[Caic-commits] r70 - in pkg: R man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Thu Oct 2 22:04:20 CEST 2008
Author: petzoldt
Date: 2008-10-02 22:04:19 +0200 (Thu, 02 Oct 2008)
New Revision: 70
Modified:
pkg/R/brunch.R
pkg/man/brunch.Rd
pkg/man/caic-package.Rd
pkg/man/caic.diagnostics.Rd
pkg/man/crunch.Rd
pkg/man/fusco.test.Rd
pkg/man/growTree.Rd
pkg/man/macrocaic.Rd
pkg/man/piclm.Rd
pkg/man/profileLik.lambda.Rd
pkg/man/write.caic.Rd
Log:
cr between references
Modified: pkg/R/brunch.R
===================================================================
--- pkg/R/brunch.R 2008-10-02 12:59:48 UTC (rev 69)
+++ pkg/R/brunch.R 2008-10-02 20:04:19 UTC (rev 70)
@@ -132,6 +132,8 @@
if(any( varLevels > 2 & ! varIsOrdered )) stop("Unordered non-binary factors included in model formula.")
# refit the model frame with numericized data
+ #data <- as.data.frame(lapply(data, function(x) as.numeric(as.factor(x))))
+ data$tip <- as.factor(data$tip)
data <- as.data.frame(lapply(data, as.numeric))
mf <- model.frame(formula, data, na.action=na.pass)
Modified: pkg/man/brunch.Rd
===================================================================
--- pkg/man/brunch.Rd 2008-10-02 12:59:48 UTC (rev 69)
+++ pkg/man/brunch.Rd 2008-10-02 20:04:19 UTC (rev 70)
@@ -50,7 +50,9 @@
}
\references{
Felsenstein, J. (1985). Phylogenies and the comparative method. Am. Nat. 125, 1-15
+
Pagel, M. D. (1992). A method for the analysis of comparative data. J. theor. Biol. 156, 431-442.
+
Purvis, A. and Rambaut, A. (1995) Comparative analysis by independent contrasts (CAIC): an Apple Macintosh application for analysing comparative data. Computer Appl. Biosciences 11, 247-251.
}
Modified: pkg/man/caic-package.Rd
===================================================================
--- pkg/man/caic-package.Rd 2008-10-02 12:59:48 UTC (rev 69)
+++ pkg/man/caic-package.Rd 2008-10-02 20:04:19 UTC (rev 70)
@@ -26,6 +26,7 @@
}
\references{
Purvis, A. and Rambaut, A. (1995) Comparative analysis by independent contrasts (CAIC): an Apple Macintosh application for analysing comparative data. Computer Appl. Biosciences 11, 247---251\\
+
Agapow, P.-M. and Isaac, N. J. B. (2002) MacroCAIC: correlates of species richness. Diversity \& Distributions, 8, 41---43\\
}
Modified: pkg/man/caic.diagnostics.Rd
===================================================================
--- pkg/man/caic.diagnostics.Rd 2008-10-02 12:59:48 UTC (rev 69)
+++ pkg/man/caic.diagnostics.Rd 2008-10-02 20:04:19 UTC (rev 70)
@@ -33,7 +33,7 @@
\value{
If \code{test.signif} is TRUE, a list with class `caic.diagonistics' containing, for each of the model terms in \code{which.terms}, a list of \code{lm} objects testing the relationship between the values in each of the specified \code{which.plots}. Otherwise, the command only produces the plots and no value is returned.
}
-\references{ ~put references to the literature/web site here ~ }
+%\references{ ~put references to the literature/web site here ~ }
\author{ David Orme }
\seealso{\code{\link{crunch}}, \code{\link{brunch}}, \code{\link{macrocaic}}}
\examples{
Modified: pkg/man/crunch.Rd
===================================================================
--- pkg/man/crunch.Rd 2008-10-02 12:59:48 UTC (rev 69)
+++ pkg/man/crunch.Rd 2008-10-02 20:04:19 UTC (rev 70)
@@ -55,7 +55,9 @@
}
\references{
Felsenstein, J. (1985). Phylogenies and the comparative method. Am. Nat. 125, 1-15
+
Pagel, M. D. (1992). A method for the analysis of comparative data. J. theor. Biol. 156, 431-442.
+
Purvis, A. and Rambaut, A. (1995) Comparative analysis by independent contrasts (CAIC): an Apple Macintosh application for analysing comparative data. Computer Appl. Biosciences 11, 247-251.
