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[R-gregmisc-users] SF.net SVN: r-gregmisc:[1329] trunk/gmodels
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From: <wa...@us...> - 2009-05-09 04:00:24
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Revision: 1329
http://r-gregmisc.svn.sourceforge.net/r-gregmisc/?rev=1329&view=rev
Author: warnes
Date: 2009-05-09 04:00:15 +0000 (Sat, 09 May 2009)
Log Message:
-----------
Update Greg's email address
Modified Paths:
--------------
trunk/gmodels/DESCRIPTION
trunk/gmodels/man/ci.Rd
trunk/gmodels/man/estimable.Rd
trunk/gmodels/man/fast.prcomp.Rd
trunk/gmodels/man/fit.contrast.Rd
trunk/gmodels/man/glh.test.Rd
trunk/gmodels/man/make.contrasts.Rd
Modified: trunk/gmodels/DESCRIPTION
===================================================================
--- trunk/gmodels/DESCRIPTION 2009-05-09 03:35:14 UTC (rev 1328)
+++ trunk/gmodels/DESCRIPTION 2009-05-09 04:00:15 UTC (rev 1329)
@@ -3,16 +3,17 @@
Title: Various R programming tools for model fitting
Author: Gregory R. Warnes. Includes R source code and/or documentation
contributed by Ben Bolker, Thomas Lumley, and Randall C Johnson.
- Contributions from Randall C. Johnson are Copyright (2005)
- SAIC-Frederick, Inc. Funded by the Intramural Research Program,
- of the NIH, National Cancer Institute, Center for Cancer Research
- under NCI Contract NO1-CO-12400.
-Maintainer: Gregory R. Warnes <wa...@bs...>
+Maintainer: Gregory R. Warnes <gr...@ra...>
Description: Various R programming tools for model fitting
Depends: R (>= 1.9.0)
-Suggests: gplots, Matrix, nlme, lme4, coda
+Suggests: gplots, Matrix, nlme, lme4
Imports: MASS, gdata
-License: GPL-2.
+License: GPL-2. Contributions from Randall C. Johnson are
+ Copyright (2005) SAIC-Frederick, Inc. Funded by
+ the Intramural Research Program, of the NIH, National
+ Cancer Institute, Center for Cancer Research under NCI
+ Contract NO1-CO-12400.
URL: http://cran.r-project.org/src/contrib/PACKAGES.html
http://www.sf.net/projects/r-gregmisc
Date: 2007-07-24
+Packaged: Fri Dec 7 17:22:36 2007; warnes
Modified: trunk/gmodels/man/ci.Rd
===================================================================
--- trunk/gmodels/man/ci.Rd 2009-05-09 03:35:14 UTC (rev 1328)
+++ trunk/gmodels/man/ci.Rd 2009-05-09 04:00:15 UTC (rev 1329)
@@ -6,20 +6,21 @@
\alias{ci.binom}
\alias{ci.lm}
\alias{ci.lme}
-\alias{ci.lmer}
+\alias{ci.mer}
\title{Compute Confidence Intervals}
\description{ Compute and display confidence intervals for model
estimates. Methods are provided for the mean of a numeric vector
\code{ci.default}, the probability of a binomial vector
- \code{ci.binom}, and for \code{lm}, \code{lme}, and \code{lmer} objects. }
+ \code{ci.binom}, and for \code{lm}, \code{lme}, and \code{mer} objects are
+ provided. }
\synopsis{
ci(x, confidence = 0.95, alpha = 1 - confidence,...)
\method{ci}{default}(x, confidence = 0.95, alpha = 1 - confidence, na.rm=FALSE)...)
\method{ci}{binom}(x, confidence = 0.95, alpha = 1 - confidence,...)
\method{ci}{lm}(x, confidence = 0.95, alpha = 1 - confidence,...)
\method{ci}{lme}(x, confidence = 0.95, alpha = 1 - confidence,...)
- \method{ci}{lmer}(x, confidence = 0.95, alpha = 1 - confidence,
- sim.lmer=TRUE, n.sim=1000, ...)
+ \method{ci}{mer}(x, confidence = 0.95, alpha = 1 - confidence,
+ sim.mer=TRUE, n.sim=1000, ...)
