diff -Nru r-cran-multcompview-0.1-7/debian/changelog r-cran-multcompview-0.1-8/debian/changelog --- r-cran-multcompview-0.1-7/debian/changelog 2018-05-31 13:45:56.000000000 +0000 +++ r-cran-multcompview-0.1-8/debian/changelog 2020-01-04 08:28:53.000000000 +0000 @@ -1,3 +1,13 @@ +r-cran-multcompview (0.1-8-1) unstable; urgency=medium + + * Team upload. + * New upstream version + * debhelper-compat 12 + * Standards-Version: 4.4.1 + * Trim trailing whitespace. + + -- Dylan Aïssi Sat, 04 Jan 2020 09:28:53 +0100 + r-cran-multcompview (0.1-7-2) unstable; urgency=medium * Rebuild for R 3.5 transition diff -Nru r-cran-multcompview-0.1-7/debian/compat r-cran-multcompview-0.1-8/debian/compat --- r-cran-multcompview-0.1-7/debian/compat 2018-05-31 13:45:56.000000000 +0000 +++ r-cran-multcompview-0.1-8/debian/compat 1970-01-01 00:00:00.000000000 +0000 @@ -1 +0,0 @@ -11 diff -Nru r-cran-multcompview-0.1-7/debian/control r-cran-multcompview-0.1-8/debian/control --- r-cran-multcompview-0.1-7/debian/control 2018-05-31 13:45:56.000000000 +0000 +++ r-cran-multcompview-0.1-8/debian/control 2020-01-04 08:28:53.000000000 +0000 @@ -4,10 +4,10 @@ Section: gnu-r Testsuite: autopkgtest-pkg-r Priority: optional -Build-Depends: debhelper (>= 11~), +Build-Depends: debhelper-compat (= 12), dh-r, r-base-dev -Standards-Version: 4.1.4 +Standards-Version: 4.4.1 Vcs-Browser: https://salsa.debian.org/r-pkg-team/r-cran-multcompview Vcs-Git: https://salsa.debian.org/r-pkg-team/r-cran-multcompview.git Homepage: https://cran.r-project.org/package=multcompView diff -Nru r-cran-multcompview-0.1-7/debian/rules r-cran-multcompview-0.1-8/debian/rules --- r-cran-multcompview-0.1-7/debian/rules 2018-05-31 13:45:56.000000000 +0000 +++ r-cran-multcompview-0.1-8/debian/rules 2020-01-04 08:28:53.000000000 +0000 @@ -2,4 +2,3 @@ %: dh $@ --buildsystem R - diff -Nru r-cran-multcompview-0.1-7/DESCRIPTION r-cran-multcompview-0.1-8/DESCRIPTION --- r-cran-multcompview-0.1-7/DESCRIPTION 2015-07-31 16:40:25.000000000 +0000 +++ r-cran-multcompview-0.1-8/DESCRIPTION 2019-12-19 16:50:10.000000000 +0000 @@ -1,8 +1,8 @@ Package: multcompView Type: Package Title: Visualizations of Paired Comparisons -Version: 0.1-7 -Date: 2015-07-25 +Version: 0.1-8 +Date: 2019-12-05 Author: Spencer Graves, Hans-Peter Piepho and Luciano Selzer with help from Sundar Dorai-Raj Maintainer: Luciano Selzer @@ -17,7 +17,8 @@ License: GPL Imports: grid Suggests: multcomp, pgirmess, MASS -Packaged: 2015-07-31 15:43:44 UTC; Luciano +Packaged: 2019-12-19 14:13:54 UTC; lucia +RoxygenNote: 7.0.2 NeedsCompilation: no Repository: CRAN -Date/Publication: 2015-07-31 18:40:25 +Date/Publication: 2019-12-19 16:50:10 UTC Binary files /tmp/tmpwdomeA/UMz69PFR5r/r-cran-multcompview-0.1-7/inst/doc/VisualizingPairedComparisons.doc and /tmp/tmpwdomeA/5i_o7aOM7L/r-cran-multcompview-0.1-8/inst/doc/VisualizingPairedComparisons.doc differ Binary files /tmp/tmpwdomeA/UMz69PFR5r/r-cran-multcompview-0.1-7/inst/doc/VisualizingPairedComparisons.pdf and /tmp/tmpwdomeA/5i_o7aOM7L/r-cran-multcompview-0.1-8/inst/doc/VisualizingPairedComparisons.pdf differ Binary files /tmp/tmpwdomeA/UMz69PFR5r/r-cran-multcompview-0.1-7/inst/doc/VisualizingPairedComparisons.ppt and /tmp/tmpwdomeA/5i_o7aOM7L/r-cran-multcompview-0.1-8/inst/doc/VisualizingPairedComparisons.ppt differ diff -Nru r-cran-multcompview-0.1-7/man/extract_p.Rd r-cran-multcompview-0.1-8/man/extract_p.Rd --- r-cran-multcompview-0.1-7/man/extract_p.Rd 2015-07-31 15:43:44.000000000 +0000 +++ r-cran-multcompview-0.1-8/man/extract_p.Rd 2019-12-19 13:30:24.000000000 +0000 @@ -1,58 +1,62 @@ -% Generated by roxygen2 (4.1.1): do not edit by hand -% Please edit documentation in R/extract_p.R -\name{extract_p} -\alias{extract_p} -\alias{extract_p.TukeyHSD} -\alias{extract_p.default} -\alias{extract_p.mc} -\title{Extracts p-values} -\usage{ -extract_p(x) - -\method{extract_p}{default}(x) - -\method{extract_p}{TukeyHSD}(x) - -\method{extract_p}{mc}(x) -} -\arguments{ -\item{x}{A object that has p-values or logical values.} -} -\value{ -A named vector with p-values or logical values. -} -\description{ -For a given object it will look for the column named "p adj" or "difference" -and extract its value mantaining its names -} -\section{Methods (by class)}{ -\itemize{ -\item \code{default}: - -\item \code{TukeyHSD}: - -\item \code{mc}: -}} -\examples{ -experiment <- data.frame(treatments = gl(11, 20, labels = c("dtl", "ctrl", "treat1", - "treat2", "treatA2", "treatB", "treatB2", - "treatC", "treatD", "treatA1", "treatX")), - y = c(rnorm(20, 10, 5), rnorm(20, 20, 5), rnorm(20, 22, 5), rnorm(20, 24, 5), - rnorm(20, 35, 5), rnorm(20, 37, 5), rnorm(20, 40, 5), rnorm(20, 43, 5), - rnorm(20, 45, 5), rnorm(20, 60, 5), rnorm(20, 60, 5))) -exp_tukey <- TukeyHSD(exp_aov <- aov(y ~ treatments, data = experiment)) - -extract_p(exp_tukey) - -require(pgirmess) -extract_p(kruskalmc(y ~ treatments, data = experiment)) -} -\author{ -Luciano Selzer -} -\seealso{ -\code{\link{multcompLetters}} \code{\link{multcompTs}} -} -\keyword{array} -\keyword{manip} - +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/extract_p.R +\name{extract_p} +\alias{extract_p} +\alias{extract_p.default} +\alias{extract_p.TukeyHSD} +\alias{extract_p.mc} +\title{Extracts p-values} +\usage{ +extract_p(x) + +\method{extract_p}{default}(x) + +\method{extract_p}{TukeyHSD}(x) + +\method{extract_p}{mc}(x) +} +\arguments{ +\item{x}{A object that has p-values or logical values.} +} +\value{ +A named vector with p-values or logical values. +} +\description{ +For a given object it will look for the column named "p adj" or "difference" +and extract its value mantaining its names +} +\section{Methods (by class)}{ +\itemize{ +\item \code{default}: + +\item \code{TukeyHSD}: extract p values from a TukeyHSD object + +\item \code{mc}: +}} + +\examples{ + +experiment <- data.frame(treatments = gl(11, 20, labels = c("dtl", "ctrl", "treat1", + "treat2", "treatA2", "treatB", "treatB2", + "treatC", "treatD", "treatA1", "treatX")), + y = c(rnorm(20, 10, 5), rnorm(20, 20, 5), rnorm(20, 22, 5), rnorm(20, 24, 5), + rnorm(20, 35, 5), rnorm(20, 37, 5), rnorm(20, 40, 5), rnorm(20, 43, 5), + rnorm(20, 45, 5), rnorm(20, 60, 5), rnorm(20, 60, 5))) +exp_tukey <- TukeyHSD(exp_aov <- aov(y ~ treatments, data = experiment)) + +extract_p(exp_tukey) + +if(require(pgirmess)){ +extract_p(kruskalmc(y ~ treatments, data = experiment)) +} + + +} +\seealso{ +\code{\link{multcompLetters}} \code{\link{multcompTs}} +} +\author{ +Luciano Selzer +} +\keyword{array} +\keyword{manip} diff -Nru r-cran-multcompview-0.1-7/man/multcompBoxplot.Rd r-cran-multcompview-0.1-8/man/multcompBoxplot.Rd --- r-cran-multcompview-0.1-7/man/multcompBoxplot.Rd 2015-07-31 15:43:44.000000000 +0000 +++ r-cran-multcompview-0.1-8/man/multcompBoxplot.Rd 2019-12-19 13:30:24.000000000 +0000 @@ -1,149 +1,156 @@ -% Generated by roxygen2 (4.1.1): do not edit by hand -% Please edit documentation in R/multcompBoxplot.R -\name{multcompBoxplot} -\alias{multcompBoxplot} -\title{boxplot with multcomp graphics} -\usage{ -multcompBoxplot(formula, data, horizontal = TRUE, compFn = "TukeyHSD", - sortFn = "mean", decreasing = TRUE, plotList = list(boxplot = list(fig = - c(0, 0.75, 0, 1)), multcompTs = list(fig = c(0.7, 0.85, 0, 1)), - multcompLetters = list(fig = c(0.87, 0.97, 0.03, 0.98), fontsize = 20, - fontface = "bold"))) -} -\arguments{ -\item{formula}{a two sided formula like "y~z", where both "y" and "z" are -columns of the data.frame "data", "y" is numeric, and "z" is a factor. This -will be passed as the first argument for both 'boxplot' and 'compFn', and so -must work in both contexts. NOTE: Any more complicated formula may produce -errors or unanticipated results.} - -\item{data}{A data.frame for evaluating 'formula'.} - -\item{horizontal}{TRUE for horizontal boxplots and vertical multcompTs and / -or multcompLetters; FALSE for the opposite.} - -\item{compFn}{a function whose output will serve as the the only non-default -input to either 'multcompTs' or 'multcompLetters'. The default "TukeyHSD" -actually translates to 'TukeyHSD(aov(formula, data))[[1]][, "p adj"]'.} - -\item{sortFn}{If sortFn is a function or a character string naming a -function, it is used to summarize the subset of y corresponding to each -level of z into a single number, which will then be used to sort the levels -of z according to the argumment 'decreasing'. This step is skipped if -sortFn is NULL or NA or if it is neither a function nor a character string -that might name a function. If sortFn is a character string but a function -by that name is not found in the search path, multcompBoxplot stops with, -'Error in do.call(sortFn, list(x = x)) : could not find function ...'