)

Arguments

phy

A timescaled phylogeny, unless analysis.type="MCMCtree" and build.tree=TRUE

analysis.type

The method used to generate the time-scale tree, one of MCMCtree, MrBayes, RevBayes, or User.

MCMC.chain

The full posterior of age estimates for all nodes (default NULL)

node.ages

List of user-supplied node ages applicable for analysis.type user. Either all nodes or a selection of nodes. Each list element must be named with its corresponding node label from the APE format.

directory.files

The directory for files to summarise for MrBayes and RevBayes analyses

plot.type

The plotting method for the phylogram corresponding to the APE definition. Phylogram is available for all analysis types, but cladogram is only avilable for MCMCtree analyses at present. Type distributions plots a phylogram with stats::density distributions on each of the nodes.

build.tree

Logical. Only applicable to MCMCtree analyses, whether to timescale the phylogeny based on the full MCMC chain

node.method

For plot.type phylogram the method to dispay age uncertainty on each node, either bar, node.length, or full.length. If 'none' is supplied plotting node uncertainty is suppressed.

all.nodes

If NULL (default) node uncertainty is plotted on all nodes. If node numbers are supplied, only these nodes will be labelled with uncertainty.

add.time.scale

Logical. Adds a timescale to the plotted phylogeny.

add.abs.time

Logical. Adds an absolute timescale alongside the geological timescale. Only applicable if add.time.scale is TRUE

scale.res

The geological age designation to add to the plot can be one or a combination of Eon, Period, Epoch, Age. The order of plot (from bottom to top) is the same as the supplied order. Subsequent arguments add.abs.time and grey.bars are based on the last supplied age designation.

label.timescale.names

Logical. Add names (Eon, Period, Epoch, Age, Ma) to axis if timescale used

time.correction

Number to place branch lengths and age estimates in absolute time, deafult to one.

col.age

The colouring of the node.method bars to summarise node age uncertainty

tip.lengths

Logical. If the tree contains non-present tip ages, the age uncertainty associated with them will be added to the plot

density.col

Colour of the node distributions (if analysis.type=distributions)

density.border.col

Colour of the node distributions (if analysis.type=distributions) borders

cex.tips

Size of the phylogeny tip labels

show.tip.label

Logical. Should the tree tip labels be displayed

col.tree

Colour of the phylogeny edges

tip.color

Colour of the phylogeny tip labels

lwd.bar

Width of the bar to summarise age uncertainty, applicable only if plot.type is phylogram and node.method is bar

grey.bars

Logical. Should grey bars be used to signify time bins, applicable only if add.time.scale is TRUE

cex.age

Size of the labels for the absolute timescale

cex.labels

Size of the labels for the geological timescale

cex.names

Logical. Add label.timescale.names, if applicable.

relative.height

the relative height of the timescale labels

tip.bar.col

The colour of uncertainty around non-contemporary tips

burn.in

The number of points in the chain to discard for MrBayes and RevBayes analyses

distribution.height

The relative height of node distributions when plot.type is distributions measured as the relative height of the descendent node

abs.age.mgp

mgp values for the absolute age axis, only applicable if add.abs.time is TRUE

abs.age.lwd.ticks

lwd values for the absolute age axis ticks, only applicable if add.abs.time is TRUE

abs.age.lwd

lwd values for the absolute age axis horizontal line, only applicable if add.abs.time is TRUE

tck.abs.age

tck values for the absolute age axis tick height, only applicable if add.abs.time is TRUE

abs.age.line

line correction for the absolute age axis tick, only applicable if add.abs.time is TRUE

pos.age

position position of absolute age axis

n.runs

For analysis.type mrbayes, the number of independent chains to summarise

ladderize.tree

Logical. Plot a ladderized tree (TRUE) or not (FALSE)

...

further arguments to be used in plot.phylo

Details

The primary inputs for the 'method' options are outputs from analysis conducting using MCMCtree, MrBayes, RevBayes, or User.

For analyses under the 'MCMCtree' option (the default) the function only requires a 'FigTree' output from MCMCtree analysis or the full MCMCtree posterior. For option "MrBayes" and "RevBayes", the method argument takes the user-supplied directory address in which all the output files are stored.