}
\arguments{
\item{x}{ object from which to compute confidence intervals. }
@@ -28,8 +29,8 @@
\item{na.rm}{boolean indicating whether missing values should be
removed. Defaults to \code{FALSE}.}
\item{\dots}{Arguments for methods}
- \item{sim.lmer}{Logical value. If TRUE confidence
- intervals will be estimated using \code{\Link[Matrix]{mcmcsamp}}. This option only takes effect for lmer
+ \item{sim.mer}{Logical value. If TRUE confidence
+ intervals will be estimated using \code{\Link[Matrix]{mcmcsamp}}. This option only takes effect for mer
objects.}
\item{n.sim}{Number of samples to take in \code{\Link[Matrix]{mcmcsamp}}.}
}
@@ -41,7 +42,7 @@
\code{Estimate}, \code{CI lower}, \code{CI upper}, \code{Std. Error},
\code{DF} (for lme objects only), and \code{p-value}.
}
-\author{ Gregory R. Warnes \email{wa...@bs...}
+\author{ Gregory R. Warnes \email{gr...@ra...}
}
\seealso{
\code{\link[stats]{confint}},
@@ -66,7 +67,7 @@
ci(reg)
\dontrun{
-# lmer example
+# mer example
library(lme4)
fm2 <- lmer(Reaction ~ Days + (1|Subject) + (0+Days|Subject), sleepstudy)
ci(fm2)
Modified: trunk/gmodels/man/estimable.Rd
===================================================================
--- trunk/gmodels/man/estimable.Rd 2009-05-09 03:35:14 UTC (rev 1328)
+++ trunk/gmodels/man/estimable.Rd 2009-05-09 04:00:15 UTC (rev 1329)
@@ -3,27 +3,27 @@
\name{estimable}
\alias{estimable}
\alias{estimable.default}
-\alias{estimable.lmer}
+\alias{estimable.mer}
\alias{estimable.mlm}
%\alias{.wald}
%\alias{.to.est}
\title{Contrasts and estimable linear functions of model coefficients}
\description{
Compute and test contrasts and other estimable linear
- functions of model coefficients for for lm, glm, lme, lmer, and geese
+ functions of model coefficients for for lm, glm, lme, mer, and geese
objects
}
\usage{
estimable(obj, cm, beta0, conf.int=NULL, show.beta0, ...)
\method{estimable}{default} (obj, cm, beta0, conf.int=NULL, show.beta0, joint.test=FALSE, ...)
-\method{estimable}{lmer}(obj, cm, beta0, conf.int=NULL,
- show.beta0, sim.lmer=TRUE, n.sim=1000, ...)
+\method{estimable}{mer}(obj, cm, beta0, conf.int=NULL,
+ show.beta0, sim.mer=TRUE, n.sim=1000, ...)
\method{estimable}{mlm}(obj, cm, beta0, conf.int=NULL, show.beta0, ...)
%.wald(obj, cm,beta0=rep(0, ifelse(is.null(nrow(cm)), 1, nrow(cm))))
%.to.est(obj, params)
}
\arguments{
- \item{obj}{Regression (lm, glm, lme, lmer, mlm) object. }
+ \item{obj}{Regression (lm, glm, lme, mer, mlm) object. }
\item{cm}{Vector, List, or Matrix specifying estimable linear functions or
contrasts. See below for details.}
\item{beta0}{Vector of null hypothesis values}
@@ -37,7 +37,7 @@
\item{show.beta0}{Logical value. If TRUE a column for beta0 will be
included in the output table. Defaults to TRUE when beta0 is
specified, FALSE otherwise.}
- \item{sim.lmer}{Logical value. If TRUE p-values and confidence
+ \item{sim.mer}{Logical value. If TRUE p-values and confidence
intervals will be estimated using \code{\Link[Matrix]{mcmcsamp}}.
}
\item{n.sim}{Number of MCMC samples to take in
@@ -95,7 +95,7 @@
}
\author{
BXC (Bendix Carstensen) \email{bxc\@novonordisk.com},
- Gregory R. Warnes \email{wa...@bs...},
+ Gregory R. Warnes \email{gr...@ra...},
Soren Hojsgaard \email{so...@ag...}, and
Randall C Johnson \email{rjo...@nc...}
}
Modified: trunk/gmodels/man/fast.prcomp.Rd
===================================================================
--- trunk/gmodels/man/fast.prcomp.Rd 2009-05-09 03:35:14 UTC (rev 1328)
+++ trunk/gmodels/man/fast.prcomp.Rd 2009-05-09 04:00:15 UTC (rev 1329)
@@ -69,7 +69,7 @@
\code{\link{svd}} .
