Revision: 966
Author: nj7w
Date: 2006-06-06 12:17:08 -0700 (Tue, 06 Jun 2006)
ViewCVS: http://svn.sourceforge.net/r-gregmisc/?rev=966&view=rev
Log Message:
-----------
Updated ci, estimable and fit.contrast as per Randall Johnson
Modified Paths:
--------------
trunk/gmodels/man/ci.Rd
trunk/gmodels/man/estimable.Rd
trunk/gmodels/man/fit.contrast.Rd
Modified: trunk/gmodels/man/ci.Rd
===================================================================
--- trunk/gmodels/man/ci.Rd 2006-06-05 21:00:28 UTC (rev 965)
+++ trunk/gmodels/man/ci.Rd 2006-06-06 19:17:08 UTC (rev 966)
@@ -18,7 +18,9 @@
\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}{lme}(x, confidence = 0.95, alpha = 1 - confidence,...)
+ \method{ci}{lmer}(x, confidence = 0.95, alpha = 1 - confidence,
+ sim.lmer=TRUE, n.sim=1000, ...)
}
\arguments{
\item{x}{ object from which to compute confidence intervals. }
@@ -27,6 +29,10 @@
\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
+ objects.}
+ \item{n.sim}{Number of samples to take in \code{\Link[Matrix]{mcmcsamp}}.}
}
%\details{
% ~~ If necessary, more details than the __description__ above ~~
Modified: trunk/gmodels/man/estimable.Rd
===================================================================
--- trunk/gmodels/man/estimable.Rd 2006-06-05 21:00:28 UTC (rev 965)
+++ trunk/gmodels/man/estimable.Rd 2006-06-06 19:17:08 UTC (rev 966)
@@ -2,6 +2,7 @@
%
\name{estimable}
\alias{estimable}
+\alias{estimable.lmer}
%\alias{.wald}
%\alias{.to.est}
\title{Contrasts and estimable linear functions of model coefficients}
@@ -10,6 +11,7 @@
objects}
\usage{
estimable(obj, cm, beta0, conf.int=NULL, joint.test=FALSE, show.beta0)
+\method{estimable}{lmer}(obj, cm, beta0, conf.int = NULL, show.beta0, sim.lmer = TRUE, n.sim = 1000) %%%%%%%%%%% added this line
%.wald(obj, cm,beta0=rep(0, ifelse(is.null(nrow(cm)), 1, nrow(cm))))
%.to.est(obj, params)
}
@@ -28,6 +30,9 @@
\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 %%%
+ intervals will be estimated using \code{\Link[Matrix]{mcmcsamp}}.} %%% Added these sections
+ \item{n.sim}{Number of MCMC samples to take in \code{\Link[Matrix]{mcmcsamp}}.}%%%
}
\details{
\code{estimable} computes an estimate, test statitic, significance
Modified: trunk/gmodels/man/fit.contrast.Rd
===================================================================
--- trunk/gmodels/man/fit.contrast.Rd 2006-06-05 21:00:28 UTC (rev 965)
+++ trunk/gmodels/man/fit.contrast.Rd 2006-06-06 19:17:08 UTC (rev 966)
@@ -4,6 +4,7 @@
\alias{fit.contrast}
\alias{fit.contrast.lm}
\alias{fit.contrast.lme}
+\alias{fit.contrast.lmer}
\title{Compute and test arbitrary contrasts for regression objects}
\description{
Compute and test arbitrary contrasts for regression objects.
@@ -14,6 +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, ...)
}
\arguments{
\item{model}{regression (lm,glm,aov,lme) object for which the
@@ -31,6 +34,10 @@
\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
+ objects.}
+ \item{n.sim}{Number of samples to use in \code{\Link[Matrix]{mcmcsamp}}.}
}
\details{
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