.} - -\item{decreasing}{If the levels of z are to be sorted using the output of -'sortFn', this is uses as the 'decreasing' in 'order' to sort the levels of -z for plotting.} - -\item{plotList}{A list with names in c("boxplot", "multcompTs", -"multcompLetters"). Replicates are allowed. If present, they produce, -e.g., multiple "multcompTs" side by side. This can be used to compare the -visual effects of different arguments to "plot.multcompTs". Each component -of 'plotList' is itself a list of arguments to pass to either "boxplot", -"plot.multcompTs" or "plot.multcompLetters". Placement can be controlled -via 'fig' arguments passed (indirectly) of the form 'c(x1, x2, y1, y2)'. -If(horizontal==TRUE), fig gives the coordinates of the figure region in the -display region of the plot device, as described on the \code{\link{par}} -help page; if(horizontal==FALSE), fig[c(3,4,1,2)] gives c(x1, x2, y1, y2) -for placement of that portion of the plot.} -} -\value{ -This function invisibly returns a list with one component for each -component of plotList containing the output of the appropriate -"plot.multcomp" call plus the output of "compFn". -} -\description{ -Create boxplots with multcompTs and / or multcompLetters -} -\details{ -For formula = y~z, if 'sortFn' is a function or the name of a function, -'multcompBoxplot' starts by applying sortFn to the subsets of y -corresponding to each level of z, and then sorting those summaries in -increasing or decreasing order, per 'decreasing'. If 'sortFn' is NULL or -NA, this sort step is skipped. - -'multcompBoxplot' then creates 'boxplot' as specified in 'plotList'. Next, -'compFn' is called to generate comparisons to feed to the functions -(\code{\link{multcompTs}} and / or \code{\link{multcompLetters}}, whose -output is then passed to (\code{\link{plot.multcomp}}) for plotting. -Components of the relevant sublists of 'plotList' are made available to -\code{\link{par}} or (for \code{\link{plot.multcompLetters}}) to -\code{\link[grid]{gpar}}. -} -\examples{ -# Example from help("TukeyHSD") -multcompBoxplot(breaks~tension, data=warpbreaks) -# 'sortFn' can be either a function or a function name -# default order is 'decreasing=TRUE' -multcompBoxplot(breaks~tension, data=warpbreaks, - sortFn=median, decreasing=FALSE) - -################## -library(multcomp) -data(recovery) -# Horizontal boxplots with both -# multcomp Ts and Letters on the right -# Using recovery{multcomp} data set -multcompBoxplot(minutes~blanket, recovery) - -# Plotting boxes rather than letters and Ts - -multcompBoxplot(minutes~blanket, recovery, - plotList=list( - boxplot=list(fig=c(0, 0.75, 0, 1), las=1, - cex.axis=1.5), - multcompTs=list(fig=c(0.7, 0.85, 0, 1), - type='boxes'), - multcompLetters=list( - fig=c(0.87, 0.97, 0.03, 0.98), - type='boxes') ) ) - -#################### - -# Vertical boxplots with both -# multcomp Ts and Letters on the top -multcompBoxplot(minutes~blanket, recovery, - horizontal=FALSE) - -# Horizontal boxplots with 2 different -# displays of the "Ts" on the left -multcompBoxplot(minutes~blanket, recovery, - plotList=list( - boxplot=list(fig=c(0.3, 1, 0, 1)), - multcompTs=list(fig=c(0, 0.15, 0, 1), - orientation="reverse"), - multcompTs=list(fig=c(0.15, 0.3, 0, 1), - type="boxes", orientation="reverse", - mar=c(5,2, 4, 0)+.1) ) ) - -library(MASS) -anorx <- -multcompBoxplot(Postwt~Treat, data=anorexia) - -\dontrun{ -# Confirm than sortFn=NULL or NA -# leaves the order unchanged -library(multcomp) -data(cholesterol) -cholesterol$trt3 <- with(cholesterol, factor( - as.character(trt), levels=levels(trt)[c(5:4,1:3)])) -multcompBoxplot(response ~ trt3, cholesterol, - sortFn=NULL) -multcompBoxplot(response ~ trt3, cholesterol, - sortFn=NA) -} -} -\author{ -Spencer Graves -} -\seealso{ -\code{\link{boxplot}} \code{\link{multcompTs}} -\code{\link{multcompLetters}} \code{\link{plot.multcomp}} -\code{\link{TukeyHSD}} \code{\link{par}} \code{\link[grid]{gpar}} -} -\keyword{aplot} - +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/multcompBoxplot.R +\name{multcompBoxplot} +\alias{multcompBoxplot} +\title{boxplot with multcomp graphics} +\usage{ +multcompBoxplot( + formula, + data, + horizontal = TRUE, + compFn = "TukeyHSD", + sortFn = "mean", + decreasing = TRUE, + plotList = list(boxplot = list(fig = c(0, 0.75, 0, 1)), multcompTs = list(fig = c(0.7, + 0.85, 0, 1)), multcompLetters = list(fig = c(0.87, 0.97, 0.03, 0.98), fontsize = 20, + fontface = "bold")) +) +} +\arguments{ +\item{formula}{a two sided formula like "y~z", where both "y" and "z" are +columns of the data.frame "data", "y" is numeric, and "z" is a factor. This +will be passed as the first argument for both 'boxplot' and 'compFn', and so +must work in both contexts. NOTE: Any more complicated formula may produce +errors or unanticipated results.} + +\item{data}{A data.frame for evaluating 'formula'.} + +\item{horizontal}{TRUE for horizontal boxplots and vertical multcompTs and / +or multcompLetters; FALSE for the opposite.} + +\item{compFn}{a function whose output will serve as the the only non-default +input to either 'multcompTs' or 'multcompLetters'. The default "TukeyHSD" +actually translates to 'TukeyHSD(aov(formula, data))[[1]][, "p adj"]'.} + +\item{sortFn}{If sortFn is a function or a character string naming a +function, it is used to summarize the subset of y corresponding to each +level of z into a single number, which will then be used to sort the levels +of z according to the argumment 'decreasing'. This step is skipped if +sortFn is NULL or NA or if it is neither a function nor a character string +that might name a function. If sortFn is a character string but a function +by that name is not found in the search path, multcompBoxplot stops with, +'Error in do.call(sortFn, list(x = x)) : could not find function ...'.} + +\item{decreasing}{If the levels of z are to be sorted using the output of +'sortFn', this is uses as the 'decreasing' in 'order' to sort the levels of +z for plotting.} + +\item{plotList}{A list with names in c("boxplot", "multcompTs", +"multcompLetters"). Replicates are allowed. If present, they produce, +e.g., multiple "multcompTs" side by side. This can be used to compare the +visual effects of different arguments to "plot.multcompTs". Each component +of 'plotList' is itself a list of arguments to pass to either "boxplot", +"plot.multcompTs" or "plot.multcompLetters". Placement can be controlled +via 'fig' arguments passed (indirectly) of the form 'c(x1, x2, y1, y2)'. +If(horizontal==TRUE), fig gives the coordinates of the figure region in the +display region of the plot device, as described on the \code{\link{par}} +help page; if(horizontal==FALSE), fig[c(3,4,1,2)] gives c(x1, x2, y1, y2) +for placement of that portion of the plot.} +} +\value{ +This function invisibly returns a list with one component for each +component of plotList containing the output of the appropriate +"plot.multcomp" call plus the output of "compFn". +} +\description{ +Create boxplots with multcompTs and / or multcompLetters +} +\details{ +For formula = y~z, if 'sortFn' is a function or the name of a function, +'multcompBoxplot' starts by applying sortFn to the subsets of y +corresponding to each level of z, and then sorting those summaries in +increasing or decreasing order, per 'decreasing'. If 'sortFn' is NULL or +NA, this sort step is skipped. + +'multcompBoxplot' then creates 'boxplot' as specified in 'plotList'. Next, +'compFn' is called to generate comparisons to feed to the functions +(\code{\link{multcompTs}} and / or \code{\link{multcompLetters}}, whose +output is then passed to (\code{\link{plot.multcomp}}) for plotting. +Components of the relevant sublists of 'plotList' are made available to +\code{\link{par}} or (for \code{\link{plot.multcompLetters}}) to +\code{\link[grid]{gpar}}. +} +\examples{ + +# Example from help("TukeyHSD") +multcompBoxplot(breaks~tension, data=warpbreaks) +# 'sortFn' can be either a function or a function name +# default order is 'decreasing=TRUE' +multcompBoxplot(breaks~tension, data=warpbreaks, + sortFn=median, decreasing=FALSE) + +################## +library(multcomp) +data(recovery) +# Horizontal boxplots with both +# multcomp Ts and Letters on the right +# Using recovery{multcomp} data set +multcompBoxplot(minutes~blanket, recovery) + +# Plotting