For the option 'User' the function requires a full posterior distribution and time-scaled phylogeny. This function can take any posterior distribution, but it may require some manipulation. The argument node.ages in MCMC.tree.plot takes a named list containing the posterior ages for each node, with the name of each element corresponding to the node in the phylogeny.

Value

If plot=TRUE plot of distributions in file 'pdfOutput' written to current working directory

Author(s)

Mark Puttick

Examples

data(MCMCtree.output)
attach(MCMCtree.output)
## if it is necessary to read in file manually
## MCMCtree.posterior <- read.csv("mcmc.posterior.file.directory", sep="\t")
MCMCtree.file <- readMCMCtree(MCMCtree.phy, from.file=FALSE)$apePhy
MCMC.tree.plot(phy=MCMCtree.file,  analysis.type="MCMCtree",
MCMC.chain=MCMCtree.posterior, plot.type="distributions", cex.tips=0.5)

MCMCtree.output

Description

Phylogeny output from MCMCtree, and posterior estimates from MCMCtree 'out' file from a re-analysis of data from Morris et al. 2018

Usage

data(MCMCtree.output)

Format

An object of class list of length 2.

References

Morris et al. 2018

Examples

data(MCMCtree.output)
attach(MCMCtree.output)
names(MCMCtree.output)

MCMCtreePhy

Description

Wrapper function to estimate node distributions and add them to tree and output MCMCtree format phylogeny file. If parameter values are in vectors shorter than the number of nodes they are recycled.

Usage

MCMCtreePhy(phy, minAges, maxAges, monoGroups, method = c("cauchy",
  "upper", "bound", "gamma", "skewNormal", "skewT", "fixed"),
  offset = 0.1, df = 1, shape = 50, scale = 1.5, minProb = 1e-08,
  addMode = 0, maxProb = 0.975, rightTail = 0.025, alpha = 188,
  beta = 100, estimateScale = TRUE, estimateShape = FALSE,
  estimateMode = FALSE, estimateAlpha = TRUE, estimateBeta = FALSE,
  plot = FALSE, pdfOutput = "nodeDistributions.pdf",
  writeMCMCtree = TRUE, MCMCtreeName = "output.tre")

Arguments

phy

fully resolved phylogeny in ape format

minAges

vector of minimum age bounds for nodes matching order in monoGroups

maxAges

vector of maximum age bounds for nodes matching order in monoGroups

monoGroups

list with each element containing species that define a node of interest

method

vector of the type of calibration distribution for each node

offset

offset value for distribution (default = 50)

df

degrees of freedom for skew-t distribution (default = 1)

shape

shape value for skew-t distribution (default = 50)

scale

scale value for distribution (default = 1.5)

minProb

probability of left tail (minimum bound) - default to hard minimum (minProb=0)

addMode

addition to the minimum age to give the location of the distribution

maxProb

probability of right tail (maximum bound. default = 0.975)

rightTail

probability of right tail (maximum bound default = 0.025)

alpha

alpha value for gamma distribution (default = 188)

beta

beta value for gamma distribution (default = 2690)

estimateScale

logical specifying whether to estimate scale with a given shape value (default = TRUE)

estimateShape

logical specifying whether to estimate shape with a given scale value

estimateMode

logical speciftying whether to estimate the scale that produces probabilities of each tail that corresponds roughly to the values given by minProb (lower tail) and maxProb (upper tail)

estimateAlpha

logical specifying whether to estimate alpha with a given beta value (default = TRUE)

estimateBeta

logical specifying whether to estimate beta with a given alpha value (default = FALSE)

plot

logical specifying whether to plot to PDF

pdfOutput

pdf output file name

writeMCMCtree

logical whether to write tree in format that is compatible with MCMCTree to file

MCMCtreeName

MCMCtree.output file name

Value

list containing node estimates for each distribution

If plot=TRUE plot of distributions in file 'pdfOutput' written to current working directory

If writeMCMCtree=TRUE tree in MCMCtree format in file "MCMCtreeName" written to current working directory

Author(s)

