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updates to man pages

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liamrevell committed Mar 28, 2017
1 parent 6e68893 commit 1aa63cb478ef4a53b7ebb64c76170b4bf4b31cd0
Showing with 112 additions and 93 deletions.
  1. +2 −2 DESCRIPTION
  2. +1 −1 man/add.arrow.Rd
  3. +4 −4 man/add.color.bar.Rd
  4. +1 −1 man/add.everywhere.Rd
  5. +2 −2 man/ancThresh.Rd
  6. +1 −1 man/anoletree.Rd
  7. +2 −0 man/as.multiPhylo.Rd
  8. +1 −1 man/averageTree.Rd
  9. +1 −1 man/bind.tip.Rd
  10. +1 −1 man/branching.diffusion.Rd
  11. +3 −3 man/brownie.lite.Rd
  12. +3 −3 man/brownieREML.Rd
  13. +2 −2 man/cladelabels.Rd
  14. +2 −2 man/contMap.Rd
  15. +2 −2 man/cospeciation.Rd
  16. +2 −2 man/densityMap.Rd
  17. +3 −2 man/densityTree.Rd
  18. +2 −1 man/dotTree.Rd
  19. +3 −3 man/evol.vcv.Rd
  20. +2 −2 man/evolvcv.lite.Rd
  21. +1 −1 man/fancyTree.Rd
  22. +2 −1 man/fastBM.Rd
  23. +1 −1 man/force.ultrametric.Rd
  24. +1 −1 man/gammatest.Rd
  25. +1 −1 man/getDescendants.Rd
  26. +3 −0 man/getSisters.Rd
  27. +5 −2 man/labelnodes.Rd
  28. +1 −1 man/ltt95.Rd
  29. +1 −3 man/make.era.map.Rd
  30. +3 −1 man/map.to.singleton.Rd
  31. +1 −1 man/midpoint.root.Rd
  32. +2 −2 man/modified.Grafen.Rd
  33. +1 −1 man/multiC.Rd
  34. +1 −1 man/optim.phylo.ls.Rd
  35. +1 −3 man/paintSubTree.Rd
  36. +2 −2 man/pbtree.Rd
  37. +8 −4 man/pgls.Ives.Rd
  38. +1 −1 man/phenogram.Rd
  39. +6 −2 man/phyl.RMA.Rd
  40. +1 −1 man/phyl.pairedttest.Rd
  41. +1 −1 man/phyl.pca.Rd
  42. +1 −1 man/phyl.resid.Rd
  43. +1 −1 man/phylomorphospace.Rd
  44. +1 −2 man/phylomorphospace3d.Rd
  45. +1 −1 man/phylosig.Rd
  46. +1 −1 man/plotBranchbyTrait.Rd
  47. +5 −4 man/plotSimmap.Rd
  48. +2 −1 man/plotThresh.Rd
  49. +1 −2 man/plotTree.errorbars.Rd
  50. +3 −2 man/plotTree.wBars.Rd
  51. +1 −1 man/rateshift.Rd
  52. +3 −3 man/roundBranches.Rd
  53. +1 −1 man/roundPhylogram.Rd
  54. +3 −3 man/untangle.Rd
  55. +2 −2 man/write.simmap.Rd
  56. +2 −1 man/writeAncestors.Rd
View
@@ -35,8 +35,8 @@ Description: Package contains various functions for phylogenetic analysis.
canonical correlation analysis, and a phylogenetic ANOVA; projecting
a tree onto a geographic map; simulating discrete character
histories on the tree; fitting a model in which a discrete character
- evolves under the threshold model; visualization of cospeciation; a
- simple statistical test for cospeciation between two trees. In
+ evolves under the threshold model; visualization of cospeciation; and
+ a simple statistical test for cospeciation between two trees. In
addition to this phylogenetic comparative method functionality, the
package also contains functions for a wide range of other purposes in
phylogenetic biology. For instance, functionality in this package
View
@@ -13,7 +13,7 @@ add.arrow(tree=NULL, tip, ...)
This function adds an arrow to a plotted tree.
