version 2.2

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: laser
-Version: 2.1
-Date: 2007-5-20
+Version: 2.2
+Date: 2008-9-21
 Title: Likelihood Analysis of Speciation/Extinction Rates from Phylogenies
 Author: Dan Rabosky
 Maintainer: Dan Rabosky <DLR32@cornell.edu>
@@ -9,4 +9,4 @@ Suggests:
 Description: laser implements maximum likelihood methods based on the birth-death
 	process to test whether diversification rates have changed over time and whether rates vary among lineages.
 License: GPL 2 or later
-Packaged: Sun May 25 21:16:25 2008; hornik
+Packaged: Sun Sep 21 09:47:21 2008; danrabosky

R/birthdeathSim.R

@@ -0,0 +1,15 @@
+birthdeathSim <- function(b=.1, d=0, CladeSize, NumberMissing, NumberOfReps){
+		v <- vector("list", NumberOfReps);
+		for (i in 1:NumberOfReps) v[[i]] <- birthdeath.tree(b = 0.1, d = 0, taxa.stop = CladeSize);
+		v <- lapply(v, old2new.phylo);
+		v <- lapply(v, drop.tip, as.character(sample(1:(CladeSize),  NumberMissing)));		
+		fx <- function(x)return(rev(sort(as.numeric(branching.times(x)))));
+		v <- lapply(v, fx);
+		v <- as.matrix(t(as.data.frame(v)));
+
+		return(v);
+}
+
+
+
+

R/fitdAICrc.R

@@ -1,5 +1,5 @@
 `fitdAICrc` <-
-function(x, modelset = c("pureBirth", "bd", "DDL", "DDX", "yule2rate", "rvbd"), ints = NULL)
+function(x, modelset = c("pureBirth", "bd", "DDL", "DDX", "yule2rate"), ints = NULL)
 {
   checkbasal(x)
   if (!is.numeric(x)) stop("object x not of class 'numeric'")

R/fitdAICrc.batch.R

@@ -0,0 +1,52 @@
+
+# laser script to fitdAICrc.batch
+
+
+
+fitdAICrc.batch <- function(x, observed=NULL, ...){
+	rc1 <- apply(x, 1, pureBirth);
+	rc2 <- apply(x, 1, bd);
+	rv1 <- apply(x, 1, DDX);
+	rv2 <- apply(x, 1, DDL);
+	rv3 <- apply(x, 1, yule2rate, ...);	
+
+	res <- matrix(0, nrow=nrow(x), ncol=6);
+	for (i in 1:nrow(x)){
+		res[i, 1] <- rc1[[i]]$aic;
+		res[i, 2] <- rc2[[i]]$aic;
+		res[i, 3] <- rv1[[i]]$aic;
+		res[i, 4] <- rv2[[i]]$aic;
+		res[i, 5] <- rv3[[i]]$aic;
+		res[i, 6] <- min(rc1[[i]]$aic, rc2[[i]]$aic) - min(rv1[[i]]$aic, rv2[[i]]$aic, rv3[[i]]$aic);
+
+	}
+
+	colnames(res) <- c('pb', 'bd', 'DDX', 'DDL', 'y2r', 'dAIC');
+	res <- as.data.frame(res);
+	if (!is.null(observed)){
+		p.value <- length(res$dAIC[res$dAIC >= observed])/(nrow(res) + 1);
+		cat('observed dAIC:', observed, '\n', 'p = ', p.value, '\n');
+	}
+	return(res);
+}
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
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+
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+
+

man/DensityDependent.Rd

@@ -46,7 +46,7 @@ revealed from molecular phylogenies. \emph{Proc. Natl. Acad. Sci. USA} 89:8322-8
 }
 \author{ Dan Rabosky \email{DLR32@cornell.edu} }
 
