Thread: [R-gregmisc-users] SF.net SVN: r-gregmisc: [1015] trunk/gmodels

Brought to you by: warnes

r-gregmisc-users

[R-gregmisc-users] SF.net SVN: r-gregmisc: [1015] trunk/gmodels

From: <wa...@us...> - 2006-11-27 20:36:32

Revision: 1015
          http://svn.sourceforge.net/r-gregmisc/?rev=1015&view=rev
Author:   warnes
Date:     2006-11-27 12:36:28 -0800 (Mon, 27 Nov 2006)

Log Message:
-----------
Add missing export of methods for estimable()

Modified Paths:
--------------
    trunk/gmodels/DESCRIPTION
    trunk/gmodels/NAMESPACE

Modified: trunk/gmodels/DESCRIPTION
===================================================================
--- trunk/gmodels/DESCRIPTION	2006-11-20 23:48:54 UTC (rev 1014)
+++ trunk/gmodels/DESCRIPTION	2006-11-27 20:36:28 UTC (rev 1015)
@@ -1,10 +1,9 @@
 Package: gmodels
-Version: 2.12.0-3
-Date: 2006-04-27
+Version: 2.13.0
 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.
-Maintainer: Nitin Jain <nit...@pf...>
+Maintainer: Gregory R. Warnes <wa...@bs...>
 Description: Various R programming tools for model fitting
 Depends: R (>= 1.9.0)
 Suggests: gplots

Modified: trunk/gmodels/NAMESPACE
===================================================================
--- trunk/gmodels/NAMESPACE	2006-11-20 23:48:54 UTC (rev 1014)
+++ trunk/gmodels/NAMESPACE	2006-11-27 20:36:28 UTC (rev 1015)
@@ -24,12 +24,12 @@
 S3method(fit.contrast, lme)
 S3method(fit.contrast, lmer)
 
+S3method(estimable, lm)
+S3method(estimable, lmer)
+
 S3method(print, glh.test)
 S3method(summary, glh.test)
 
-S3method(fit.contrast,lm)
-S3method(fit.contrast,lme)
-
 importFrom(MASS, ginv)
 importFrom(gdata, frameApply)
 importFrom(gdata, nobs)


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

[R-gregmisc-users] SF.net SVN: r-gregmisc: [1016] trunk/gmodels

From: <wa...@us...> - 2006-11-27 20:45:59

Revision: 1016
          http://svn.sourceforge.net/r-gregmisc/?rev=1016&view=rev
Author:   warnes
Date:     2006-11-27 12:45:56 -0800 (Mon, 27 Nov 2006)

Log Message:
-----------
Update for 2.13.1

Modified Paths:
--------------
    trunk/gmodels/DESCRIPTION
    trunk/gmodels/NEWS

Modified: trunk/gmodels/DESCRIPTION
===================================================================
--- trunk/gmodels/DESCRIPTION	2006-11-27 20:36:28 UTC (rev 1015)
+++ trunk/gmodels/DESCRIPTION	2006-11-27 20:45:56 UTC (rev 1016)
@@ -1,5 +1,5 @@
 Package: gmodels
-Version: 2.13.0
+Version: 2.13.1
 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.

Modified: trunk/gmodels/NEWS
===================================================================
--- trunk/gmodels/NEWS	2006-11-27 20:36:28 UTC (rev 1015)
+++ trunk/gmodels/NEWS	2006-11-27 20:45:56 UTC (rev 1016)
@@ -1,6 +1,19 @@
-CHANGES IN GMODELS 2.12.0
--------------------------
+Version 2.13.1
+--------------
 
+Bug Fixes:
+
+- Problem: estimable() was failing for lmer objects.
+  Solution: Add estimable.lmer() to the exported methods list in NAMESPACE
+
+
+Version 2.13.0
+--------------
+
+
+Version 2.12.0
+--------------
+
 - Updated Greg's email address.
 
 - Add support for lmer (lme version 4) objects to ci(), estimable(),
@@ -14,11 +27,11 @@
         estimable(reg, c(    0,   1,	 0,   -1)) 
   which should make estimable() much easier to use for large models.
 