Mark Puttick

Examples

data(apeData)
attach(apeData)
## extract taxon descending from calibrated nodes 8, 10, 11, 13
## these nodes can be visualised using plot.phylo
## and nodelabels from ape
monophyleticGroups <- tipDes(apeData$apeTree, c(8,10,11,13))
minimumTimes <- c("nodeOne"=15, "nodeTwo"=6,
"nodeThree"=8, "nodeFour"=13) / 10
maximumTimes <- c("nodeOne" = 30, "nodeTwo" = 12,
"nodeThree"=12, "nodeFour" = 20) / 10
# Cauchy, upper age, bound, and gamma applied individually to each node
MCMCtreePhy(phy=apeTree, minAge=minimumTimes, maxAge=maximumTimes, 
monoGroups=monophyleticGroups, plot=FALSE, 
method=c("cauchy", "upper", "bound", "gamma"), writeMCMCtree=FALSE)

ApeData Ape phylogeny in ape format, monophyletic clades, and maximum and minimum ages

Description

ApeData Ape phylogeny in ape format, monophyletic clades, and maximum and minimum ages

Usage

data(apeData)

Format

An object of class list of length 4.

References

Yang 2014

Examples

data(apeData)
attach(apeData)
names(apeData)

Estimate a Uniform Distribution for MCMCtree

Description

Estimate the paramaters of a soft-bounded uniform distribution and output trees for MCMCtree input

Usage

estimateBound(minAge, maxAge, minProb = 0.025, rightTail = 0.025, phy,
  monoGroups, writeMCMCtree = FALSE, plot = TRUE,
  MCMCtreeName = "bound.tre", pdfOutput = "uniformPlot.pdf")

Arguments

minAge

vector of minimum age bounds for nodes matching order in monoGroups

maxAge

vector of maximum age bounds for nodes matching order in monoGroups

minProb

probability of left tail (minimum bound) - default to hard minimum (minProb=0)

rightTail

probability of right tail (maximum bound default = 0.975)

phy

fully resolved phylogeny in ape format

monoGroups

list with each element containing species that define a node of interest

writeMCMCtree

logical whether to write tree in format that is compatible with MCMCTree to file

plot

logical specifying whether to plot to PDF

MCMCtreeName

MCMCtree.output file name

pdfOutput

pdf output file name

Value

list containing node estimates for each distribution

If plot=TRUE plot of distributions in file 'pdfOutput' written to current working directory

If writeMCMCtree=TRUE tree in MCMCtree format in file "MCMCtreeName" written to current working directory

Author(s)

Mark Puttick

Examples

data(apeData)
attach(apeData)
## extract taxon descending from calibrated nodes 8, 10, 11, 13
## these nodes can be visualised using plot.phylo
## and nodelabels from ape
monophyleticGroups <- tipDes(apeData$apeTree, c(8,10,11,13))
minimumTimes <- c("nodeOne"=15, "nodeTwo"=6,
"nodeThree"=8, "nodeFour"=13) / 10
maximumTimes <- c("nodeOne" = 30, "nodeTwo" = 12,
"nodeThree"=12, "nodeFour" = 20) / 10
estimateBound(minAge=minimumTimes, maxAge=maximumTimes, 
monoGroups=monophyleticGroups, phy=apeTree, plot=FALSE)$MCMCtree

Estimate Cauchy Distribution for MCMCtree

Description

Estimate the offset and scale paramaters of a soft-tailed cauchy distribution and output trees for MCMCtree input

Usage

estimateCauchy(minAge, maxAge, phy, monoGroups, scale = 1.5,
  offset = 50, estimateScale = TRUE, minProb = 0, maxProb = 0.975,
  plot = FALSE, pdfOutput = "cauchyPlot.pdf", writeMCMCtree = FALSE,
  MCMCtreeName = "cauchyInput.tre")

Arguments

minAge

vector of minimum age bounds for nodes matching order in monoGroups

maxAge

vector of maximum age bounds for nodes matching order in monoGroups

phy

fully resolved phylogeny in ape format

monoGroups

list with each element containing species that define a node of interest

scale

scale value for cauchy distribution (default = 1.5) (c in PAML manual page 49)

offset

offset value for cauchy distribution (default = 50) (p in PAML manual page 49)

estimateScale

logical specifying whether to estimate scale with a given shape value (default = TRUE)

minProb

probability of left tail (minimum bound) - default to hard minimum (minProb=0)

maxProb

probability of right tail (maximum bound. default = 0.975)

plot

logical specifying whether to plot to PDF

pdfOutput

pdf output file name

writeMCMCtree

logical whether to write tree in format that is compatible with MCMCTree to file

MCMCtreeName

MCMCtree.output file name

Value

list containing node estimates for each distribution

If plot=TRUE plot of distributions in file 'pdfOutput' written to current working directory