boxes rather than letters and Ts + +multcompBoxplot(minutes~blanket, recovery, + plotList=list( + boxplot=list(fig=c(0, 0.75, 0, 1), las=1, + cex.axis=1.5), + multcompTs=list(fig=c(0.7, 0.85, 0, 1), + type='boxes'), + multcompLetters=list( + fig=c(0.87, 0.97, 0.03, 0.98), + type='boxes') ) ) + +#################### + +# Vertical boxplots with both +# multcomp Ts and Letters on the top +multcompBoxplot(minutes~blanket, recovery, + horizontal=FALSE) + +# Horizontal boxplots with 2 different +# displays of the "Ts" on the left +multcompBoxplot(minutes~blanket, recovery, + plotList=list( + boxplot=list(fig=c(0.3, 1, 0, 1)), + multcompTs=list(fig=c(0, 0.15, 0, 1), + orientation="reverse"), + multcompTs=list(fig=c(0.15, 0.3, 0, 1), + type="boxes", orientation="reverse", + mar=c(5,2, 4, 0)+.1) ) ) + +library(MASS) +anorx <- +multcompBoxplot(Postwt~Treat, data=anorexia) + +\dontrun{ +# Confirm than sortFn=NULL or NA +# leaves the order unchanged +library(multcomp) +data(cholesterol) +cholesterol$trt3 <- with(cholesterol, factor( + as.character(trt), levels=levels(trt)[c(5:4,1:3)])) +multcompBoxplot(response ~ trt3, cholesterol, + sortFn=NULL) +multcompBoxplot(response ~ trt3, cholesterol, + sortFn=NA) +} + +} +\seealso{ +\code{\link{boxplot}} \code{\link{multcompTs}} +\code{\link{multcompLetters}} \code{\link{plot.multcomp}} +\code{\link{TukeyHSD}} \code{\link{par}} \code{\link[grid]{gpar}} +} +\author{ +Spencer Graves +} +\keyword{aplot} diff -Nru r-cran-multcompview-0.1-7/man/multcompLetters.Rd r-cran-multcompview-0.1-8/man/multcompLetters.Rd --- r-cran-multcompview-0.1-7/man/multcompLetters.Rd 2015-07-31 15:43:44.000000000 +0000 +++ r-cran-multcompview-0.1-8/man/multcompLetters.Rd 2019-12-19 13:30:24.000000000 +0000 @@ -1,217 +1,226 @@ -% Generated by roxygen2 (4.1.1): do not edit by hand -% Please edit documentation in R/multcompLetters.R -\name{multcompLetters} -\alias{multcompLetters} -\alias{multcompLetters2} -\alias{multcompLetters3} -\alias{multcompLetters4} -\title{Letter summary of similarities and differences} -\usage{ -multcompLetters(x, compare = "<", threshold = 0.05, Letters = c(letters, - LETTERS, "."), reversed = FALSE) - -multcompLetters2(formula, x, data, ...) - -multcompLetters3(z, y, x, data, ...) - -multcompLetters4(object, comp, ...) -} -\arguments{ -\item{x}{One of the following: (1) A square, symmetric matrix with row -names. (2) A vector with hyphenated names, which identify individual items -or factor levels after "strsplit". (3) An object of class "dist". If x (or -x[1]) is not already of class "logical", it is replaced with -do.call(compare, list(x, threshold)), which by default converts numbers -(typically p-values) less than 0.05 to TRUE and everything else to FALSE. -If x is a matrix, its diagonal must be or must convert to FALSE.} - -\item{compare}{function or binary operator; not used if class(x) is -"logical".} - -\item{threshold}{Second (reference) argument to "compare".} - -\item{Letters}{Vector of distinct characters (or character strings) used to -connect levels that are not significantly different. They should be -recogizable when concatonated. The last element of "Letters" is used as a -prefix for a reuse of "Letters" if more are needed than are provided. For -example, with the default "Letters", if 53 distinct connection colums are -required, they will be "a", ..., "z", "A", ..., "Z", and ".a". If 54 are -required, the last one will be ".b". If 105 are required, the last one will -be "..a", etc. (If the algorithm generates that many distinct groups, the -display may be too busy to be useful, but the algorithm shouldn't break.)} - -\item{reversed}{A logical value indicating whether the order of the letters -should be reversed. Defaults to FALSE.} - -\item{formula}{The formula used to make the test (lm, aov, glm, etc.). Like -y ~ x.} - -\item{data}{Data used to make the test.} - -\item{...}{Extra arguments passed to multcompLetters.} - -\item{z}{Categorical variables used in the test.} - -\item{y}{Value of the response variable.} - -\item{object}{An object of class aov or lm for the time being.} - -\item{comp}{A object with multiple comparison or a function name to perform -a multiple comparison.} -} -\value{ -An object of class 'multcompLetters', which is a list with the -following components: \item{Letters }{character vector with names = the -names of the levels or groups compared and with values = character strings -in which common values of the function argument "Letters" identify levels or -groups that are not significantly different (or more precisely for which the -corresponding element of "x" was FALSE or was converted to FALSE by -"compare"). } \item{monospacedLetters }{ Same as "Letters" but with spaces -so the individual grouping letters will line up with a monspaced type font. -} \item{LetterMatrix }{Logical matrix with one row for each level compared -and one column for each "Letter" in the "letter-based representation". The -output component "Letters" is obtained by concatonating the column names of -all columns with TRUE in that row. } multcompLetters4 will return a named -list with the terms containing a object of class 'multcompLetters' as -produced by \code{multcompLetters}. -} -\description{ -Convert a logical vector or a vector of p-values or a correlation or -distance matrix into a character-based display in which common characters -identify levels or groups that are not significantly different. Designed -for use with the output of functions like TukeyHSD, diststats, simint, -simtest, csimint, csimtestmultcomp, friedmanmc, kruskalmcpgirmess. -} -\details{ -Produces a "Letter-Based Representation of All- Pairwise Comparisons" as -described by Piepho (2004). (The present algorithm does NOT perform his -"sweeping" step.) \code{multcompLettersx} are wrapper of multcompLetters -that will reorder the levels of the data so that the letters appear in a -descending order of the mean. \code{mulcompletters3} is similar to -\code{multcompletters2} except that it uses vector names to separte and the -later has an formula interface. \code{multcompLetters4} will take a aov or -lm object and a comparison test and will produce all the letters for the -terms and interactions. -} -\section{Functions}{ -\itemize{ -\item \code{multcompLetters2}: - -\item \code{multcompLetters3}: - -\item \code{multcompLetters4}: -}} -\examples{ -## -## 1. a logical vector indicating signficant differences -## -dif3 <- c(FALSE, FALSE, TRUE) -names(dif3) <- c("A-B", "A-C", "B-C") -dif3L <- multcompLetters(dif3) -dif3L -print(dif3L) -print(dif3L, TRUE) - -## -## 2. numeric vector indicating statistical significance -## -dif4 <- c(.01, .02, .03, 1) -names(dif4) <- c("a-b", "a-c", "b-d", "a-d") -(diff4.T <- multcompLetters(dif4)) - -(dif4.L1 <- multcompLetters(dif4, - Letters=c("*", "."))) -# "Letters" can be any character strings, -# but they should be recognizable when -# concatonated. - -## -## 3. distance matrix -## -dJudge <- dist(USJudgeRatings) -dJl <- multcompLetters(dJudge, compare='>', threshold = median(dJudge)) -# comparison of 43 judges; compact but undecipherable: -dJl - -x <- array(1:9, dim=c(3,3), - dimnames=list(LETTERS[1:3], NULL) ) -d3 <- dist(x) -dxLtrs <- multcompLetters(d3, compare=">", threshold=2) - -d3d <- dist(x, diag=TRUE) -dxdLtrs <- multcompLetters(d3d, compare=">", threshold=2) - -\dontshow{stopifnot(} -all.equal(dxLtrs, dxdLtrs) -\dontshow{)} - -d3u <- dist(x, upper=TRUE) -dxuLtrs <- multcompLetters(d3d, compare=">", threshold=2) - -\dontshow{stopifnot(} -all.equal(dxLtrs, dxuLtrs) -\dontshow{)} - -## -## 4. cor matrix -## -set.seed(4) -x100 <- matrix(rnorm(100), ncol=5, - dimnames=list(NULL, LETTERS[1:5]) ) -cx <- cor(x100) -cxLtrs <- multcompLetters(abs(cx), threshold=.3) - - -## -##5. reversed -## - -dif3 <- c(FALSE, FALSE, TRUE) -names(dif3) <- c("A-B", "A-C", "B-C") -dif3L <- multcompLetters(dif3) -dif3L.R <- multcompLetters(dif3, rev = TRUE) -dif3L -dif3L.R - - -## -##6. multcompletters2 usage - -experiment <- data.frame(treatments = gl(11, 20, labels = c("dtl", "ctrl", "treat1", - "treat2", "treatA2", "treatB", "treatB2", - "treatC", "treatD", "treatA1", "treatX")), - y = c(rnorm(20, 10, 5), rnorm(20, 20, 5), rnorm(20, 22, 5), rnorm(20, 24, 5), - rnorm(20, 35, 5), rnorm(20, 37, 5), rnorm(20, 40, 5), rnorm(20, 43, 5), - rnorm(20, 45, 5), rnorm(20, 60, 5), rnorm(20, 60, 5))) -exp_tukey <- TukeyHSD(exp_aov <- aov(y ~ treatments, data = experiment)) -exp_letters1 <- multcompLetters(exp_tukey$treatments[,4]) -exp_letters1 -#Notice lowest mean treatments gets a "e" -#Ordered letters -multcompLetters2(y ~ treatments, exp_tukey$treatments[,"p adj"], experiment) -multcompLetters2(y ~ treatments, exp_tukey$treatments[,"p adj"], experiment, reversed = TRUE) - -##7. multcompletters3 usage - -multcompLetters3("treatments", "y", exp_tukey$treatments[,"p adj"], experiment) - -##8. multcompletters4 usage - - -multcompLetters4(exp_aov, exp_tukey) -} -\author{ -Spencer Graves, Hans-Peter Piepho and Luciano Selzer -} -\references{ -Piepho, Hans-Peter (2004) "An Algorithm for a Letter-Based -Representation of All-Pairwise Comparisons", Journal of Computational and -Graphical Statistics, 13(2)456-466. -} -\seealso{ -\code{\link{multcompBoxplot}} \code{\link{plot.multcompLetters}} -\code{\link{print.multcompLetters}} \code{\link{multcompTs}} -\code{\link{vec2mat}} -} -\keyword{dplot} - +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/multcompLetters.R +\name{multcompLetters} +\alias{multcompLetters} +\alias{multcompLetters2} +\alias{multcompLetters3} +\alias{multcompLetters4} +\title{Letter summary of similarities and differences} +\usage{ +multcompLetters( + x, + compare = "<", + threshold = 0.05, + Letters = c(letters, LETTERS, "."), + reversed = FALSE +) + +multcompLetters2(formula, x, data, ...) + +multcompLetters3(z, y, x, data, ...) + +multcompLetters4(object, comp, ...) +} +\arguments{ +\item{x}{One of the following: (1) A square, symmetric matrix with row +names. (2) A vector with hyphenated names, which identify individual items +or factor levels after "strsplit". (3) An object of class "dist". If x (or +x[1]) is not already of class "logical", it is replaced with +do.call(compare, list(x, threshold)), which by default converts numbers +(typically p-values) less than 0.05 to TRUE and everything else to FALSE. +If x is a matrix, its diagonal must be or must convert to FALSE.} + +\item{compare}{function or binary operator; not used if class(x) is +"logical".} + +\item{threshold}{Second (reference) argument to "compare".} + +\item{Letters}{Vector of distinct characters (or character strings) used to +connect levels that are not significantly different. They should be +recogizable when concatonated. The last element of "Letters" is used as a +prefix for a reuse of "Letters" if more are needed than are provided. For +example, with the default "Letters", if 53 distinct connection colums are +required, they will be "a", ..., "z", "A", ..., "Z", and ".a". If 54 are +required, the last one will be ".b". If 105 are required, the last one will +be "..a", etc. (If the algorithm generates that many distinct groups, the +display may be too busy to be useful, but the algorithm shouldn't break.)} + +\item{reversed}{A logical value indicating whether the order of the letters +should be reversed. Defaults to FALSE.} + +\item{formula}{The formula used to make the test (lm, aov, glm, etc.). Like +y ~ x.} + +\item{data}{Data used to make the test.} + +\item{...}{Extra arguments passed to multcompLetters.} + +\item{z}{Categorical variables used in the test.} + +\item{y}{Value of the response variable.} + +\item{object}{An object of class aov or lm for the time being.} + +\item{comp}{A object with multiple comparison or a function name to perform +a multiple comparison.} +} +\value{ +An object of class 'multcompLetters', which is a list with the +following components: \item{Letters }{character vector with names = the +names of the levels or groups compared and with values = character strings +in which common values of the function argument "Letters" identify levels or +groups that are not significantly different (or more precisely for which the +corresponding element of "x" was FALSE or was converted to FALSE by +"compare"). } \item{monospacedLetters }{ Same as "Letters" but with spaces +so the individual grouping letters will line up with a monspaced type font. +} \item{LetterMatrix }{Logical matrix with one row for each level compared +and one column for each "Letter" in the "letter-based representation". The +output component "Letters" is obtained by concatonating the column names of +all columns with TRUE in that row. } multcompLetters4 will return a named +list with the terms containing a object of class 'multcompLetters' as +produced by \code{multcompLetters}. +} +\description{ +Convert a logical vector or a vector of p-values or a correlation or +distance matrix into a character-based display in which common characters +identify levels or groups that are not significantly different. Designed +for use with the output of functions like TukeyHSD, diststats, simint, +simtest, csimint, csimtestmultcomp, friedmanmc, kruskalmcpgirmess. +} +\details{ +Produces a "Letter-Based Representation of All- Pairwise Comparisons" as +described by Piepho (2004). (The present algorithm does NOT perform his +"sweeping" step.) \code{multcompLettersx} are wrapper of multcompLetters +that will reorder the levels of the data so that the letters appear in a +descending order of the mean. \code{mulcompletters3} is similar to +\code{multcompletters2} except that it uses vector names to separte and the +later has an formula interface. \code{multcompLetters4} will take a aov or +lm object and a comparison test and will produce all the letters for the +terms and interactions. +} +\section{Functions}{ +\itemize{ +\item \code{multcompLetters2}: + +\item \code{multcompLetters3}: create a compact letters display and order the +letters + +\item \code{multcompLetters4}: create a compact letters display using a aov object +}} + +\examples{ + +## +## 1. a logical vector indicating signficant differences +## +dif3 <- c(FALSE, FALSE, TRUE) +names(dif3) <- c("A-B", "A-C", "B-C") +dif3L <- multcompLetters(dif3) +dif3L +print(dif3L) +print(dif3L, TRUE) + +## +## 2. numeric vector indicating statistical significance +## +dif4 <- c(.01, .02, .03, 1) +names(dif4) <- c("a-b", "a-c", "b-d", "a-d") +(diff4.T <- multcompLetters(dif4)) + +(dif4.L1 <- multcompLetters(dif4, + Letters=c("*", "."))) +# "Letters" can be any character strings, +# but they should be recognizable when +# concatonated. + +## +## 3. distance matrix +## +dJudge <- dist(USJudgeRatings) +dJl <- multcompLetters(dJudge, compare='>', threshold = median(dJudge)) +# comparison of 43 judges; compact but undecipherable: +dJl + +x <- array(1:9, dim=c(3,3), + dimnames=list(LETTERS[1:3], NULL) ) +d3 <- dist(x) +dxLtrs <- multcompLetters(d3, compare=">", threshold=2) + +d3d <- dist(x, diag=TRUE) +dxdLtrs <- multcompLetters(d3d, compare=">", threshold=2) + +\dontshow{stopifnot(} +all.equal(dxLtrs, dxdLtrs) +\dontshow{)} + +d3u <- dist(x, upper=TRUE) +dxuLtrs <- multcompLetters(d3d, compare=">", threshold=2) + +\dontshow{stopifnot(} +all.equal(dxLtrs, dxuLtrs) +\dontshow{)} + +## +## 4. cor matrix +## +set.seed(4) +x100 <- matrix(rnorm(100), ncol=5, + dimnames=list(NULL, LETTERS[1:5]) ) +cx <- cor(x100) +cxLtrs <- multcompLetters(abs(cx), threshold=.3) + + +## +##5. reversed +## + +dif3 <- c(FALSE, FALSE, TRUE) +names(dif3) <- c("A-B", "A-C", "B-C") +dif3L <- multcompLetters(dif3) +dif3L.R <- multcompLetters(dif3, rev = TRUE) +dif3L +dif3L.R + + +## +##6. multcompletters2 usage + +experiment <- data.frame(treatments = gl(11, 20, labels = c("dtl", "ctrl", "treat1", + "treat2", "treatA2", "treatB", "treatB2", + "treatC", "treatD", "treatA1", "treatX")), + y = c(rnorm(20, 10, 5), rnorm(20, 20, 5), rnorm(20, 22, 5), rnorm(20, 24, 5), + rnorm(20, 35, 5), rnorm(20, 37, 5), rnorm(20, 40, 5), rnorm(20, 43, 5), + rnorm(20, 45, 5), rnorm(20, 60, 5), rnorm(20, 60, 5))) +exp_tukey <- TukeyHSD(exp_aov <- aov(y ~ treatments, data = experiment)) +exp_letters1 <- multcompLetters(exp_tukey$treatments[,4]) +exp_letters1 +#Notice lowest mean treatments gets a "e" +#Ordered letters +multcompLetters2(y ~ treatments, exp_tukey$treatments[,"p adj"], experiment) +multcompLetters2(y ~ treatments, exp_tukey$treatments[,"p adj"], experiment, reversed = TRUE) + +##7. multcompletters3 usage + +multcompLetters3("treatments", "y", exp_tukey$treatments[,"p adj"], experiment) + +##8. multcompletters4 usage + + +multcompLetters4(exp_aov, exp_tukey) + + +} +\references{ +Piepho, Hans-Peter (2004) "An Algorithm for a Letter-Based +Representation of All-Pairwise Comparisons", Journal of Computational and +Graphical Statistics, 13(2)456-466. +} +\seealso{ +\code{\link{multcompBoxplot}} \code{\link{plot.multcompLetters}} +\code{\link{print.multcompLetters}} \code{\link{multcompTs}} +\code{\link{vec2mat}} +} +\author{ +Spencer Graves, Hans-Peter Piepho and Luciano Selzer +} +\keyword{dplot} diff -Nru r-cran-multcompview-0.1-7/man/multcompTs.Rd r-cran-multcompview-0.1-8/man/multcompTs.Rd --- r-cran-multcompview-0.1-7/man/multcompTs.Rd 2015-07-31 15:43:44.000000000 +0000 +++ r-cran-multcompview-0.1-8/man/multcompTs.Rd 2019-12-19 13:30:24.000000000 +0000 @@ -1,136 +1,137 @@ -% Generated by roxygen2 (4.1.1): do not edit by hand -% Please edit documentation in R/multcompTs.R -\name{multcompTs} -\alias{multcompTs} -\title{"T" depiction of undiffentiated classes} -\usage{ -multcompTs(x, compare = "<", threshold = 0.05, sep = ".") -} -\arguments{ -\item{x}{One of the following: (1) A square, symmetric matrix with row -names. (2) A vector with hyphenated names, which identify individual items -or factor levels after "strsplit(..., '-')". (3) An object of class "dist". - -If x (or x[1]) is not already of class "logical", it is replaced with -do.call(compare, list(x, threshold)), which by default converts numbers -(typically p-values) less than 0.05 to TRUE and everything else to FALSE. -If x is a matrix, its diagonal must be or must convert to FALSE.