-CHANGES IN GMODELS 2.1.0
-------------------------
+Version 2.1.0
+-------------
 
-CHANGES IN GMODELS 2.0.8
------------------------
+Version 2.0.8
+-------------
 
  - Added DESCRIPTION and removed DESCRIPTION.in
 


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

[R-gregmisc-users] SF.net SVN: r-gregmisc: [1026] trunk/gmodels

From: <wa...@us...> - 2006-11-29 00:04:56

Revision: 1026
          http://svn.sourceforge.net/r-gregmisc/?rev=1026&view=rev
Author:   warnes
Date:     2006-11-28 16:04:54 -0800 (Tue, 28 Nov 2006)

Log Message:
-----------
- Add generic
- Fix code vs. doc inconsistiencies

Modified Paths:
--------------
    trunk/gmodels/R/estimable.R
    trunk/gmodels/man/estimable.Rd

Modified: trunk/gmodels/R/estimable.R
===================================================================
--- trunk/gmodels/R/estimable.R	2006-11-28 22:38:11 UTC (rev 1025)
+++ trunk/gmodels/R/estimable.R	2006-11-29 00:04:54 UTC (rev 1026)
@@ -1,12 +1,10 @@
 # $Id$
-estimable <- function (obj, cm, beta0, conf.int=NULL, joint.test=FALSE,
-                       show.beta0, ...)
+estimable <- function (obj, cm, beta0, conf.int=NULL,  show.beta0, ...)
   {
     UseMethod("estimable")
   }
 
-estimable.default <- function (obj, cm, beta0, conf.int=NULL, joint.test=FALSE,
-                           show.beta0, ...)
+estimable.default <- function (obj, cm, beta0, conf.int=NULL, show.beta0, joint.test=FALSE, ...)
 {
   if (is.matrix(cm) || is.data.frame(cm))
     {
@@ -202,8 +200,8 @@
     print(as.data.frame(retval))
 }
 
-estimable.lmer <- function (obj, cm, beta0, conf.int=NULL,
-                            show.beta0, sim.lmer=TRUE, n.sim=1000, ...)
+estimable.lmer <- function (obj, cm, beta0, conf.int=NULL, show.beta0,
+                                             sim.lmer=TRUE, n.sim=1000, ...)
 {
   if (is.matrix(cm) || is.data.frame(cm))
     {

Modified: trunk/gmodels/man/estimable.Rd
===================================================================
--- trunk/gmodels/man/estimable.Rd	2006-11-28 22:38:11 UTC (rev 1025)
+++ trunk/gmodels/man/estimable.Rd	2006-11-29 00:04:54 UTC (rev 1026)
@@ -2,16 +2,21 @@
 %
 \name{estimable}
 \alias{estimable}
+\alias{estimable.default}
 \alias{estimable.lmer}
 %\alias{.wald}
 %\alias{.to.est}
 \title{Contrasts and estimable linear functions of model coefficients}
-\description{Compute and test contrasts and other estimable linear
+\description{
+  Compute and test contrasts and other estimable linear
   functions of model coefficients for for lm, glm, lme, lmer, and geese
-  objects}
+  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
+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, ...) 
 %.wald(obj, cm,beta0=rep(0, ifelse(is.null(nrow(cm)), 1, nrow(cm))))
 %.to.est(obj, params)
 }
@@ -30,9 +35,13 @@
    \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}}.}%%%
+   \item{sim.lmer}{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
+     \code{\Link[Matrix]{mcmcsamp}}.
+   }
+   \item{...}{ignored}
 }
 \details{
   \code{estimable} computes an estimate, test statitic, significance


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

[R-gregmisc-users] SF.net SVN: r-gregmisc: [1075] trunk/gmodels

From: <wa...@us...> - 2007-03-09 20:06:36

Revision: 1075
          http://svn.sourceforge.net/r-gregmisc/?rev=1075&view=rev
Author:   warnes
Date:     2007-03-09 12:06:05 -0800 (Fri, 09 Mar 2007)

Log Message:
-----------
Flip lower and upper interval in ci.lmer(). Add example to man page.