}
Modified: pkg/man/fusco.test.Rd
===================================================================
--- pkg/man/fusco.test.Rd 2008-10-02 12:59:48 UTC (rev 69)
+++ pkg/man/fusco.test.Rd 2008-10-02 20:04:19 UTC (rev 70)
@@ -79,6 +79,7 @@
}
\references{
Fusco, G. & Cronk, Q.C.B. (1995) A New Method for Evaluating the Shape of Large Phylogenies. J. theor. Biol. 175, 235-243
+
Purvis A., Katzourakis A. & Agapow, P-M (2002) Evaluating Phylogenetic Tree Shape: Two Modifications to Fusco & Cronk's Method. J. theor. Biol. 214, 93-103.
}
\author{David Orme, Andy Purvis}
Modified: pkg/man/growTree.Rd
===================================================================
--- pkg/man/growTree.Rd 2008-10-02 12:59:48 UTC (rev 69)
+++ pkg/man/growTree.Rd 2008-10-02 20:04:19 UTC (rev 70)
@@ -46,7 +46,7 @@
\item{ct.set}{If continuous characters were simulated, a list of the \code{ct.start}, \code{ct.change} and \code{ct.var} details provided.}
\item{dt.rates}{If discrete characters were simulated, a list containing the \code{dt.rates} details provided.}
}
-\references{ ~put references to the literature/web site here ~ }
+%\references{ ~put references to the literature/web site here ~ }
\author{David Orme, drawing heavily on discussions with Paul-Michael Agapow.}
\examples{
Modified: pkg/man/macrocaic.Rd
===================================================================
--- pkg/man/macrocaic.Rd 2008-10-02 12:59:48 UTC (rev 69)
+++ pkg/man/macrocaic.Rd 2008-10-02 20:04:19 UTC (rev 70)
@@ -42,6 +42,7 @@
}
\references{
Felsenstein, J. (1985). Phylogenies and the comparative method. Am. Nat. 125, 1-15
+
Agapow, P.-M. and Isaac, N. J. B. (2002) MacroCAIC: correlates of species richness. Diversity & Distributions, 8, 41-43
}
\author{David Orme}
Modified: pkg/man/piclm.Rd
===================================================================
--- pkg/man/piclm.Rd 2008-10-02 12:59:48 UTC (rev 69)
+++ pkg/man/piclm.Rd 2008-10-02 20:04:19 UTC (rev 70)
@@ -46,7 +46,9 @@
}
\references{
Felsenstein, J. (1985). Phylogenies and the comparative method. Am. Nat. 125, 1-15
+
Pagel, M. D. (1992). A method for the analysis of comparative data. J. theor. Biol. 156, 431-442.
+
Purvis, A. and Rambaut, A. (1995) Comparative analysis by independent contrasts (CAIC): an Apple Macintosh application for analysing comparative data. Computer Appl. Biosciences 11, 247-251.
}
Modified: pkg/man/profileLik.lambda.Rd
===================================================================
--- pkg/man/profileLik.lambda.Rd 2008-10-02 12:59:48 UTC (rev 69)
+++ pkg/man/profileLik.lambda.Rd 2008-10-02 20:04:19 UTC (rev 70)
@@ -61,7 +61,7 @@
The \code{maxLik} functions return \code{optimize} output: namely, a list with components maximum and objective which give the location of the maximum likelihood and the value of the lambda or kappa at that point.
}
-\references{ ~put references to the literature/web site here ~ }
+%\references{ ~put references to the literature/web site here ~ }
\author{Rob Freckleton; David Orme; Gavin Thomas}
\seealso{\code{\link{pglm}}}
\examples{
Modified: pkg/man/write.caic.Rd
===================================================================
--- pkg/man/write.caic.Rd 2008-10-02 12:59:48 UTC (rev 69)
+++ pkg/man/write.caic.Rd 2008-10-02 20:04:19 UTC (rev 70)
@@ -23,6 +23,7 @@
}
\references{
Purvis, A. and Rambaut, A. (1995) Comparative analysis by independent contrasts (CAIC): an Apple Macintosh application for analysing comparative data. Computer Appl. Biosciences 11, 247-251.
+
Agapow, P.-M. and Isaac, N. J. B. (2002) MacroCAIC: correlates of species richness. Diversity & Distributions, 8, 41-43
}
\author{David Orme}
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