}
\details{
- This function presently works for radial (\code{type="fan"}) and right facing square phylograms (\code{type="phylogram"}). Trees can be plotted using phytools function \code{plotTree}, \code{plotSimmap}, \code{contMap}, \code{densityMap}, and ape method \code{plot.phylo}.
+ This function presently works for radial (\code{type="fan"}) and right facing square phylograms (\code{type="phylogram"}). Trees can be plotted using phytools function \code{plotTree}, \code{plotSimmap}, \code{contMap}, \code{densityMap}, and ape S3 method \code{plot.phylo}.
}
\references{
Revell, L. J. (2012) phytools: An R package for phylogenetic comparative biology (and other things). \emph{Methods Ecol. Evol.}, \bold{3}, 217-223.
View
@@ -3,7 +3,7 @@
\title{Add color bar to a plot}
\usage{
add.color.bar(leg, cols, title=NULL, lims=c(0,1), digits=1, prompt=TRUE,
- lwd=4, outline=TRUE, ...)
+ lwd=4, outline=TRUE, ...)
}
\arguments{
\item{leg}{numerical value for the length of the legend.}
@@ -14,17 +14,17 @@ add.color.bar(leg, cols, title=NULL, lims=c(0,1), digits=1, prompt=TRUE,
\item{prompt}{logical value indicating whether the location of the legend should be obtained interactively.}
\item{lwd}{width of the plotted bar.}
\item{outline}{logical value indicated whether or not to outline the plotted color bar with a 1 pt line.}
- \item{...}{optional arguments including: \code{x} x-coordinate of the legend (if \code{prompt=FALSE}); \code{y} y-coordinate of the legend; \code{subtitle} optional legend subtitle; \code{direction} direction of the color bar (i.e., increase from left to right or from right to left).}
+ \item{...}{optional arguments including: \code{x} x-coordinate of the legend (if \code{prompt=FALSE}); \code{y} y-coordinate of the legend; \code{subtitle} optional legend subtitle; \code{direction} direction of the color bar (i.e., increase from left to right or from right to left); and \code{fsize}, font size for the legend text.}
}
\description{
- This function adds a color bar to a plot created by \code{\link{plotBranchbyTrait}}. A color bar can be added by clicking on a location within the plot (when \code{prompt=TRUE}) or by setting \code{prompt=FALSE} and supplying x & y coordinates for the object. This function is also used internally by \code{plot.contMap} and \code{plot.densityMap}.
+ This function adds a color bar to a plot created by \code{\link{plotBranchbyTrait}}. A color bar can be added by clicking on a location within the plot (when \code{prompt=TRUE}) or by setting \code{prompt=FALSE} and supplying x & y coordinates for the object. This function is also used internally by S3 methods \code{\link{plot.contMap}} and \code{\link{plot.densityMap}}, as well as by \code{\link{errobar.contMap}}.
}
\references{
Revell, L. J. (2013) Two new graphical methods for mapping trait evolution on phylogenies. \emph{Methods in Ecology and Evolution}, \bold{4}, 754-759.
}
\author{Liam Revell \email{liam.revell@umb.edu}}
\seealso{
- \code{\link{contMap}}, \code{\link{densityMap}}, \code{\link{plotBranchbyTrait}}
+ \code{\link{contMap}}, \code{\link{densityMap}}, \code{\link{errorbar.contMap}}, \code{\link{plotBranchbyTrait}}
}
\keyword{phylogenetics}
\keyword{plotting}
View
@@ -9,7 +9,7 @@ add.everywhere(tree, tip.name)
\item{tip.name}{a string containing the name of the tip to add.}
}
\description{
- This function adds a tip to all branches to the tree and returns a a list of trees as an object of class \code{"multiPhylo"}.
+ This function adds a tip to all branches of the tree and returns a a list of trees as an object of class \code{"multiPhylo"}.
}
\value{
A list of trees as an object of class \code{"multiPhylo"}. Since the tip can be added to any branch, the length of the list is equal to the number of edges in \code{tree}.