} - -\item{compare}{function or binary operator; not used if class(x) is -"logical".} - -\item{threshold}{Second (reference) argument to "compare".} - -\item{sep}{Concatonation character for names of objects with identical -similarity / dissimilarity patterns. The output of multcompTs is matrix for -which the number of rows = (number of columns + number of uses of the "sep" -character).} -} -\value{ -An object of class "multcompTs", which is a matrix of values -1, 0, -1, with one row for each level compared and one column for each "T", read as -follows: 1 = base of the "T" represented by that column, 0 = level(s) not -significantly different, and (-1) = leves(s) significantly different. If -two or more levels have the same pattern of significant and insignificant -differences, they are combined into a single column that can be represented -by a "T" with multiple bases. The column name will be a character string -concatonating all row names with "1" in that column separated by the "sep" -character. Thus, the matrix should have as many 1's as it has rows. Also, -the lower triangular portion should have as many "-1's" as there are "TRUE" -(e.g., significant) differences among the comparisons. -} -\description{ -Convert a logical vector or a vector of p-values or a correlation or -distance matrix into a matrix with an associated visual display to show -whether the differences between items exceed a threshold. Designed for use -with the output of functions like TukeyHSD, diststats, simint, simtest, -csimint, csimtestmultcomp, friedmanmc, kruskalmcpgirmess. -} -\details{ -Produces a matrix of class "multcompTs", describing the "undifferentiated -classes" that identify the other factor levels or items that are not -distinct or not significantly different from the "base" of the "T"; if two -or more levels have the same pattern of significant differences, the two are -combined into one "T" with two "bases". The resulting T's are similar to -the "undifferentiated classes" discussed by Donaghue (2004). -} -\examples{ -## -## 0. Conference presentation comparing Ts and Letters -## -dir(system.file('doc', package='multcompView'), - pattern='\\\\.pdf$', full.name=TRUE) - -## -## 1. logical vector indicating different pairs -## -dif3 <- c(FALSE, FALSE, TRUE) -names(dif3) <- c("a-b", "a-c", "b-c") -multcompTs(dif3) - -## -## 2. numeric vector indicating statistical significance -## -dif4 <- c(.01, .02, .03, 1) -names(dif4) <- c("a-b", "a-c", "b-d", "a-d") -(diff4.T <- multcompTs(dif4)) -plot(diff4.T) - -## -## 3. Distance matrix -## -dJudge <- dist(USJudgeRatings) -dJt <- multcompTs(dJudge, compare='>', threshold = median(dJudge)) -# comparison of 43 judges; compact but undecipherable: -plot(dJt, cex.axis=.5) - -x <- array(1:9, dim=c(3,3), - dimnames=list(LETTERS[1:3], NULL) ) -d3 <- dist(x) -dxTs <- multcompTs(d3, compare=">", threshold=2) -plot(dxTs) - -d3d <- dist(x, diag=TRUE) -dxdTs <- multcompTs(d3d, compare=">", threshold=2) - -\dontshow{stopifnot(} -all.equal(dxTs, dxdTs) -\dontshow{)} - -d3u <- dist(x, upper=TRUE) -dxuTs <- multcompTs(d3d, compare=">", threshold=2) - -\dontshow{stopifnot(} -all.equal(dxTs, dxuTs) -\dontshow{)} - -## -## 4. cor matrix -## -set.seed(4) -x100 <- matrix(rnorm(100), ncol=5, - dimnames=list(NULL, LETTERS[1:5]) ) -cx <- cor(x100) -cxTs <- multcompTs(abs(cx), threshold=.3) -plot(cxTs) -} -\author{ -Spencer Graves and Hans-Peter Piepho -} -\references{ -John R. Donaghue (2004) "Implementing Shaffer's multiple -comparison procedure for a large number of groups", pp. 1-23 in Benjamini, -Bretz and Sarkar (eds) Recent Developments in Multiple Comparison Procedures -(Institute of Mathematical Statistics Lecture Notes-Monograph Series vol. -47) - -Spencer Graves and Hans-Peter Piepho (2006) "Simple Visualizations of Paired -Comparisons", \url{dir(system.file('doc', package='multcompView'), -pattern='\.pdf$', full.name=TRUE)} -} -\seealso{ -\code{\link{multcompBoxplot}} \code{\link{multcompLetters}} -\code{\link{plot.multcompTs}} \code{\link{vec2mat}} \code{\link{dist}} -} -\keyword{dplot} - +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/multcompTs.R +\name{multcompTs} +\alias{multcompTs} +\title{"T" depiction of undiffentiated classes} +\usage{ +multcompTs(x, compare = "<", threshold = 0.05, sep = ".") +} +\arguments{ +\item{x}{One of the following: (1) A square, symmetric matrix with row +names. (2) A vector with hyphenated names, which identify individual items +or factor levels after "strsplit(..., '-')". (3) An object of class "dist". + +If x (or x[1]) is not already of class "logical", it is replaced with +do.call(compare, list(x, threshold)), which by default converts numbers +(typically p-values) less than 0.05 to TRUE and everything else to FALSE. +If x is a matrix, its diagonal must be or must convert to FALSE.} + +\item{compare}{function or binary operator; not used if class(x) is +"logical".} + +\item{threshold}{Second (reference) argument to "compare".} + +\item{sep}{Concatonation character for names of objects with identical +similarity / dissimilarity patterns. The output of multcompTs is matrix for +which the number of rows = (number of columns + number of uses of the "sep" +character).} +} +\value{ +An object of class "multcompTs", which is a matrix of values -1, 0, +1, with one row for each level compared and one column for each "T", read as +follows: 1 = base of the "T" represented by that column, 0 = level(s) not +significantly different, and (-1) = leves(s) significantly different. If +two or more levels have the same pattern of significant and insignificant +differences, they are combined into a single column that can be represented +by a "T" with multiple bases. The column name will be a character string +concatonating all row names with "1" in that column separated by the "sep" +character. Thus, the matrix should have as many 1's as it has rows. Also, +the lower triangular portion should have as many "-1's" as there are "TRUE" +(e.g., significant) differences among the comparisons. +} +\description{ +Convert a logical vector or a vector of p-values or a correlation or +distance matrix into a matrix with an associated visual display to show +whether the differences between items exceed a threshold. Designed for use +with the output of functions like TukeyHSD, diststats, simint, simtest, +csimint, csimtestmultcomp, friedmanmc, kruskalmcpgirmess. +} +\details{ +Produces a matrix of class "multcompTs", describing the "undifferentiated +classes" that identify the other factor levels or items that are not +distinct or not significantly different from the "base" of the "T"; if two +or more levels have the same pattern of significant differences, the two are +combined into one "T" with two "bases". The resulting T's are similar to +the "undifferentiated classes" discussed by Donaghue (2004). +} +\examples{ + +## +## 0. Conference presentation comparing Ts and Letters +## +dir(system.file('doc', package='multcompView'), + pattern='\\\\.pdf$', full.name=TRUE) + +## +## 1. logical vector indicating different pairs +## +dif3 <- c(FALSE, FALSE, TRUE) +names(dif3) <- c("a-b", "a-c", "b-c") +multcompTs(dif3) + +## +## 2. numeric vector indicating statistical significance +## +dif4 <- c(.01, .02, .03, 1) +names(dif4) <- c("a-b", "a-c", "b-d", "a-d") +(diff4.T <- multcompTs(dif4)) +plot(diff4.T) + +## +## 