Thread: [R-gregmisc-users] SF.net SVN: r-gregmisc:[1329] trunk/gmodels

SourceForge Headquarters 225 Broadway Suite 1600 San Diego, CA 92101 +1 (858) 422-6466

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:


This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.




Thread: [R-gregmisc-users] SF.net SVN: r-gregmisc:[1329] trunk/gmodels

r-gregmisc-users