View
@@ -2,8 +2,8 @@
\alias{ancThresh}
\title{Ancestral character estimation under the threshold model using Bayesian MCMC}
\usage{
-ancThresh(tree, x, ngen=1000, sequence=NULL, method="mcmc", model=c("BM","OU","lambda"),
- control=list(), ...)
+ancThresh(tree, x, ngen=1000, sequence=NULL, method="mcmc",
+ model=c("BM","OU","lambda"), control=list(), ...)
}
\arguments{
\item{tree}{phylogenetic tree.}
View
@@ -8,7 +8,7 @@
data(anoletree)
}
\format{
- The data are stored as a modified object of class \code{"simmap"} with a mapped discrete character. (E.g., see \code{read.simmap}.)
+ The data are stored as a modified object of class \code{"simmap"} with a mapped discrete character. (E.g., see \code{\link{read.simmap}}.)
}
\source{
Mahler, D. L, L. J. Revell, R. E. Glor, and J. B. Losos. (2010) Ecological opportunity and the rate of morphological evolution in the diversification of Greater Antillean anoles. \emph{Evolution}, \bold{64}, 2731-2745.
View
@@ -1,10 +1,12 @@
\name{as.multiPhylo}
\alias{as.multiPhylo}
\alias{as.multiPhylo.multiSimmap}
+\alias{as.multiPhylo.phylo}
\title{Conversion to object of class \code{"multiPhylo"}}
\usage{
as.multiPhylo(x, ...)
\method{as.multiPhylo}{multiSimmap}(x, ...)
+\method{as.multiPhylo}{phylo}(x, ...)
}
\arguments{
\item{x}{object to be converted to \code{"multiPhylo"}. Presently an object of class \code{"multiSimmap"}, or an object of class \code{"phylo"}. In the latter case an object of class \code{"multiPhylo"} with length \code{1} is generated.}
View
@@ -5,7 +5,7 @@
\title{Compute an average tree from a set of trees and related operations}
\usage{
averageTree(trees, start=NULL, method="quadratic.path.difference",
- tol=1e-12, quiet=FALSE, ...)
+ tol=1e-12, quiet=FALSE, ...)
ls.consensus(trees, start=NULL, tol=1e-12, quiet=FALSE, ...)
minTreeDist(tree, trees, method="quadratic.path.difference", ...)
}
View
@@ -3,7 +3,7 @@
\title{Attaches a new tip to a tree}
\usage{
bind.tip(tree, tip.label, edge.length=NULL, where=NULL, position=0,
- interactive=FALSE, ...)
+ interactive=FALSE, ...)
}
\arguments{
\item{tree}{receptor tree.}
@@ -3,7 +3,7 @@
\title{Animation of branching random diffusion}
\usage{
branching.diffusion(sig2=1, b=0.0023, time.stop=1000, ylim=NULL,
- smooth=TRUE, pause=0.02, record=NULL, path=NULL)
+ smooth=TRUE, pause=0.02, record=NULL, path=NULL)
}
\arguments{
\item{sig2}{variance of BM process.}
View
@@ -14,13 +14,13 @@ brownie.lite(tree, x, maxit=2000, test="chisq", nsim=100, se=NULL, ...)
\item{...}{optional arguments.}
}
\description{
- This function takes a modified \code{"phylo"} object with a mapped binary or multistate trait (see \code{\link{read.simmap}}) and data for a single continuously valued character. It then fits the Brownian rate variation ("noncensored") model of O'Meara et al. (2006; \emph{Evolution}). This is also the basic model implemented in Brian O'Meara's "Brownie" program.
+ This function takes an object of class \code{"simmap"} with a mapped binary or multistate trait (see \code{\link{read.simmap}}) and data for a single continuously valued character. It then fits the Brownian rate variation ("noncensored") model of O'Meara et al. (2006; \emph{Evolution}). This is also the basic model implemented in Brian O'Meara's \emph{Brownie} software.
}
\details{
Sampling error in the estimation of species means can also be accounted for by assigning the vector \code{se} with the species specific sampling errors for \code{x}.
