[Sleuth2-commits] r39 - in pkg/Sleuth3: . inst/doc man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Sat Aug 25 09:25:14 CEST 2012
Author: berwin
Date: 2012-08-25 09:25:14 +0200 (Sat, 25 Aug 2012)
New Revision: 39
Modified:
pkg/Sleuth3/DESCRIPTION
pkg/Sleuth3/inst/doc/Sleuth3-manual.pdf
pkg/Sleuth3/man/case0501.Rd
pkg/Sleuth3/man/case0502.Rd
pkg/Sleuth3/man/case0601.Rd
pkg/Sleuth3/man/case0602.Rd
pkg/Sleuth3/man/case1602.Rd
pkg/Sleuth3/man/case1702.Rd
pkg/Sleuth3/man/ex1620.Rd
Log:
Sleuth3:
Edited a few .Rd files so that examples can be run without error on R
versions that have suggested packages not installed.
Updated inst/doc/Sleuth3-manual.pdf
Updated publication date in DESCRIPTION file and bumped version number.
Modified: pkg/Sleuth3/DESCRIPTION
===================================================================
--- pkg/Sleuth3/DESCRIPTION 2012-08-24 14:47:28 UTC (rev 38)
+++ pkg/Sleuth3/DESCRIPTION 2012-08-25 07:25:14 UTC (rev 39)
@@ -1,7 +1,7 @@
Package: Sleuth3
Title: Data sets from Ramsey and Schafer's "Statistical Sleuth (3rd ed)"
-Version: 0.0-6
-Date: 2012-08-24
+Version: 0.0-7
+Date: 2012-08-25
Author: Original by F.L. Ramsey and D.W. Schafer,
modifications by Daniel W. Schafer, Jeannie Sifneos and Berwin A. Turlach
Description: Data sets from Ramsey, F.L. and Schafer, D.W. (2013), "The
Modified: pkg/Sleuth3/inst/doc/Sleuth3-manual.pdf
===================================================================
(Binary files differ)
Modified: pkg/Sleuth3/man/case0501.Rd
===================================================================
--- pkg/Sleuth3/man/case0501.Rd 2012-08-24 14:47:28 UTC (rev 38)
+++ pkg/Sleuth3/man/case0501.Rd 2012-08-25 07:25:14 UTC (rev 39)
@@ -68,9 +68,9 @@
"dietRR50 - dietNR50 = 0",
"dietlopro - dietNR50 = 0",
"dietNN85 - dietNP = 0") )
- }
summary(myComparisons,test=adjusted("none")) # No multiple comparison adjust.
confint(myComparisons, calpha = univariate_calpha()) # No adjustment
+}
## EXAMPLE 5: BOXPLOTS FOR PRESENTATION
boxplot(Lifetime ~ myDiet, ylab= "Lifetime (months)", names=myNames,
Modified: pkg/Sleuth3/man/case0502.Rd
===================================================================
--- pkg/Sleuth3/man/case0502.Rd 2012-08-24 14:47:28 UTC (rev 38)
+++ pkg/Sleuth3/man/case0502.Rd 2012-08-25 07:25:14 UTC (rev 39)
@@ -66,9 +66,9 @@
myContrast <- rbind(c(1/6, 1/6, 1/6, 1/6, 1/6, 1/6, - 1))
if(require(multcomp)){ # use multcomp library
myComparison <- glht(myAov3, linfct=myContrast)
-}
summary(myComparison, test=adjusted("none"))
confint(myComparison)
+}
## BOXPLOTS FOR PRESENTATION
boxplot(Percent ~ Judge, ylab= "Percent of Women on Judges' Venires",
Modified: pkg/Sleuth3/man/case0601.Rd
===================================================================
--- pkg/Sleuth3/man/case0601.Rd 2012-08-24 14:47:28 UTC (rev 38)
+++ pkg/Sleuth3/man/case0601.Rd 2012-08-25 07:25:14 UTC (rev 39)
@@ -49,29 +49,29 @@
## COMPARE MEAN QUALIFICATION SCORE OF EVERY HANDICAP GROUP TO "NONE"
if(require(multcomp)){ # Use the multcomp library
myDunnett <- glht(myAov, linfct = mcp(myHandicap = "Dunnett"))
+ summary(myDunnett)
+ confint(myDunnett,level=.95)
+ opar <- par(no.readonly=TRUE) # Save current graphics parameter settings
+ par(mar=c(4.1,8.1,4.1,1.1)) # Change margins
+ plot(myDunnett,
+ xlab="Difference in Mean Qualification Score (and Dunnet-adjusted CIs)")
+ par(opar) # Restore original graphics parameter settings
}
-summary(myDunnett)