If writeMCMCtree=TRUE tree in MCMCtree format in file "MCMCtreeName" written to current working directory

Author(s)

Mark Puttick data(apeData) attach(apeData) ## extract taxon descending from calibrated nodes 8, 10, 11, 13 ## these nodes can be visualised using plot.phylo ## and nodelabels from ape monophyleticGroups <- tipDes(apeData$apeTree, c(8,10,11,13)) minimumTimes <- c("nodeOne"=15, "nodeTwo"=6, "nodeThree"=8, "nodeFour"=13) / 10 maximumTimes <- c("nodeOne" = 30, "nodeTwo" = 12, "nodeThree"=12, "nodeFour" = 20) / 10 estimateCauchy(minAge=minimumTimes, maxAge=maximumTimes, monoGroups=monophyleticGroups, offset=0.5, phy=apeTree, plot=FALSE)$MCMCtree

Fixed Age for MCMCtree analysis input

Description

Produce fixed age trees for MCMCtree analysis

Usage

estimateFixed(minAge, phy, monoGroups, writeMCMCtree = FALSE,
  MCMCtreeName = "estimateFixed.tre")

Arguments

minAge

vector of fixed age bounds for nodes matching order in monoGroups

phy

fully resolved phylogeny in ape format

monoGroups

list with each element containing species that define a node of interest

writeMCMCtree

logical whether to write tree in format that is compatible with MCMCTree to file

MCMCtreeName

MCMCtree.output file name

Value

list containing node estimates for each distribution

If writeMCMCtree=TRUE tree in MCMCtree format in file "MCMCtreeName" written to current working directory

Author(s)

Mark Puttick

Examples

data(apeData)
attach(apeData)
## extract taxon descending from calibrated nodes 8, 10, 11, 13
## these nodes can be visualised using plot.phylo
## and nodelabels from ape
monophyleticGroups <- tipDes(apeData$apeTree, c(8,10,11,13))
minimumTimes <- c("nodeOne"=15, "nodeTwo"=6,
"nodeThree"=8, "nodeFour"=13) / 10
maximumTimes <- c("nodeOne" = 30, "nodeTwo" = 12,
"nodeThree"=12, "nodeFour" = 20) / 10
estimateFixed(minAge=minimumTimes[1],
monoGroups=monophyleticGroups[[1]], phy=apeTree)$MCMCtree

Estimate Gamma Distribution for MCMCtree analysis

Description

Estimate the shape and rate paramaters of Gamma distribution and output trees for MCMCtree input

Usage

estimateGamma(minAge, maxAge, phy, monoGroups, alpha = 188,
  beta = 2690, offset = 0.1, estimateAlpha = TRUE,
  estimateBeta = FALSE, plot = FALSE, pdfOutput = "gammaPlot.pdf",
  writeMCMCtree = FALSE, MCMCtreeName = "gammaInput.tre")

Arguments

minAge

vector of minimum age bounds for nodes matching order in monoGroups

maxAge

vector of maximum age bounds for nodes matching order in monoGroups

phy

fully resolved phylogeny in ape format

monoGroups

list with each element containing species that define a node of interest

alpha

alpha value for gamma distribution (default = 188)

beta

beta value for gamma distribution (default = 2690)

offset

distance of mean value from minimum bound

estimateAlpha

logical specifying whether to estimate alpha with a given beta value (default = TRUE)

estimateBeta

logical specifying whether to estimate beta with a given alpha value (default = FALSE)

plot

logical specifying whether to plot to PDF

pdfOutput

pdf output file name

writeMCMCtree

logical whether to write tree in format that is compatible with MCMCTree to file

MCMCtreeName

MCMCtree.output file name

Value

list containing node estimates for each distribution

If plot=TRUE plot of distributions in file 'pdfOutput' written to current working directory

If writeMCMCtree=TRUE tree in MCMCtree format in file "MCMCtreeName" written to current working directory

Author(s)