3. Distance matrix +## +dJudge <- dist(USJudgeRatings) +dJt <- multcompTs(dJudge, compare='>', threshold = median(dJudge)) +# comparison of 43 judges; compact but undecipherable: +plot(dJt, cex.axis=.5) + +x <- array(1:9, dim=c(3,3), + dimnames=list(LETTERS[1:3], NULL) ) +d3 <- dist(x) +dxTs <- multcompTs(d3, compare=">", threshold=2) +plot(dxTs) + +d3d <- dist(x, diag=TRUE) +dxdTs <- multcompTs(d3d, compare=">", threshold=2) + +\dontshow{stopifnot(} +all.equal(dxTs, dxdTs) +\dontshow{)} + +d3u <- dist(x, upper=TRUE) +dxuTs <- multcompTs(d3d, compare=">", threshold=2) + +\dontshow{stopifnot(} +all.equal(dxTs, dxuTs) +\dontshow{)} + +## +## 4. cor matrix +## +set.seed(4) +x100 <- matrix(rnorm(100), ncol=5, + dimnames=list(NULL, LETTERS[1:5]) ) +cx <- cor(x100) +cxTs <- multcompTs(abs(cx), threshold=.3) +plot(cxTs) + + +} +\references{ +John R. Donaghue (2004) "Implementing Shaffer's multiple +comparison procedure for a large number of groups", pp. 1-23 in Benjamini, +Bretz and Sarkar (eds) Recent Developments in Multiple Comparison Procedures +(Institute of Mathematical Statistics Lecture Notes-Monograph Series vol. +47) + +Spencer Graves and Hans-Peter Piepho (2006) "Simple Visualizations of Paired +Comparisons", \href{../doc/VisualizingPairedComparisons.pdf}{\code{vignette("VisualizingPairedComparisons", package = "multcompView")}} +} +\seealso{ +\code{\link{multcompBoxplot}} \code{\link{multcompLetters}} +\code{\link{plot.multcompTs}} \code{\link{vec2mat}} \code{\link{dist}} +} +\author{ +Spencer Graves and Hans-Peter Piepho +} +\keyword{dplot} diff -Nru r-cran-multcompview-0.1-7/man/multcompView-package.Rd r-cran-multcompview-0.1-8/man/multcompView-package.Rd --- r-cran-multcompview-0.1-7/man/multcompView-package.Rd 2015-07-31 15:43:44.000000000 +0000 +++ r-cran-multcompview-0.1-8/man/multcompView-package.Rd 2019-12-19 13:30:24.000000000 +0000 @@ -1,53 +1,54 @@ -% Generated by roxygen2 (4.1.1): do not edit by hand -% Please edit documentation in R/multcompView-package.R -\docType{package} -\name{multcompView-package} -\alias{multcompView} -\alias{multcompView-package} -\title{Summarize multiple paired comparisons} -\description{ -Convert a logical vector or a vector of p-values or a difference or distance -matrix into a display identifying the pairs for which the differences were -not significantly different or for which the difference exceeded a -threshold. -} -\details{ -\tabular{ll}{ Package: \tab multcompView\cr Type: \tab Package\cr Version: -\tab 0.1-0\cr Date: \tab 2006-08-06\cr License: \tab GPL\cr } Convert a -logical vector or a vector of p-values or a difference or distance matrix -into either a letter-based display using "multcompLetters" or a graphic -roughly like a "T" using "multcompTs" to identify factor levels or similar -groupings that are or are not significantly different. Designed for use in -conjunction with the output of functions like TukeyHSD, diststats, simint, -simtest, csimint, csimtestmultcomp, friedmanmc, kruskalmcpgirmess. -} -\examples{ -dif3 <- c(FALSE, FALSE, TRUE) -names(dif3) <- c("a-b", "a-c", "b-c") -multcompTs(dif3) -multcompLetters(dif3) - -library(MASS) -multcompBoxplot(Postwt~Treat, data=anorexia) -} -\author{ -Spencer Graves and Hans-Peter Piepho with help from Sundar Dorai-Raj - -Maintainer: Spencer Graves -} -\references{ -Piepho, Hans-Peter (2004) "An Algorithm for a Letter-Based -Representation of All-Pairwise Comparisons", Journal of Computational and -Graphical Statistics, 13(2)456-466. - -John R. Donaghue (2004) "Implementing Shaffer's multiple comparison -procedure for a large number of groups", pp. 1-23 in Benjamini, Bretz and -Sarkar (eds) Recent Developments in Multiple Comparison Procedures -(Institute of Mathematical Statistics Lecture Notes-Monograph Series vol. -47) -} -\keyword{aplot} -\keyword{dplot} -\keyword{htest} -\keyword{package} - +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/multcompView-package.R +\docType{package} +\name{multcompView-package} +\alias{multcompView-package} +\alias{multcompView} +\title{Summarize multiple paired comparisons} +\description{ +Convert a logical vector or a vector of p-values or a difference or distance +matrix into a display identifying the pairs for which the differences were +not significantly different or for which the difference exceeded a +threshold. +} +\details{ +\tabular{ll}{ Package: \tab multcompView\cr Type: \tab Package\cr Version: +\tab 0.1-0\cr Date: \tab 2006-08-06\cr License: \tab GPL\cr } Convert a +logical vector or a vector of p-values or a difference or distance matrix +into either a letter-based display using "multcompLetters" or a graphic +roughly like a "T" using "multcompTs" to identify factor levels or similar +groupings that are or are not significantly different. Designed for use in +conjunction with the output of functions like TukeyHSD, diststats, simint, +simtest, csimint, csimtestmultcomp, friedmanmc, kruskalmcpgirmess. +} +\examples{ + +dif3 <- c(FALSE, FALSE, TRUE) +names(dif3) <- c("a-b", "a-c", "b-c") +multcompTs(dif3) +multcompLetters(dif3) + +library(MASS) +multcompBoxplot(Postwt~Treat, data=anorexia) + +} +\references{ +Piepho, Hans-Peter (2004) "An Algorithm for a Letter-Based +Representation of All-Pairwise Comparisons", Journal of Computational and +Graphical Statistics, 13(2)456-466. + +John R. Donaghue (2004) "Implementing Shaffer's multiple comparison +procedure for a large number of groups", pp. 1-23 in Benjamini, Bretz and +Sarkar (eds) Recent Developments in Multiple Comparison Procedures +(Institute of Mathematical Statistics Lecture Notes-Monograph Series vol. +47) +} +\author{ +Spencer Graves and Hans-Peter Piepho with help from Sundar Dorai-Raj + +Maintainer: Spencer Graves +} +\keyword{aplot} +\keyword{dplot} +\keyword{htest} +\keyword{package} diff -Nru r-cran-multcompview-0.1-7/man/plotBoxes.Rd r-cran-multcompview-0.1-8/man/plotBoxes.Rd --- r-cran-multcompview-0.1-7/man/plotBoxes.Rd 2015-07-31 15:43:44.000000000 +0000 +++ r-cran-multcompview-0.1-8/man/plotBoxes.Rd 2019-12-19 13:30:24.000000000 +0000 @@ -1,119 +1,129 @@ -% Generated by roxygen2 (4.1.1): do not edit by hand -% Please edit documentation in R/plotBoxes.R -\name{plotBoxes} -\alias{plotBoxes} -\title{plot multcomp displays} -\usage{ -plotBoxes(obj, at, width, horizontal, col, add, label.levels, label.groups, - orientation = "", ...) -} -\arguments{ -\item{obj}{a matrix describing which levels (rows) will be plotted with -which groups (columns). For plotTs and plotBoxes, obj is a matrix of -numbers from (-1, 0, 1). For plotLetters, obj is a logical matrix = TRUE if -that "letter" (group or column of obj) is to be plotted with that level (row -of obj).} - -\item{at}{an array with one row for each level and 3 columns giving low, -middle and high levels for the display for that level.} - -\item{width}{an array with one row for each group of levels in the display -and 3 columns giving low, middle and high levels for the display for that -group.} - -\item{horizontal}{A logical scalar indicating whether the list of items -compared reads left to right (horizontal = TRUE) or top to bottom -(horizontal = FALSE). If this multcomp graphic accompanies boxplots for -different levels or groups compared, the 'boxplot' argument 'horizontal' is -the negation of the multcomp plot 'horizontal' argument.} - -\item{col}{The color for each group of items or factor levels. The colors -will cross the different items or factor levels and will therefore have the -orientation specified via 'horizontal'. If the number of columns exceeds -length(col), col is recycled. For alternative choices for col, see "Color -Specification" in the \code{\link{par}} help page.} - -\item{add}{TRUE to add to an existing plot; FALSE to start a new plot. The -names of the factor levels or items compared will be plotted only if -add=FALSE.} - -\item{label.levels}{Distance from the plot region to print the names of the -levels as a proportion of the plot range; NA for no level labels.} - -\item{label.groups}{Distance from the plot region to print the names of the -groups as a proportion of the plot range; NA for no level labels.} - -\item{orientation}{If 'reversed', the base(s) of each "T" or traingle -indicating the master level(s) of that "undifferentiated class" will point -right or up (depending on horizontal) rather than down or left.} - -\item{...}{graphical parameters can be given as described on the -\code{\link{plot}} help page or the \code{\link[grid]{gpar}} help page.