[Lme4-commits] r1677 - in pkg/lme4.0: . man tests

[noreply at r-forge.r-project.org]

Author: bbolker
Date: 2012-03-17 23:31:07 +0100 (Sat, 17 Mar 2012)
New Revision: 1677

Added:
   pkg/lme4.0/man/sigma.Rd
   pkg/lme4.0/tests/sigma.R
Modified:
   pkg/lme4.0/DESCRIPTION
   pkg/lme4.0/NAMESPACE
Log:

   added sigma() for forward-compatibility with lme4 
(request of A. Galecki)



Modified: pkg/lme4.0/DESCRIPTION
===================================================================
--- pkg/lme4.0/DESCRIPTION	2012-03-17 21:13:54 UTC (rev 1676)
+++ pkg/lme4.0/DESCRIPTION	2012-03-17 22:31:07 UTC (rev 1677)
@@ -1,6 +1,6 @@
 Package: lme4.0
-Version: 0.9999-0
-Date: 2011-12-31
+Version: 0.9999-1
+Date: 2012-03-17
 Title: Linear mixed-effects models using S4 classes
 Description: Fit linear and generalized linear mixed-effects models.
   This is the implementation of lme4 available on CRAN and developed up to 2011.

Modified: pkg/lme4.0/NAMESPACE
===================================================================
--- pkg/lme4.0/NAMESPACE	2012-03-17 21:13:54 UTC (rev 1676)
+++ pkg/lme4.0/NAMESPACE	2012-03-17 22:31:07 UTC (rev 1677)
@@ -40,6 +40,7 @@
        "nlmer",
        #"pooledSD",
        "refit",
+       "sigma",
        "VarCorr")
 
 

Added: pkg/lme4.0/man/sigma.Rd
===================================================================
--- pkg/lme4.0/man/sigma.Rd	                        (rev 0)
+++ pkg/lme4.0/man/sigma.Rd	2012-03-17 22:31:07 UTC (rev 1677)
@@ -0,0 +1,25 @@
+\name{sigma}
+\alias{sigma}
+\alias{sigma,mer-method}
+\title{Extract residual standard error}
+\usage{
+  sigma(object, ...)
+}
+\arguments{
+  \item{object}{a fitted model.}
+
+  \item{...}{additional, optional arguments.  (None are
+  used in the \code{mer} method)}
+}
+\value{
+  the residual standard error as a scalar
+}
+\description{
+  Extract the residual standard error from a fitted model.
+}
+\details{
+  This is a generic function.  At present the only methods
+  are for mixed-effects models of class
+  \code{\linkS4class{mer}}.
+}
+

Added: pkg/lme4.0/tests/sigma.R
===================================================================
--- pkg/lme4.0/tests/sigma.R	                        (rev 0)
+++ pkg/lme4.0/tests/sigma.R	2012-03-17 22:31:07 UTC (rev 1677)
@@ -0,0 +1,3 @@
+library(lme4.0)
+fm1 <- lmer(Reaction ~ Days + (Days|Subject), sleepstudy)
+stopifnot(all.equal(attr(VarCorr(fm1),"sc"),sigma(fm1)))