}
\value{
- A list with the following components:
+ An object of class \code{"brownie.lite"} containing the following components:
\item{sig2.single}{is the rate for a single rate model - this is usually the "null" model.}
\item{a.single}{is the estimated state at the root node for the single rate model.}
\item{var.single}{variance on the single rate estimator - obtained from the Hessian.}
@@ -42,7 +42,7 @@ brownie.lite(tree, x, maxit=2000, test="chisq", nsim=100, se=NULL, ...)
}
\author{Liam Revell \email{liam.revell@umb.edu}}
\seealso{
- \code{\link{brownieREML}}, \code{\link{evol.vcv}}
+ \code{\link{brownieREML}}, \code{\link{evol.vcv}}, \code{\link{ratebytree}}
}
\keyword{phylogenetics}
\keyword{comparative method}
View
@@ -11,10 +11,10 @@ brownieREML(tree, x, maxit=2000, ...)
\item{...}{optional arguments.}
}
\description{
- This function takes a modified \code{"phylo"} object with a mapped binary or multistate trait (see \code{\link{read.simmap}}) and data for a single continuously valued character. It then uses restricted maximum likelihood (REML) to fit the Brownian rate variation ("noncensored") model of O'Meara et al. (2006; \emph{Evolution}). This function is similar to \code{\link{brownie.lite}} but uses REML (which is faster and unbiased) instead of ML. REML optimization takes advantage of Felsenstein's (1985) contrasts algorithm.
+ This function takes an object of class \code{"simmap"} with a mapped binary or multistate trait (see \code{\link{read.simmap}}) and data for a single continuously valued character. It then uses restricted maximum likelihood (REML) to fit the Brownian rate variation ("noncensored") model of O'Meara et al. (2006; \emph{Evolution}). This function is similar to \code{\link{brownie.lite}} but uses REML (which is faster and unbiased) instead of ML. REML optimization takes advantage of Felsenstein's (1985) contrasts algorithm.
}
\value{
- A list with the following components:
+ An object of class \code{"brownieREML"} containing the following components:
\item{sig2.single}{is the rate for a single rate model - this is usually the "null" model.}
\item{logL1}{log-likelihood of the single-rate model.}
\item{sig2.multiple}{is a length \emph{p} (for \emph{p} rates) vector of BM rates from the multi-rate model.}
@@ -30,7 +30,7 @@ brownieREML(tree, x, maxit=2000, ...)
}
\author{Liam Revell \email{liam.revell@umb.edu}}
\seealso{
- \code{\link{brownie.lite}}, \code{\link{evol.vcv}}, \code{\link{evol.rate.mcmc}}
+ \code{\link{brownie.lite}}, \code{\link{evol.vcv}}, \code{\link{evol.rate.mcmc}}, \code{\link{ratebytree}}
}
\keyword{phylogenetics}
\keyword{comparative method}
View
@@ -4,9 +4,9 @@
\title{Add labels to subtrees of a plotted phylogeny}
\usage{
cladelabels(tree=NULL, text, node, offset=NULL, wing.length=NULL, cex=1,
- orientation="vertical")
+ orientation="vertical")
arc.cladelabels(tree=NULL, text, node, ln.offset=1.02,
- lab.offset=1.06, cex=1, orientation="curved",...)
+ lab.offset=1.06, cex=1, orientation="curved",...)
}
\arguments{
\item{tree}{an object of class \code{"phylo"}. If not supplied, the function will obtain the last plotted phylogeny from the environmental variable \code{last_plot.phylo}.}
View
@@ -5,8 +5,8 @@
\title{Map continuous trait evolution on the tree}
\usage{
contMap(tree, x, res=100, fsize=NULL, ftype=NULL, lwd=4, legend=NULL,
- lims=NULL, outline=TRUE, sig=3, type="phylogram", direction="rightwards",
- plot=TRUE, ...)
+ lims=NULL, outline=TRUE, sig=3, type="phylogram", direction="rightwards",
+ plot=TRUE, ...)
\method{plot}{contMap}(x, ...)
errorbar.contMap(obj, ...)
}
View
@@ -5,8 +5,8 @@
\title{Conducts a statistical test of cospeciation between two trees}
\usage{
cospeciation(t1, t2, distance=c("RF","SPR"),
- method=c("simulation","permutation"), assoc=NULL,
- nsim=100, ...)