} - -\item{lwd}{line width for the display outline.} - -\item{T.base}{A numeric scalar giving the proportion of the available space -devoted to the base of the Ts.} - -\item{font.family}{character string naming the font family used by -"plotLetters". This function plots the different "Letters" in different -colors by plotting one color at a time. It's currently not smart enough to -align the letters properly except by assuming a mono-spaced font.} - -\item{fig}{figure region = (x0, x1, y0, y1) as a proportion of the device -region.} - -\item{mar}{margin = (lower, left, upper, right) in lines.} -} -\value{ -"Done" -} -\description{ -Helper functions for plot.multcompTs and plot.multcompLetters. These not -intended to be called directly and are hidden in a namespace. You can use -'getAnywhere' to see them. -} -\details{ -The requested graphic is either plotted by itself or added to an existing -plot as specified by the arguments. - -"plotTs" and "plotBoxes" use traditional R graphics and will not be -discussed further here. - -"plotLetters" uses 'grid' graphics, because it seems to provide more support -for controlling the side-by-side placement of "Letters" of possibly -different colors and widths. The "Letters" display will be positioned in -the "plot region" defined by fig and mar, assuming the entire device region -is 37 lines both wide and tall. Thus, the plot region is diff(fig[1:2])*37 -lines wide and diff(fig(1:2])*37 lines high. If, for example, fig = c(0.9, -1, 0, 1), this makes the plot region 3.7 lines wide. With the default -mar=c(5, 4, 4, 2)+0.1 lines, the "width" of the plot region is therefore 3.7 -- (4.1+2.1) = (-2.5) lines. "plotLetters" initially ignores this -contradictory negative width, and centers the plot at the midpoint of h0 = -fig[1]+mar[2]/37, h1 = fig[2]-mar[4]/37, v0 = fig[3]+mar[1]/37, and v1 = -fig[4]-mar[3]/37. The "Letters" for the different levels compared are -rescaled from at[, "center"] to fit inside At.rng = if(horizontal) c(h0, h1) -else c(v0, v1). With "n" levels compared and at.rng = range(at[, -"center"]), at[, "center"] is expanded to (at.rng+/-0.5) and rescaled to -match At.rng; if(diff(At.rng)<=0), an error message is issued. - -Meanwhile, the "Letters" are centered at the midpoint of W.rng = -if(horizontal) c(v0, v1) else v(h0, h1) [the opposite of At.rng]; the -argument "width" used by plotTs and plotBoxes is not used (and not even -accepted) by plotLetters. If(label.levels), these are positioned in the -midpoint of the right margin in the "W" direction. -} -\examples{ -# Designed to be called from plot.multcompTs -# or plot.multcompLetters, NOT directly by users. -} -\author{ -Spencer Graves -} -\seealso{ -\code{\link{plot.multcompTs}} \code{\link{plot.multcompLetters}} -\code{\link[grid]{gpar}} -} -\keyword{aplot} -\keyword{internal} - +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/plotBoxes.R +\name{plotBoxes} +\alias{plotBoxes} +\title{plot multcomp displays} +\usage{ +plotBoxes( + obj, + at, + width, + horizontal, + col, + add, + label.levels, + label.groups, + orientation = "", + ... +) +} +\arguments{ +\item{obj}{a matrix describing which levels (rows) will be plotted with +which groups (columns). For plotTs and plotBoxes, obj is a matrix of +numbers from (-1, 0, 1). For plotLetters, obj is a logical matrix = TRUE if +that "letter" (group or column of obj) is to be plotted with that level (row +of obj).} + +\item{at}{an array with one row for each level and 3 columns giving low, +middle and high levels for the display for that level.} + +\item{width}{an array with one row for each group of levels in the display +and 3 columns giving low, middle and high levels for the display for that +group.} + +\item{horizontal}{A logical scalar indicating whether the list of items +compared reads left to right (horizontal = TRUE) or top to bottom +(horizontal = FALSE). If this multcomp graphic accompanies boxplots for +different levels or groups compared, the 'boxplot' argument 'horizontal' is +the negation of the multcomp plot 'horizontal' argument.} + +\item{col}{The color for each group of items or factor levels. The colors +will cross the different items or factor levels and will therefore have the +orientation specified via 'horizontal'. If the number of columns exceeds +length(col), col is recycled. For alternative choices for col, see "Color +Specification" in the \code{\link{par}} help page.} + +\item{add}{TRUE to add to an existing plot; FALSE to start a new plot. The +names of the factor levels or items compared will be plotted only if +add=FALSE.} + +\item{label.levels}{Distance from the plot region to print the names of the +levels as a proportion of the plot range; NA for no level labels.} + +\item{label.groups}{Distance from the plot region to print the names of the +groups as a proportion of the plot range; NA for no level labels.} + +\item{orientation}{If 'reversed', the base(s) of each "T" or traingle +indicating the master level(s) of that "undifferentiated class" will point +right or up (depending on horizontal) rather than down or left.} + +\item{...}{graphical parameters can be given as described on the +\code{\link{plot}} help page or the \code{\link[grid]{gpar}} help page.} + +\item{lwd}{line width for the display outline.} + +\item{T.base}{A numeric scalar giving the proportion of the available space +devoted to the base of the Ts.} + +\item{font.family}{character string naming the font family used by +"plotLetters". This function plots the different "Letters" in different +colors by plotting one color at a time. It's currently not smart enough to +align the letters properly except by assuming a mono-spaced font.} + +\item{fig}{figure region = (x0, x1, y0, y1) as a proportion of the device +region.} + +\item{mar}{margin = (lower, left, upper, right) in lines.} +} +\value{ +"Done" +} +\description{ +Helper functions for plot.multcompTs and plot.multcompLetters. These not +intended to be called directly and are hidden in a namespace. You can use +'getAnywhere' to see them. +} +\details{ +The requested graphic is either plotted by itself or added to an existing +plot as specified by the arguments. + +"plotTs" and "plotBoxes" use traditional R graphics and will not be +discussed further here. + +"plotLetters" uses 'grid' graphics, because it seems to provide more support +for controlling the side-by-side placement of "Letters" of possibly +different colors and widths. The "Letters" display will be positioned in +the "plot region" defined by fig and mar, assuming the entire device region +is 37 lines both wide and tall. Thus, the plot region is diff(fig[1:2])*37 +lines wide and diff(fig(1:2])*37 lines high. If, for example, fig = c(0.9, +1, 0, 1), this makes the plot region 3.7 lines wide. With the default +mar=c(5, 4, 4, 2)+0.1 lines, the "width" of the plot region is therefore 3.7 +- (4.1+2.1) = (-2.5) lines. "plotLetters" initially ignores this +contradictory negative width, and centers the plot at the midpoint of h0 = +fig[1]+mar[2]/37, h1 = fig[2]-mar[4]/37, v0 = fig[3]+mar[1]/37, and v1 = +fig[4]-mar[3]/37. The "Letters" for the different levels compared are +rescaled from at[, "center"] to fit inside At.rng = if(horizontal) c(h0, h1) +else c(v0, v1). With "n" levels compared and at.rng = range(at[, +"center"]), at[, "center"] is expanded to (at.rng+/-0.5) and rescaled to +match At.rng; if(diff(At.rng)<=0), an error message is issued. + +Meanwhile, the "Letters" are centered at the midpoint of W.rng = +if(horizontal) c(v0, v1) else v(h0, h1) [the opposite of At.rng]; the +argument "width" used by plotTs and plotBoxes is not used (and not even +accepted) by plotLetters. If(label.levels), these are positioned in the +midpoint of the right margin in the "W" direction. +} +\examples{ + +# Designed to be called from plot.multcompTs +# or plot.multcompLetters, NOT directly by users. +} +\seealso{ +\code{\link{plot.multcompTs}} \code{\link{plot.multcompLetters}} +\code{\link[grid]{gpar}} +} +\author{ +Spencer Graves +} +\keyword{aplot} +\keyword{internal} diff -Nru r-cran-multcompview-0.1-7/man/plotLetters.Rd r-cran-multcompview-0.1-8/man/plotLetters.Rd --- r-cran-multcompview-0.1-7/man/plotLetters.Rd 2015-07-31 15:43:44.000000000 +0000 +++ r-cran-multcompview-0.1-8/man/plotLetters.Rd 2019-12-19 13:30:24.000000000 +0000 @@ -1,119 +1,129 @@ -% Generated by roxygen2 (4.1.1): do not edit by hand -% Please edit documentation in R/plotLetters.R -\name{plotLetters} -\alias{plotLetters} -\title{plot multcomp displays} -\usage{ -plotLetters(obj, at, horizontal, col, add, label.levels, font.family = "mono", - fig = par("fig"), mar = par("mar"), ...) -} -\arguments{ -\item{obj}{a matrix describing which levels (rows) will be plotted with -which groups (columns). For plotTs and plotBoxes, obj is a matrix of -numbers from (-1, 0, 1). For plotLetters, obj is a logical matrix = TRUE if -that "letter" (group or column of obj) is to be plotted with that level (row -of obj).