[R-gregmisc-users] SF.net SVN: r-gregmisc: [966] trunk/gmodels/man

[<nj...@us...>]

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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