}
\author{Modifications by Gregory R. Warnes
- \email{wa...@bs...} }
+ \email{gr...@ra...} }
\seealso{
\code{\link[stats]{prcomp}}, \code{\link{svd}}, \code{\link{La.svd}}
Modified: trunk/gmodels/man/fit.contrast.Rd
===================================================================
--- trunk/gmodels/man/fit.contrast.Rd 2009-05-09 03:35:14 UTC (rev 1328)
+++ trunk/gmodels/man/fit.contrast.Rd 2009-05-09 04:00:15 UTC (rev 1329)
@@ -4,7 +4,7 @@
\alias{fit.contrast}
\alias{fit.contrast.lm}
\alias{fit.contrast.lme}
-\alias{fit.contrast.lmer}
+\alias{fit.contrast.mer}
\title{Compute and test arbitrary contrasts for regression objects}
\description{
Compute and test arbitrary contrasts for regression objects.
@@ -15,8 +15,8 @@
conf.int=NULL, df=FALSE, ...)
\method{fit.contrast}{lme}(model, varname, coeff, showall=FALSE,
conf.int=NULL, df=FALSE, ...)
-\method{fit.contrast}{lmer}(model, varname, coeff, showall=FALSE,
- conf.int=NULL, sim.lmer = TRUE, n.sim = 1000, ...)
+\method{fit.contrast}{mer}(model, varname, coeff, showall=FALSE,
+ conf.int=NULL, sim.mer = TRUE, n.sim = 1000, ...)
}
\arguments{
\item{model}{regression (lm,glm,aov,lme) object for which the
@@ -34,8 +34,8 @@
\item{df}{boolean indicating whether to return a column containing the
degrees of freedom.}
\item{\dots}{optional arguments provided by methods.}
- \item{sim.lmer}{Logical value. If TRUE p-values and confidence
- intervals will be estimated using \code{\Link[Matrix]{mcmcsamp}}. This option only takes effect for lmer
+ \item{sim.mer}{Logical value. If TRUE p-values and confidence
+ intervals will be estimated using \code{\Link[Matrix]{mcmcsamp}}. This option only takes effect for mer
objects.}
\item{n.sim}{Number of samples to use in \code{\Link[Matrix]{mcmcsamp}}.}
}
@@ -52,7 +52,7 @@
specified lower and upper confidence limits are also returned.}
\references{Venables & Ripley, Section 6.2}
-\author{ Gregory R. Warnes \email{wa...@bs...}}
+\author{ Gregory R. Warnes \email{gr...@ra...}}
\seealso{ \code{\link{lm}}, \code{\link{contrasts}},
\code{\link{contr.treatment}}, \code{\link{contr.poly}},
Modified: trunk/gmodels/man/glh.test.Rd
===================================================================
--- trunk/gmodels/man/glh.test.Rd 2009-05-09 03:35:14 UTC (rev 1328)
+++ trunk/gmodels/man/glh.test.Rd 2009-05-09 04:00:15 UTC (rev 1329)
@@ -67,7 +67,7 @@
}
\references{ R.H. Myers, Classical and Modern Regression with
Applications, 2nd Ed, 1990, p. 105}
-\author{Gregory R. Warnes \email{wa...@bs...} }
+\author{Gregory R. Warnes \email{gr...@ra...} }
\seealso{\code{\link{fit.contrast}}, \code{\link{estimable}},
\code{\link{contrasts}} }
\examples{
Modified: trunk/gmodels/man/make.contrasts.Rd
===================================================================
--- trunk/gmodels/man/make.contrasts.Rd 2009-05-09 03:35:14 UTC (rev 1328)
+++ trunk/gmodels/man/make.contrasts.Rd 2009-05-09 04:00:15 UTC (rev 1329)
@@ -31,7 +31,7 @@
\code{\link{contrasts}} or to the \code{contrasts} argument of model
functions (eg, \code{\link{lm}}).
}
-\author{ Gregory R. Warnes \email{wa...@bs...}}
+\author{ Gregory R. Warnes \email{gr...@ra...}}
\seealso{ \code{\link{lm}}, \code{\link{contrasts}},
\code{\link{contr.treatment}}, \code{\link{contr.poly}},
Computation and testing of General Linear Hypothesis:
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