Mark Puttick

Examples

data(apeData)
attach(apeData)
## extract taxon descending from calibrated nodes 8, 10, 11, 13
## these nodes can be visualised using plot.phylo
## and nodelabels from ape
monophyleticGroups <- tipDes(apeData$apeTree, c(8,10,11,13))
minimumTimes <- c("8"=15, "10"=6,
"11"=8, "13"=13) / 10
maximumTimes <- c("8" = 30, "10" = 12,
"11"=12, "13" = 20) / 10
gamma.nodes <- estimateGamma(minAge=minimumTimes, maxAge=maximumTimes, 
monoGroups=monophyleticGroups, alpha=188, beta=2690, 
offset=0.1, phy=apeTree, plot=FALSE)
gamma.nodes

Estimate Skew Normal for MCMCtree analysis

Description

Estimate the shape, scale, and location paramaters of a skew normal distribution and output trees for MCMCtree input

Usage

estimateSkewNormal(minAge, maxAge, monoGroups, phy, shape = 50,
  scale = 1.5, addMode = 0, maxProb = 0.975, minProb = 0.003,
  estimateScale = TRUE, estimateShape = FALSE, estimateMode = FALSE,
  plot = FALSE, pdfOutput = "skewNormalPlot.pdf",
  writeMCMCtree = FALSE, MCMCtreeName = "skewNormalInput.tre")

Arguments

minAge

vector of minimum age bounds for nodes matching order in monoGroups

maxAge

vector of maximum age bounds for nodes matching order in monoGroups

monoGroups

list with each element containing species that define a node of interest

phy

fully resolved phylogeny in ape format

shape

shape value for skew normal distribution (default = 50)

scale

scale value for skew normal distribution (default = 1.5)

addMode

addition to the minimum age to give the location of the distribution

maxProb

probability of right tail (maximum bound default = 0.975)

minProb

probability of left tail (maximum bound default = 0.003)

estimateScale

logical specifying whether to estimate scale with a given shape value (default = TRUE)

estimateShape

logical specifying whether to estimate shape with a given scale value (default = FALSE)

estimateMode

logical speciftying whether to estimate the scale that produces probabilities of each tail that corresponds roughly to the values given by minProb (lower tail) and maxProb (upper tail)

plot

logical specifying whether to plot to PDF

pdfOutput

pdf output file name

writeMCMCtree

logical whether to write tree in format that is compatible with MCMCTree to file

MCMCtreeName

MCMCtree.output file name

Value

list containing node estimates for each distribution

If plot=TRUE plot of distributions in file 'pdfOutput' written to current working directory

If writeMCMCtree=TRUE tree in MCMCtree format in file "MCMCtreeName" written to current working directory

Author(s)

Mark Puttick

See Also

qst

Examples

data(apeData)
attach(apeData)
monophyleticGroups <- list()
## extract taxon descending from calibrated nodes 8, 10, 11, 13
## these nodes can be visualised using plot.phylo
## and nodelabels from ape
monophyleticGroups <- tipDes(apeData$apeTree, c(8,10,11,13))
minimumTimes <- c("nodeOne"=15, "nodeTwo"=6,
"nodeThree"=8, "nodeFour"=13) / 10
maximumTimes <- c("nodeOne" = 30, "nodeTwo" = 12,
"nodeThree"=12, "nodeFour" = 20) / 10
estimateSkewNormal(minAge=minimumTimes, maxAge=maximumTimes, 
monoGroups=monophyleticGroups, phy=apeTree, plot=FALSE)

Estimate Skew-t Distribution for MCMCtree analysis

Description

Estimate the shape, scale, and location paramaters of a Skew-t distribution and output trees for MCMCtree input

Usage

estimateSkewT(minAge, maxAge, monoGroups, phy, shape = 50, scale = 1.5,
  df = 1, addMode = 0, maxProb = 0.975, minProb = 0.003,
  estimateScale = TRUE, estimateShape = FALSE, estimateMode = FALSE,
  plot = FALSE, pdfOutput = "skewTPlot.pdf", writeMCMCtree = FALSE,
  MCMCtreeName = "skewTInput.tre")

