Revision: 1076
http://svn.sourceforge.net/r-gregmisc/?rev=1076&view=rev
Author: warnes
Date: 2007-03-09 12:06:36 -0800 (Fri, 09 Mar 2007)
Log Message:
-----------
Minor code formatting changes
Modified Paths:
--------------
trunk/gmodels/R/ci.R
Modified: trunk/gmodels/R/ci.R
===================================================================
--- trunk/gmodels/R/ci.R 2007-03-09 20:06:05 UTC (rev 1075)
+++ trunk/gmodels/R/ci.R 2007-03-09 20:06:36 UTC (rev 1076)
@@ -3,21 +3,22 @@
ci <- function(x, confidence=0.95,alpha=1-confidence,...)
UseMethod("ci")
-ci.default <- function(x, confidence=0.95,alpha=1-confidence,na.rm=FALSE,...) {
- est <- mean(x, na.rm=na.rm)
- stderr <- sd(x, na.rm=na.rm)/sqrt(nobs(x));
- ci.low <- est + qt(alpha/2, nobs(x)-1) * stderr
- ci.high <- est - qt(alpha/2, nobs(x)-1) * stderr
- retval <- c(
- Estimate=est,
- "CI lower"=ci.low,
- "CI upper"=ci.high,
- "Std. Error"=stderr
- )
+ci.default <- function(x, confidence=0.95,alpha=1-confidence,na.rm=FALSE,...)
+ {
+ est <- mean(x, na.rm=na.rm)
+ stderr <- sd(x, na.rm=na.rm)/sqrt(nobs(x));
+ ci.low <- est + qt(alpha/2, nobs(x)-1) * stderr
+ ci.high <- est - qt(alpha/2, nobs(x)-1) * stderr
+ retval <- c(
+ Estimate=est,
+ "CI lower"=ci.low,
+ "CI upper"=ci.high,
+ "Std. Error"=stderr
+ )
+
+ retval
+ }
- retval
-}
-
ci.binom <- function(x, confidence=0.95,alpha=1-confidence,...)
{
if( !(all(x) %in% c(0,1)) ) stop("Binomial values must be either 0 or 1.")
@@ -37,48 +38,55 @@
}
ci.lm <- function(x,confidence=0.95,alpha=1-confidence,...)
-{
- x <- summary(x)
- est <- coef(x)[,1] ;
- ci.low <- est + qt(alpha/2, x$df[2]) * coef(x)[,2] ;
- ci.high <- est - qt(alpha/2, x$df[2]) * coef(x)[,2] ;
- retval <- cbind(Estimate=est,
- "CI lower"=ci.low,
- "CI upper"=ci.high,
- "Std. Error"= coef(x)[,2],
- "p-value" = coef(x)[,4])
+ {
+ x <- summary(x)
+ est <- coef(x)[,1] ;
+ ci.low <- est + qt(alpha/2, x$df[2]) * coef(x)[,2] ;
+ ci.high <- est - qt(alpha/2, x$df[2]) * coef(x)[,2] ;
+ retval <- cbind(Estimate=est,
+ "CI lower"=ci.low,
+ "CI upper"=ci.high,
+ "Std. Error"= coef(x)[,2],
+ "p-value" = coef(x)[,4])
+
+ reqtval
+ }
- retval
-}
-
ci.lme <- function(x,confidence=0.95,alpha=1-confidence,...)
{
- x <- summary(x)
- est <- x$tTable[,"Value"] ;
- ci.low <- est + qt(alpha/2, x$tTable[,"DF"]) * x$tTable[,"Std.Error"] ;
- ci.high <- est - qt(alpha/2, x$tTable[,"DF"]) * x$tTable[,"Std.Error"] ;
- retval <- cbind(Estimate=est,
- "CI lower"=ci.low,
- "CI upper"=ci.high,
- "Std. Error"= x$tTable[,"Std.Error"],
- "DF" = x$tTable[,"DF"],
- "p-value" = x$tTable[,"p-value"])
- rownames(retval) <- rownames(x$tTable)
- retval
-}
+ x <- summary(x)
+ est <- x$tTable[,"Value"] ;
+ ci.low <- est + qt(alpha/2, x$tTable[,"DF"]) * x$tTable[,"Std.Error"] ;
+ ci.high <- est - qt(alpha/2, x$tTable[,"DF"]) * x$tTable[,"Std.Error"] ;
+ retval <- cbind(Estimate=est,
+ "CI lower"=ci.low,
+ "CI upper"=ci.high,
+ "Std. Error"= x$tTable[,"Std.Error"],
+ "DF" = x$tTable[,"DF"],
+ "p-value" = x$tTable[,"p-value"])
+ rownames(retval) <- rownames(x$tTable)
+ retval
+ }
-ci.lmer <- function(x, confidence=0.95, alpha=1-confidence, sim.lmer=TRUE, n.sim=1000, ...) ################### changed this function
+ci.lmer <- function(x,
+ confidence=0.95,
+ alpha=1-confidence,
+ sim.lmer=TRUE,
+ n.sim=1000,
+ ...
+ )
{
if(!(require(coda, quietly=TRUE) & require(Matrix, quietly=TRUE)))
stop("coda and Matrix packages required for ci.lmer")
x.effects <- fixef(x)
n <- length(x.effects)
-
+
retval <- est.lmer(obj = x, cm = diag(n), beta0 = rep(0, n),
conf.int = confidence, show.beta0 = FALSE,
- n.sim = n.sim)[,c("Estimate", "Lower.CI", "Upper.CI", "Std. Error", "p value")]
-
+ n.sim = n.sim)[,c("Estimate", "Lower.CI", "Upper.CI",
+ "Std. Error", "p value")]
+
colnames(retval)[c(2:3, 5)] <- c("CI lower", "CI upper", "p-value")
rownames(retval) <- names(x.effects)
retval
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