[R-gregmisc-users] SF.net SVN: r-gregmisc:[1868] trunk/gmodels

[<wa...@us...>]

Revision: 1868
          http://sourceforge.net/p/r-gregmisc/code/1868
Author:   warnes
Date:     2014-07-24 15:14:30 +0000 (Thu, 24 Jul 2014)
Log Message:
-----------
- Estimable now adds the class 'estimable' to returned objects.
- New ci() method for estimable objects.
- Minor improvemets to man page formatting.

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

Modified: trunk/gmodels/DESCRIPTION
===================================================================
--- trunk/gmodels/DESCRIPTION	2014-07-22 15:07:54 UTC (rev 1867)
+++ trunk/gmodels/DESCRIPTION	2014-07-24 15:14:30 UTC (rev 1868)
@@ -1,6 +1,6 @@
 Package: gmodels
-Version: 2.15.5
-Date: 2013-07-18
+Version: 2.16.0
+Date: 2014-07-24
 Title: Various R programming tools for model fitting
 Author: Gregory R. Warnes, Ben Bolker, Thomas Lumley, and Randall C
         Johnson. Contributions from Randall C. Johnson are Copyright

Modified: trunk/gmodels/NAMESPACE
===================================================================
--- trunk/gmodels/NAMESPACE	2014-07-22 15:07:54 UTC (rev 1867)
+++ trunk/gmodels/NAMESPACE	2014-07-24 15:14:30 UTC (rev 1868)
@@ -19,6 +19,7 @@
 S3method(ci, lm)
 S3method(ci, lme)
 S3method(ci, mer)
+S3method(ci, estimable)
 
 S3method(fit.contrast, lm)
 S3method(fit.contrast, lme)

Modified: trunk/gmodels/R/ci.R
===================================================================
--- trunk/gmodels/R/ci.R	2014-07-22 15:07:54 UTC (rev 1867)
+++ trunk/gmodels/R/ci.R	2014-07-24 15:14:30 UTC (rev 1868)
@@ -93,3 +93,19 @@
     
     retval
 }
+
+
+ci.estimable  <-  function(x,confidence=0.95,alpha=1-confidence,...)
+  {
+    ci.low  <- x$Estimate + qt(alpha/2, x$DF) * x$"Std. Error"
+    ci.high <- x$Estimate - qt(alpha/2, x$DF) * x$"Std. Error"
+    retval  <- cbind(Estimate=x$Estimate,
+                     "CI lower"=ci.low,
+                     "CI upper"=ci.high,
+                     "Std. Error"= x$"Std. Error",
+                     "p-value" = x$"Pr(>|t|)"
+                     )
+    rownames(retval) <- rownames(x)
+    
+    retval
+  }

Modified: trunk/gmodels/R/estimable.R
===================================================================
--- trunk/gmodels/R/estimable.R	2014-07-22 15:07:54 UTC (rev 1867)
+++ trunk/gmodels/R/estimable.R	2014-07-24 15:14:30 UTC (rev 1868)
@@ -161,6 +161,9 @@
       rownames(retval) <- make.unique(rownames(retval))
       retval <- as.data.frame(retval)
       if(!show.beta0) retval$beta0 <- NULL
+
+      class(retval) <- c("estimable", class(retval))
+      
       return(retval)
     }
 }
@@ -273,6 +276,9 @@
   rownames(retval) <- make.unique(rownames(retval))
   retval <- as.data.frame(retval)
   if(!show.beta0) retval$beta0 <- NULL
+
+  class(retval) <- c("estimable", class(retval))
+
   return(retval)
 
 }

Modified: trunk/gmodels/man/ci.Rd
===================================================================
--- trunk/gmodels/man/ci.Rd	2014-07-22 15:07:54 UTC (rev 1867)
+++ trunk/gmodels/man/ci.Rd	2014-07-24 15:14:30 UTC (rev 1868)
@@ -7,6 +7,7 @@
 \alias{ci.lm}
 \alias{ci.lme}
 \alias{ci.mer}
+\alias{ci.estimable}
 \title{Compute Confidence Intervals}
 \description{ Compute and display confidence intervals for model
   estimates.  Methods are provided for the mean of a numeric vector
@@ -14,12 +15,13 @@
   \code{ci.binom}, and for \code{lm}, \code{lme}, and \code{mer} objects are
   provided. }
 \usage{
-  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}{mer}(x, confidence = 0.95, alpha = 1 - confidence, n.sim=10000, ...) 
+  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}{mer}(x, confidence=0.95, alpha=1-confidence, n.sim=10000, ...) 
+  \method{ci}{estimable}(x, confidence=0.95, alpha=1-confidence, ...) 
 }
 \arguments{
   \item{x}{ object from which to compute confidence intervals. }

Modified: trunk/gmodels/man/estimable.Rd
===================================================================
--- trunk/gmodels/man/estimable.Rd	2014-07-22 15:07:54 UTC (rev 1867)
+++ trunk/gmodels/man/estimable.Rd	2014-07-24 15:14:30 UTC (rev 1868)
@@ -104,7 +104,7 @@
   \code{\link[stats]{lm}},
   \code{\link[nlme]{lme}},
   \code{\link[stats]{contrasts}},
-  \code{\link[rms]{contrast.rms}},
+  \code{\link[rms]{contrast}}
   }
 
 \examples{

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