-\seealso{ \code{\link{yule-n-rate}}, \code{\link{rvbd}}, \code{\link{fitdAICrc}} }
+\seealso{ \code{\link{yule-n-rate}}, \code{\link{fitdAICrc}} }
 \examples{
   data(plethodon)
   resX <- DDX(plethodon)

man/bd.Rd

@@ -47,7 +47,7 @@ Nee, S., R. M. May, and P. H. Harvey.  1994b.  The reconstructed evolutionary pr
 }
 \author{ Dan Rabosky \email{DLR32@cornell.edu} }
 
-\seealso{ \code{\link{pureBirth}}, \code{\link{fitdAICrc}},\code{\link{yule-n-rate}},\code{\link{rvbd}}}
+\seealso{ \code{\link{pureBirth}}, \code{\link{fitdAICrc}},\code{\link{yule-n-rate}}}
 \examples{
   data(plethodon)
   result <- bd(plethodon)  

man/birthdeathSim.Rd

@@ -0,0 +1 @@
+\name{birthdeathSim}\alias{birthdeathSim}\title{ birthdeathSim }\description{  Simulate Branching Times Under the birth-death model and/or with incomplete sampling}\usage{birthdeathSim(b, d, CladeSize, NumberMissing, NumberOfReps)}\arguments{  \item{b}{ the speciation rate }  \item{d}{ the extinction rate }  \item{CladeSize}{ the true clade size you wish to simulate }  \item{NumberMissing}{ the number of taxa missing from the 'real' tree }  \item{NumberOfReps}{ the number of phylogenies to simulated }}\details{	This generates a matrix of branching times that can be used with 	\code{fitdAICrc.batch} under any parameterization of a general birth-death	model with or without incomplete sampling.		To simulate a clade with incomplete sampling, note that \code{CladeSize} is 	the true size of a phylogeny, and \code{NumberMissing} is the number of missing taxa,	so if you specified \code{CladeSize = 100} and \code{NumberMissing = 20}, your resulting	trees would have 80 tips (Trees with 100 tips would be simulated, but then 20 taxa	would be dropped randomly to simulate incomplete sampling).		THis function is basically a wrapper for the \code{birthdeath.tree} function	from Geiger, but makes it more amenable to calculation of the delta AIC test	statistic for detecting temporal changes in diversification rates.  }\value{  an n x m matrix of branching times, where n is size \code{CladeSize} - \code{NumberMissing}   and m is size \code{ NumberOfReps }.}\author{ Dan Rabosky \email{DLR32@cornell.edu} }\examples{}\keyword{ datagen }

man/calcLHbd.Rd

@@ -34,7 +34,7 @@ Nee, S., R. M. May, and P. H. Harvey.  1994b.  The reconstructed evolutionary pr
 }
 \author{ Dan Rabosky \email{DLR32@cornell.edu} }
 
-\seealso{ \code{bd}, \code{rvbd}, \code{pureBirth} }
+\seealso{ \code{bd}, \code{pureBirth} }
 \examples{
 
 #plot a likelihood surface for the plethodon dataset

man/fitdAICrc.Rd

@@ -8,8 +8,7 @@
   in AIC scores between the best rate-constant and rate-variable models.
 }
 \usage{
-fitdAICrc(x, modelset = c("pureBirth", "bd", "DDL", "DDX", "yule2rate", 
-                "rvbd"), ints = NULL)
+fitdAICrc(x, modelset = c("pureBirth", "bd", "DDL", "DDX", "yule2rate"), ints = NULL)
 }
 \arguments{
   \item{x}{ a numeric vector of branching times }
@@ -22,12 +21,14 @@ fitdAICrc(x, modelset = c("pureBirth", "bd", "DDL", "DDX", "yule2rate",
 
   \code{modelset} is a list of the rate-constant and rate-variable models to consider.  You should include 
   both rate-constant models (\code{\link{pureBirth}} and \code{\link{bd}}), as well as one or more candidate rate-variable
-  models.  Available options are \code{\link{DDX}}, \code{\link{DDL}}, \code{\link{yule2rate}}, \code{\link{rvbd}}, and \code{\link{yule3rate}}. 
+  models.  Available options are \code{\link{DDX}}, \code{\link{DDL}}, \code{\link{yule2rate}}, and \code{\link{yule3rate}}. 
   See full descriptions of each of these models this document.
 