+ method=c("simulation","permutation"), assoc=NULL,
+ nsim=100, ...)
\method{plot}{cospeciation}(x, ...)
\method{print}{cospeciation}(x, ...)
}
View
@@ -4,8 +4,8 @@
\title{Plot posterior density of stochastic mapping on a tree}
\usage{
densityMap(trees, res=100, fsize=NULL, ftype=NULL, lwd=3, check=FALSE,
- legend=NULL, outline=FALSE, type="phylogram", direction="rightwards",
- plot=TRUE, ...)
+ legend=NULL, outline=FALSE, type="phylogram", direction="rightwards",
+ plot=TRUE, ...)
\method{plot}{densityMap}(x, ...)
}
\arguments{
View
@@ -3,8 +3,9 @@
\alias{make.transparent}
\title{Plots a posterior sample of trees}
\usage{
-densityTree(trees, colors="blue", alpha=NULL, method="plotTree", fix.depth=FALSE,
- use.edge.length=TRUE, compute.consensus=FALSE, ...)
+densityTree(trees, colors="blue", alpha=NULL, method="plotTree",
+ fix.depth=FALSE, use.edge.length=TRUE, compute.consensus=FALSE,
+ ...)
make.transparent(color, alpha)
}
\arguments{
View
@@ -4,7 +4,8 @@
\title{Creates a phylogenetic dot plot}
\usage{
dotTree(tree, x, legend=TRUE, method="plotTree", standardize=FALSE, ...)
-dot.legend(x, y, min, max, Ntip, length=5, prompt=FALSE, method="plotTree", ...)
+dot.legend(x, y, min, max, Ntip, length=5, prompt=FALSE, method="plotTree",
+ ...)
}
\arguments{
\item{tree}{an object of class \code{"phylo"}.}
View
@@ -5,20 +5,20 @@
evol.vcv(tree, X, maxit=2000, vars=FALSE, ...)
}
\arguments{
- \item{tree}{a phylogenetic tree in modified \code{"phylo"} format (see \code{\link{read.simmap}}).}
+ \item{tree}{an object of class \code{"simmap"}.}
\item{X}{an \code{n} x \code{m} matrix of tip values for \code{m} continuously valued traits in \code{n} species - row names should be species names.}
\item{maxit}{an optional integer value indicating the maximum number of iterations for optimization - may need to be increased for large trees.}
\item{vars}{an optional logical value indicating whether or not to estimate the variances of the parameter estimates from the Hessian matrix.}
\item{...}{optional arguments.}
}
\description{
- This function takes a modified \code{"phylo"} object with a mapped binary or multistate trait and data for an arbitrary number of continuously valued character. It then fits the multiple evolutionary variance-covariance matrix (rate matrix) model of Revell & Collar (2009; \emph{Evolution}).
+ This function takes an object of class \code{"simmap"} with a mapped binary or multistate trait and data for an arbitrary number of continuously valued character. It then fits the multiple evolutionary variance-covariance matrix (rate matrix) model of Revell & Collar (2009; \emph{Evolution}).
}
\details{
This function performs optimization by first optimizing the likelihood with respect to the Cholesky matrices using \code{\link{optim}}. Optimization is by \code{method="Nelder-Mead"}. Using box constraints does not make sense here as they would be applied to the Cholesky matrix rather than the target parameters. May have to increase \code{maxit} for large trees and more than 2 traits.
}
\value{
- A list with the following components:
+ An object of class \code{"evol.vcv"} with the following components:
\item{R.single}{vcv matrix for the single rate matrix model.}
\item{vars.single}{optionally, a matrix containing the variances of the elements of \code{R.single}.}
\item{logL1}{log-likelihood for single matrix model.}
View
@@ -5,13 +5,13 @@
evolvcv.lite(tree, X, maxit=2000, tol=1e-10)
}
\arguments{
- \item{tree}{a phylogenetic tree in modified \code{"phylo"} format (see \code{\link{read.simmap}}).}
+ \item{tree}{an object of class \code{"simmap"}.}
\item{X}{an \code{n} x \code{m} matrix of tip values for \code{m} continuously valued traits in \code{n} species - row names should be species names.}
\item{maxit}{an optional integer value indicating the maximum number of iterations for optimization - may need to be increased for large trees.}
\item{tol}{tolerance value for \code{"L-BFGS-B"} optimization.}
}
\description{
- This function takes a modified \code{"phylo"} object with a mapped binary or multistate trait and data for two and only two continuously valued character. It then fits four different evolutionary models: common rates and correlation; different rates, common correlation; different correlations, common rates; no common structure.