Modified Paths:
--------------
    trunk/gmodels/R/est.lmer.R
    trunk/gmodels/man/ci.Rd

Modified: trunk/gmodels/R/est.lmer.R
===================================================================
--- trunk/gmodels/R/est.lmer.R	2007-03-09 19:43:05 UTC (rev 1074)
+++ trunk/gmodels/R/est.lmer.R	2007-03-09 20:06:05 UTC (rev 1075)
@@ -24,7 +24,8 @@
   est <- drop(cm %*% samp.summ$statistics[1:n,1])
   stderr <- sd(samp.cm)
   
-  pval <- sapply(1:length(beta0), function(i){percentile(beta0[i], samp.cm[,i])})
+  pval <- sapply(1:length(beta0),
+                 function(i){percentile(beta0[i], samp.cm[,i])})
   pval <- ifelse(pval <= .5, 2*pval, 2*(1-pval))
 
   if(is.null(conf.int))
@@ -33,10 +34,15 @@
     upper.ci <- NULL
   }else{
     alpha <- 1-conf.int
-    samp.ci <- sapply(1:length(beta0), function(i){quantile(samp.cm[,i], probs=c(alpha/2, 1-alpha/2))})
+    samp.ci <- sapply(1:length(beta0),
+                      function(i)
+                        {
+                          quantile(samp.cm[,i], probs=c(alpha/2, 1-alpha/2))
+                        }
+                      )
 
-    lower.ci <- samp.ci[2,]
-    upper.ci <- samp.ci[1,]
+    lower.ci <- samp.ci[1,]
+    upper.ci <- samp.ci[2,]
   }
 
   # return results

Modified: trunk/gmodels/man/ci.Rd
===================================================================
--- trunk/gmodels/man/ci.Rd	2007-03-09 19:43:05 UTC (rev 1074)
+++ trunk/gmodels/man/ci.Rd	2007-03-09 20:06:05 UTC (rev 1075)
@@ -66,5 +66,13 @@
 reg  <-  lm(Area ~ Population, data=as.data.frame(state.x77))
 ci(reg) 
 
+\dontrun{
+# lmer example
+library(lme4)
+fm2 <- lmer(Reaction ~ Days + (1|Subject) + (0+Days|Subject), sleepstudy)
+ci(fm2)
 }
+
+
+}
 \keyword{ regression }


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

[R-gregmisc-users] SF.net SVN: r-gregmisc: [1105] trunk/gmodels

From: <wa...@us...> - 2007-07-26 00:20:02

Revision: 1105
          http://r-gregmisc.svn.sourceforge.net/r-gregmisc/?rev=1105&view=rev
Author:   warnes
Date:     2007-07-25 17:20:00 -0700 (Wed, 25 Jul 2007)

Log Message:
-----------
Add support for mlm to estimable().

Modified Paths:
--------------
    trunk/gmodels/DESCRIPTION
    trunk/gmodels/NAMESPACE
    trunk/gmodels/NEWS
    trunk/gmodels/R/estimable.mlm.R
    trunk/gmodels/man/estimable.Rd

Modified: trunk/gmodels/DESCRIPTION
===================================================================
--- trunk/gmodels/DESCRIPTION	2007-07-26 00:10:03 UTC (rev 1104)
+++ trunk/gmodels/DESCRIPTION	2007-07-26 00:20:00 UTC (rev 1105)
@@ -1,5 +1,5 @@
 Package: gmodels
-Version: 2.13.2
+Version: 2.14.0
 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.
@@ -15,5 +15,4 @@
 	 Contract NO1-CO-12400.
 URL: http://cran.r-project.org/src/contrib/PACKAGES.html 
      http://www.sf.net/projects/r-gregmisc
-Packaged: Mon Jun  5 16:19:14 2006; root
-Date: 2007-03-09
\ No newline at end of file
+Date: 2007-07-24
\ No newline at end of file

Modified: trunk/gmodels/NAMESPACE
===================================================================
--- trunk/gmodels/NAMESPACE	2007-07-26 00:10:03 UTC (rev 1104)
+++ trunk/gmodels/NAMESPACE	2007-07-26 00:20:00 UTC (rev 1105)
@@ -26,6 +26,7 @@
 