-confint(myDunnett,level=.95)
-opar <- par(no.readonly=TRUE) # Save current graphics parameter settings
-par(mar=c(4.1,8.1,4.1,1.1)) # Change margins
-plot(myDunnett,
- xlab="Difference in Mean Qualification Score (and Dunnet-adjusted CIs)")
-par(opar) # Restore original graphics parameter settings
## COMPARE EVERY MEAN TO EVERY OTHER MEAN
if(require(multcomp)){ # Use the multcomp library
myTukey <- glht(myAov, linfct = mcp(myHandicap = "Tukey"))
+ summary(myTukey)
}
-summary(myTukey)
## TEST THE CONTRAST OF DISPLAY 6.4
myAov2 <- aov(Score ~ myHandicap - 1)
myContrast <- rbind(c(0, -1/2, 1/2, -1/2, 1/2))
if(require(multcomp)){ # Use the multcomp library
myComparison <- glht(myAov2, linfct=myContrast)
- }
-summary(myComparison, test=adjusted("none"))
-confint(myComparison)
+ summary(myComparison, test=adjusted("none"))
+ confint(myComparison)
+}
# BOXPLOTS FOR PRESENTATION
Modified: pkg/Sleuth3/man/case0602.Rd
===================================================================
--- pkg/Sleuth3/man/case0602.Rd 2012-08-24 14:47:28 UTC (rev 38)
+++ pkg/Sleuth3/man/case0602.Rd 2012-08-25 07:25:14 UTC (rev 39)
@@ -56,8 +56,8 @@
myContrast <- rbind(c(5, -3, 1, 3, -9, 3))
if(require(multcomp)){ # Use the multcomp library
myComparison <- glht(myAov2, linfct=myContrast)
+ summary(myComparison, test=adjusted("none"))
}
-summary(myComparison, test=adjusted("none"))
# Simpler exploration of linear effect, via regression (Ch. 7)
Modified: pkg/Sleuth3/man/case1602.Rd
===================================================================
--- pkg/Sleuth3/man/case1602.Rd 2012-08-24 14:47:28 UTC (rev 38)
+++ pkg/Sleuth3/man/case1602.Rd 2012-08-25 07:25:14 UTC (rev 39)
@@ -62,7 +62,7 @@
n <- length(highMinusBase) # 20: sample size
multiplier <- sqrt(2*((n-1)/(n-2))*qf(.95,2,n-2)) # See Sleuth, page 495
HighMinusBase + c(-1,1)*multiplier*seHighMinusBase # 95% CI for High - Base
-HighMinusLow + c(-1,2)*multiplier*seHighMinusLow # 95% CI for High - Low)
+HighMinusLow + c(-1,2)*multiplier*seHighMinusLow # 95% CI for High - Low
## GRAPHICAL DISPLAY FOR PRESENTATION
Modified: pkg/Sleuth3/man/case1702.Rd
===================================================================
--- pkg/Sleuth3/man/case1702.Rd 2012-08-24 14:47:28 UTC (rev 38)
+++ pkg/Sleuth3/man/case1702.Rd 2012-08-25 07:25:14 UTC (rev 39)
@@ -56,7 +56,6 @@
myCCA <- cc(x,y) # Store canonical correlation computations
canCor <- myCCA$cor # Extract the canonical correlations
canCor #[1] 0.9506990 0.8665601 0.5571876 0.1106555
-}
# Make a function to test the number of canonical correlations (advanced).
# Bartlett modification of likelihood ratio test
@@ -176,8 +175,7 @@
abline(myLm2)
par(opar) # Restore previous graphics parameter settings
-
-
+}
detach(case1702)
}
\keyword{datasets}
Modified: pkg/Sleuth3/man/ex1620.Rd
===================================================================
--- pkg/Sleuth3/man/ex1620.Rd 2012-08-24 14:47:28 UTC (rev 38)
+++ pkg/Sleuth3/man/ex1620.Rd 2012-08-25 07:25:14 UTC (rev 39)
@@ -10,7 +10,7 @@
in the two groups were performed for each gene individually. The data are the
p-values from all these tests. The goal is to use a identify a set of genes
that differentially express in the two groups, subject to some specified value
- for expected false discovery rate, such as 5%.
+ for expected false discovery rate, such as 5\%.
}
\usage{ex1620}
\format{
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