Arguments

minAge

vector of minimum age bounds for nodes matching order in monoGroups

maxAge

vector of maximum age bounds for nodes matching order in monoGroups

monoGroups

list with each element containing species that define a node of interest

phy

fully resolved phylogeny in ape format

shape

shape value for skew-t distribution (default = 50)

scale

scale value for skew-t distribution (default = 1.5)

df

degrees of freedom for skew-t distribution (default = 1)

addMode

addition to the minimum age to give the location of the distribution

maxProb

probability of right tail (maximum bound default = 0.975)

minProb

probability of left tail (maximum bound default = 0.003)

estimateScale

logical specifying whether to estimate scale with a given shape value (default = TRUE)

estimateShape

logical specifying whether to estimate shape with a given scale value (default = FALSE)

estimateMode

logical speciftying whether to estimate the scale that produces probabilities of each tail that corresponds roughly to the values given by minProb (lower tail) and maxProb (upper tail)

plot

logical specifying whether to plot to PDF

pdfOutput

pdf output file name

writeMCMCtree

logical whether to write tree in format that is compatible with MCMCTree to file

MCMCtreeName

MCMCtree.output file name

Value

list containing node estimates for each distribution

If plot=TRUE plot of distributions in file 'pdfOutput' written to current working directory

If writeMCMCtree=TRUE tree in MCMCtree format in file "MCMCtreeName" written to current working directory

Author(s)

Mark Puttick

See Also

qst

Examples

data(apeData)
attach(apeData)
## extract taxon descending from calibrated nodes 8, 10, 11, 13
## these nodes can be visualised using plot.phylo
## and nodelabels from ape
monophyleticGroups <- tipDes(apeData$apeTree, c(8,10,11,13))
minimumTimes <- c("nodeOne"=15, "nodeTwo"=6,
"nodeThree"=8, "nodeFour"=13) / 10
maximumTimes <- c("nodeOne" = 30, "nodeTwo" = 12,
"nodeThree"=12, "nodeFour" = 20) / 10
estimateSkewT(minAge=minimumTimes, maxAge=maximumTimes,
monoGroups=monophyleticGroups, phy=apeTree, plot=FALSE)$MCMCtree

Estimate Upper Age for MCMCtree analysis

Description

Estimate the upper age distribution and output trees for MCMCtree input

Usage

estimateUpper(maxAge, rightTail = 0.025, phy, monoGroups,
  writeMCMCtree = FALSE, MCMCtreeName = "estimateUpper.tre")

Arguments

maxAge

vector of maximum age bounds for nodes matching order in monoGroups

rightTail

probability of right tail (maximum bound default = 0.025)

phy

fully resolved phylogeny in ape format

monoGroups

list with each element containing species that define a node of interest

writeMCMCtree

logical whether to write tree in format that is compatible with MCMCTree to file

MCMCtreeName

MCMCtree.output file name

Value

list containing node estimates for each distribution

If plot=TRUE plot of distributions in file 'pdfOutput' written to current working directory

If writeMCMCtree=TRUE tree in MCMCtree format in file "MCMCtreeName" written to current working directory

Author(s)

Mark Puttick

Examples

data(apeData)
attach(apeData)
## extract taxon descending from calibrated nodes 8, 10, 11, 13
## these nodes can be visualised using plot.phylo
## and nodelabels from ape
monophyleticGroups <- tipDes(apeData$apeTree, c(8,10,11,13))
minimumTimes <- c("nodeOne"=15, "nodeTwo"=6,
"nodeThree"=8, "nodeFour"=13) / 10
maximumTimes <- c("nodeOne" = 30, "nodeTwo" = 12,
"nodeThree"=12, "nodeFour" = 20) / 10
estimateUpper(maxAge=maximumTimes, monoGroups=monophyleticGroups,
rightTail=0.025, phy=apeTree)

Add Node Constraints to Tree in MCMCtree Format

Description

Produce tree with node labels in MCMCtree format

Usage

nodeToPhy(phy, monoGroups, nodeCon, returnPhy = TRUE)

Arguments

phy

fully resolved phylogeny in ape format

monoGroups

list with each element containing species that define a node of interest

nodeCon

node distributions in MCMCtreeR format

returnPhy

logical specifying whether to return phy to console or write MCMCtree for input (default = TRUE)

Value

If returnPhy=TRUE phylogeny with node labels in ape format

If returnPhy=FALSE phylogeny with node labels in MCMCtree format

Author(s)