 S3method(estimable, default)
 S3method(estimable, lmer)
+S3method(estimable, mlm)
 
 S3method(print, glh.test)
 S3method(summary, glh.test)

Modified: trunk/gmodels/NEWS
===================================================================
--- trunk/gmodels/NEWS	2007-07-26 00:10:03 UTC (rev 1104)
+++ trunk/gmodels/NEWS	2007-07-26 00:20:00 UTC (rev 1105)
@@ -1,6 +1,14 @@
 Version 2.13.2
 --------------
 
+New Features:
+
+- Add support for 'mlm' objects to estimable
+
+
+Version 2.13.2
+--------------
+
 Bug Fixes:
 
 - Lower and upper end of confidence interval for lmer objects were

Modified: trunk/gmodels/R/estimable.mlm.R
===================================================================
--- trunk/gmodels/R/estimable.mlm.R	2007-07-26 00:10:03 UTC (rev 1104)
+++ trunk/gmodels/R/estimable.mlm.R	2007-07-26 00:20:00 UTC (rev 1105)
@@ -1,5 +1,5 @@
 `estimable.mlm` <-
-  function (object, ...) 
+  function (obj, cm, beta0, conf.int=NULL,  show.beta0, ...)
 {
   coef <- coef(object)
   ny <- ncol(coef)
@@ -23,7 +23,7 @@
     object$fitted.values <- fitted[, i]
     object$effects <- effects[, i]
     object$call$formula[[2]] <- object$terms[[2]] <- as.name(ynames[i])
-    value[[i]] <- estimable(object, ...)
+    value[[i]] <- estimable(obj, cm, beta0, conf.int=NULL,  show.beta0, ...)
   }
   class(value) <- "listof"
   value

Modified: trunk/gmodels/man/estimable.Rd
===================================================================
--- trunk/gmodels/man/estimable.Rd	2007-07-26 00:10:03 UTC (rev 1104)
+++ trunk/gmodels/man/estimable.Rd	2007-07-26 00:20:00 UTC (rev 1105)
@@ -4,6 +4,7 @@
 \alias{estimable}
 \alias{estimable.default}
 \alias{estimable.lmer}
+\alias{estimable.mlm}
 %\alias{.wald}
 %\alias{.to.est}
 \title{Contrasts and estimable linear functions of model coefficients}
@@ -17,11 +18,12 @@
 \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}{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) object. }
+   \item{obj}{Regression (lm,glm,lme,lmer,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}


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

[R-gregmisc-users] SF.net SVN: r-gregmisc: [1232] trunk/gmodels

From: <wa...@us...> - 2007-12-07 22:21:45

Revision: 1232
          http://r-gregmisc.svn.sourceforge.net/r-gregmisc/?rev=1232&view=rev
Author:   warnes
Date:     2007-12-07 14:21:41 -0800 (Fri, 07 Dec 2007)

Log Message:
-----------
Update DESCRIPTION and NEWS for release 2.14.1

Modified Paths:
--------------
    trunk/gmodels/DESCRIPTION
    trunk/gmodels/NEWS

Modified: trunk/gmodels/DESCRIPTION
===================================================================
--- trunk/gmodels/DESCRIPTION	2007-12-07 22:10:30 UTC (rev 1231)
+++ trunk/gmodels/DESCRIPTION	2007-12-07 22:21:41 UTC (rev 1232)
@@ -1,5 +1,5 @@
 Package: gmodels
-Version: 2.14.0
+Version: 2.14.1
 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.

Modified: trunk/gmodels/NEWS
===================================================================
--- trunk/gmodels/NEWS	2007-12-07 22:10:30 UTC (rev 1231)
+++ trunk/gmodels/NEWS	2007-12-07 22:21:41 UTC (rev 1232)
@@ -1,6 +1,17 @@
-Version 2.13.2
+Version 2.14.1
 --------------
 
+New features:
+
+- Add support for 'lme' objects to estimable().
+
+Other:
+
+- Fix minor typos in manual page for estimable().
+
+Version 2.14.0
+--------------
+
 New Features:
 
 - Add support for 'mlm' objects to estimable


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