   'ints' is used in determining the number of shift points to consider.  If 'ints = NULL' (the 
   default), the model will consider only observed branching times as possible shift points.  See
-  \code{\link{yule-n-rate}} for additional discussion of the 'ints' option.   
+  \code{\link{yule-n-rate}} for additional discussion of the 'ints' option.  ]
+
+  Note that the rvbd function is no longer suppored ('rate variable birth death').
 
 }
 \value{

man/fitdAICrc.batch.Rd

@@ -0,0 +1,52 @@
+\name{fitdAICrc.batch}
+\alias{fitdAICrc.batch}
+
+
+\title{ Generate Null Distribution of dAICrc}
+\description{
+  Generates null distribution of dAICrc test statistic and determines significance
+  of dAICrc indices calculated for 'real' phylogenies.  
+}
+\usage{
+fitdAICrc.batch(x, observed=NULL, ...)
+}
+
+\arguments{
+  \item{x}{ a numeric matrix or dataframe of branching times }
+  \item{observed}{ the dAICrc statistic for the 'real' phylogeny }
+  \item{...}{ other parameters, e.g., ints for yule2rate }
+}
+\details{
+  For details on input format, see \code{\link{getBtimes.batch}}.  
+
+  This fits the following models: pure birth, birth death, density-dependent (exponential),
+  density-dependent (logistic), yule-2-rate
+
+
+  'observed' is the calculated dAICrc statistic obtained for a test phylogeny for which you would like to
+  obtain a p-value (using \code{\link{fitdAICrc}}).
+
+}
+\value{
+  A dataframe with N rows, where N is the number of sets of branching times analyzed.  Columns of the data frame
+  are the AIC scores for each of the models. The final column, with name dAIC, is the deltaAICrc test statistic
+  for that particular tree.
+
+}
+\references{ 
+Rabosky, D. L. 2006.  Likelihood methods for inferring temporal shifts in 
+diversification rates.  \emph{Evolution} 60:1152-1164. 
+
+}
+\author{ Dan Rabosky \email{DLR32@cornell.edu} }
+\note{ 
+	Make sure that you are using the exact same set of models for the real phylogeny and for the simulated 
+	phylogenies. If not, your results are invalid.
+
+}
+
+\examples{
+
+}
+\keyword{ models }
+\keyword{ htest }

man/laser-internals.Rd

@@ -3,7 +3,6 @@
 \alias{yuleint2}
 \alias{combinations}
 \alias{Ibd}
-\alias{Irvbd}
 \alias{IDDX}
 \alias{IDDL}
 \alias{IpureBirth}

man/laser-package.Rd

@@ -12,8 +12,8 @@ LASER
 \tabular{ll}{
 Package: \tab laser\cr
 Type: \tab Package\cr
-Version: \tab 2.0\cr
-Date: \tab 2008-05-19\cr
+Version: \tab 2.2\cr
+Date: \tab 2008-09-21\cr
 License: \tab GPL 2.0 ? \cr
 LazyLoad: \tab yes\cr
 }

man/pureBirth.Rd

@@ -30,7 +30,7 @@ of Dr.  J. C. Willis. \emph{Phil. Trans. R. Soc. Lond. B} 213:21-87.
 }
 \author{ Dan Rabosky \email{DLR32@cornell.edu} }
 
-\seealso{ \code{\link{yule-n-rate}}, \code{\link{bd}}, \code{\link{yuleWindow}}, \code{\link{rvbd}} }
+\seealso{ \code{\link{yule-n-rate}}, \code{\link{bd}}, \code{\link{yuleWindow}} }
 \examples{
   data("plethodon")
   ### loads branching times for plethodontid salamander dataset