Mark Puttick

Plot distribution from MCMCtree node estimations

Description

Estimate the offset and scale paramaters of a soft-tailed cauchy distribution and output trees for MCMCtree input

Usage

plotMCMCtree(parameters, method = c("skewT", "skewNormal", "cauchy",
  "gamma", "bound"), title, upperTime, lowerTime = 0,
  plotMCMCtreeData = TRUE)

Arguments

parameters

output parameters from node estimation function

method

one of skewT, skewNormal, cauchy, gamma, or bound

title

title for the plot

upperTime

maxmimum age for x-axis plot

lowerTime

maxmimum age for x-axis plot (default = 0)

plotMCMCtreeData

If TRUE returns co-ordinates to plot distributions to allow greater flexibility (default = TRUE)

Value

plot of the specified prior applied for a node

If plotMCMCtreeData=TRUE x and y coordinates of distributions from 0 to upperTime on x axis

Author(s)

Mark Puttick

Examples

data(apeData)
attach(apeData)
# create monophyletic groups descending from nodes 8, 10, 11, and 13
monophyleticGroups <- tipDes(apeData$apeTree, c(8,10,11,13))
minimumTimes <- c("nodeOne"=15, "nodeTwo"=6,
"nodeThree"=8, "nodeFour"=13) / 10
maximumTimes <- c("nodeOne" = 30, "nodeTwo" = 12,
"nodeThree"=12, "nodeFour" = 20) / 10
cauchy <- estimateCauchy(minAge=minimumTimes[1], maxAge=maximumTimes[1],
monoGroups=monophyleticGroups[[1]], offset=0.5, phy=apeTree, plot=FALSE)
## un-comment to run
plotMCMCtree(parameters=cauchy$parameters, method="cauchy",
title="cauchyPlot", upperTime=maximumTimes[1]+1)

priorPosterior

Description

Analyse prior and posterior node distributions from MCMCtree analysis

Usage

priorPosterior(MCMCPrior, MCMCPosterior = NULL, inputTree,
  return.density = FALSE, rootCalibration = NULL)

Arguments

MCMCPrior

prior of MCMC file from MCMCtree analysis using data=0

MCMCPosterior

posterior of MCMC file from MCMCtree analysis using data

inputTree

phylogeny in MCMCtree format used in MCMCtree analysis

return.density

Logical. Whether to return the density or original values for the effective prior and posterior.

rootCalibration

= NULL If NULL, then behaves as by default. Alternatively, if a user has specified a root prior in the MCMCtreeR control file it can be added here as a vector in the form it would appear tree.

Value

list containing node estimates for each distribution

Author(s)

Mark Puttick, Pascal Title

Examples

data(MCMCtree.output)
# priorPosterior(MCMCPrior, 
# MCMCPosterior=MCMCtree.output$MCMCtree.posterior, 
# path.to.input.tree)

Read MCMCtree output tree into R

Description

Read MCMCtree output tree into R to produce time-scaled tree in APE format, and a table of the mean and 95

Usage

readMCMCtree(inputPhy, forceUltrametric = TRUE, from.file = TRUE)

Arguments

inputPhy

file directory of 'Figtree' output from MCMCtree

forceUltrametric

alters branch lengths at tips so tree is fully ultrametric (default = TRUE)

from.file

Logical. Read a tree from file or locally from within R?

Value

apePhy time-scaled output tree from MCMCtree in APE format

nodeAges mean and 95

Author(s)

Mark Puttick

Examples

data(MCMCtree.output)
attach(MCMCtree.output)
# tree and node ages
readMCMCtree(MCMCtree.phy, from.file=FALSE)

Find Descendent Tips From A Common Ancestor

Description

This function finds tip descendants from a common ancestor

Usage

tipDes(phy, node)

Arguments

phy

user tree in ape format

node

one or more nodes from the ape format that designate the crown monophyletic group

Details

If a single node number is supplied the function returns a vector of tip labels. When more than one node number is supplied the function returns a list with each element a vector of tip labels for that node.

Author(s)

Mark Puttick

Examples

set.seed(1029)
# one node
phy <- rcoal(10)
node <- 13
tipDes(phy, node)
## multiple nodes
node <- c(13,14,15)
tipDes(phy, node)