+ This function takes an object of class \code{"simmap"} with a mapped binary or multistate trait and data for two and only two continuously valued character. It then fits four different evolutionary models: common rates and correlation; different rates, common correlation; different correlations, common rates; no common structure.
}
\value{
A list with the results summarized for each model.
View
@@ -3,7 +3,7 @@
\title{Plots special types of phylogenetic trees}
\usage{
fancyTree(tree, type=c("extinction","traitgram3d","droptip","densitymap",
- "contmap","phenogram95","scattergram"), ..., control=list())
+ "contmap","phenogram95","scattergram"), ..., control=list())
}
\arguments{
\item{tree}{a phylogenetic tree in \code{"phylo"} format.}
View
@@ -2,7 +2,8 @@
\alias{fastBM}
\title{Fast Brownian simulation}
\usage{
-fastBM(tree, a=0, mu=0, sig2=1, bounds=c(-Inf,Inf), internal=FALSE, nsim=1, ...)
+fastBM(tree, a=0, mu=0, sig2=1, bounds=c(-Inf,Inf), internal=FALSE, nsim=1,
+ ...)
}
\arguments{
\item{tree}{is a phylogenetic tree in \code{"phylo"} format.}
View
@@ -9,7 +9,7 @@ force.ultrametric(tree, method=c("nnls","extend"))
\item{method}{the method to use to force the tree to be ultrametric. Options are \code{"nnls"} (which uses the phangorn function \code{\link{nnls.tree}} internally), or \code{"extend"}.}
}
\description{
- This function forces an object of class \code{"phylo"} to be ultrametric. This is achieved either by using \code{\link{nnls.tree}} from the phangorn package to compute the set of edge lengths that result in a minimized sum-of-squares distance between the patristic distance of the output and input trees (\code{method="nnls"}); or by simplying extend all the external edges of the tree to match the external edge with the greatest total height (\code{method="extend"}). Note that neither of these should be treated as formal statistical methods for inferring an ultrametric tree. Rather, they should be employed when a genuinely ultrametric tree read from file fails \code{\link{is.ultrametric}} for reasons of numerical precision.
+ This function forces an object of class \code{"phylo"} to be ultrametric. This is achieved either by using \code{\link{nnls.tree}} from the phangorn package to compute the set of edge lengths that result in a minimized sum-of-squares distance between the patristic distance of the output and input trees (\code{method="nnls"}); or by simply extending all the external edges of the tree to match the external edge with the greatest total height (\code{method="extend"}). Note that neither of these should be treated as formal statistical methods for inferring an ultrametric tree. Rather, this method can be deployed when a genuinely ultrametric tree read from file fails \code{\link{is.ultrametric}} for reasons of numerical precision.
}
\value{
An ultrametric tree in an object of class \code{"phylo"}.
View
@@ -5,7 +5,7 @@
gammatest(x)
}
\arguments{
- \item{x}{list from function call of \code{\link{ltt}} in which \code{ltt(...,gamma=F)}.}
+ \item{x}{an object of class \code{"ltt"} resulting from a call of the function \code{\link{ltt}}.}
}
\description{
Conducts \eqn{\gamma}-test of Pybus & Harvey (2000).
View
@@ -20,7 +20,7 @@ getDescendants(tree, node, curr=NULL)
}
\author{Liam Revell \email{liam.revell@umb.edu}}
\seealso{
- \code{\link{paintSubTree}}
+ \code{\link{Descendants}}, \code{\link{paintSubTree}}
}
\keyword{phylogenetics}
\keyword{utilities}
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