} - -\item{at}{an array with one row for each level and 3 columns giving low, -middle and high levels for the display for that level.} - -\item{horizontal}{A logical scalar indicating whether the list of items -compared reads left to right (horizontal = TRUE) or top to bottom -(horizontal = FALSE). If this multcomp graphic accompanies boxplots for -different levels or groups compared, the 'boxplot' argument 'horizontal' is -the negation of the multcomp plot 'horizontal' argument.} - -\item{col}{The color for each group of items or factor levels. The colors -will cross the different items or factor levels and will therefore have the -orientation specified via 'horizontal'. If the number of columns exceeds -length(col), col is recycled. For alternative choices for col, see "Color -Specification" in the \code{\link{par}} help page.} - -\item{add}{TRUE to add to an existing plot; FALSE to start a new plot. The -names of the factor levels or items compared will be plotted only if -add=FALSE.} - -\item{label.levels}{Distance from the plot region to print the names of the -levels as a proportion of the plot range; NA for no level labels.} - -\item{font.family}{character string naming the font family used by -"plotLetters". This function plots the different "Letters" in different -colors by plotting one color at a time. It's currently not smart enough to -align the letters properly except by assuming a mono-spaced font.} - -\item{fig}{figure region = (x0, x1, y0, y1) as a proportion of the device -region.} - -\item{mar}{margin = (lower, left, upper, right) in lines.} - -\item{...}{graphical parameters can be given as described on the -\code{\link{plot}} help page or the \code{\link[grid]{gpar}} help page.} - -\item{width}{an array with one row for each group of levels in the display -and 3 columns giving low, middle and high levels for the display for that -group.} - -\item{lwd}{line width for the display outline.} - -\item{label.groups}{Distance from the plot region to print the names of the -groups as a proportion of the plot range; NA for no level labels.} - -\item{T.base}{A numeric scalar giving the proportion of the available space -devoted to the base of the Ts.} - -\item{orientation}{If 'reversed', the base(s) of each "T" or traingle -indicating the master level(s) of that "undifferentiated class" will point -right or up (depending on horizontal) rather than down or left.} -} -\value{ -"Done" -} -\description{ -Helper functions for plot.multcompTs and plot.multcompLetters. These not -intended to be called directly and are hidden in a namespace. You can use -'getAnywhere' to see them. -} -\details{ -The requested graphic is either plotted by itself or added to an existing -plot as specified by the arguments. - -"plotTs" and "plotBoxes" use traditional R graphics and will not be -discussed further here. - -"plotLetters" uses 'grid' graphics, because it seems to provide more support -for controlling the side-by-side placement of "Letters" of possibly -different colors and widths. The "Letters" display will be positioned in -the "plot region" defined by fig and mar, assuming the entire device region -is 37 lines both wide and tall. Thus, the plot region is diff(fig[1:2])*37 -lines wide and diff(fig(1:2])*37 lines high. If, for example, fig = c(0.9, -1, 0, 1), this makes the plot region 3.7 lines wide. With the default -mar=c(5, 4, 4, 2)+0.1 lines, the "width" of the plot region is therefore 3.7 -- (4.1+2.1) = (-2.5) lines. "plotLetters" initially ignores this -contradictory negative width, and centers the plot at the midpoint of h0 = -fig[1]+mar[2]/37, h1 = fig[2]-mar[4]/37, v0 = fig[3]+mar[1]/37, and v1 = -fig[4]-mar[3]/37. The "Letters" for the different levels compared are -rescaled from at[, "center"] to fit inside At.rng = if(horizontal) c(h0, h1) -else c(v0, v1). With "n" levels compared and at.rng = range(at[, -"center"]), at[, "center"] is expanded to (at.rng+/-0.5) and rescaled to -match At.rng; if(diff(At.rng)<=0), an error message is issued. - -Meanwhile, the "Letters" are centered at the midpoint of W.rng = -if(horizontal) c(v0, v1) else v(h0, h1) [the opposite of At.rng]; the -argument "width" used by plotTs and plotBoxes is not used (and not even -accepted) by plotLetters. If(label.levels), these are positioned in the -midpoint of the right margin in the "W" direction. -} -\examples{ -# Designed to be called from plot.multcompTs -# or plot.multcompLetters, NOT directly by users. -} -\author{ -Spencer Graves -} -\seealso{ -\code{\link{plot.multcompTs}} \code{\link{plot.multcompLetters}} -\code{\link[grid]{gpar}} -} -\keyword{aplot} -\keyword{internal} - +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/plotLetters.R +\name{plotLetters} +\alias{plotLetters} +\title{plot multcomp displays} +\usage{ +plotLetters( + obj, + at, + horizontal, + col, + add, + label.levels, + font.family = "mono", + fig = par("fig"), + mar = par("mar"), + ... +) +} +\arguments{ +\item{obj}{a matrix describing which levels (rows) will be plotted with +which groups (columns). For plotTs and plotBoxes, obj is a matrix of +numbers from (-1, 0, 1). For plotLetters, obj is a logical matrix = TRUE if +that "letter" (group or column of obj) is to be plotted with that level (row +of obj).} + +\item{at}{an array with one row for each level and 3 columns giving low, +middle and high levels for the display for that level.} + +\item{horizontal}{A logical scalar indicating whether the list of items +compared reads left to right (horizontal = TRUE) or top to bottom +(horizontal = FALSE). If this multcomp graphic accompanies boxplots for +different levels or groups compared, the 'boxplot' argument 'horizontal' is +the negation of the multcomp plot 'horizontal' argument.} + +\item{col}{The color for each group of items or factor levels. The colors +will cross the different items or factor levels and will therefore have the +orientation specified via 'horizontal'. If the number of columns exceeds +length(col), col is recycled. For alternative choices for col, see "Color +Specification" in the \code{\link{par}} help page.} + +\item{add}{TRUE to add to an existing plot; FALSE to start a new plot. The +names of the factor levels or items compared will be plotted only if +add=FALSE.} + +\item{label.levels}{Distance from the plot region to print the names of the +levels as a proportion of the plot range; NA for no level labels.} + +\item{font.family}{character string naming the font family used by +"plotLetters". This function plots the different "Letters" in different +colors by plotting one color at a time. It's currently not smart enough to +align the letters properly except by assuming a mono-spaced font.} + +\item{fig}{figure region = (x0, x1, y0, y1) as a proportion of the device +region.} + +\item{mar}{margin = (lower, left, upper, right) in lines.} + +\item{...}{graphical parameters can be given as described on the +\code{\link{plot}} help page or the \code{\link[grid]{gpar}} help page.} + +\item{width}{an array with one row for each group of levels in the display +and 3 columns giving low, middle and high levels for the display for that +group.} + +\item{lwd}{line width for the display outline.} + +\item{label.groups}{Distance from the plot region to print the names of the +groups as a proportion of the plot range; NA for no level labels.} + +\item{T.base}{A numeric scalar giving the proportion of the available space +devoted to the base of the Ts.} + +\item{orientation}{If 'reversed', the base(s) of each "T" or traingle +indicating the master level(s) of that "undifferentiated class" will point +right or up (depending on horizontal) rather than down or left.} +} +\value{ +"Done" +} +\description{ +Helper functions for plot.multcompTs and plot.multcompLetters. These not +intended to be called directly and are hidden in a namespace. You can use +'getAnywhere' to see them. +} +\details{ +The requested graphic is either plotted by itself or added to an existing +plot as specified by the arguments. + +"plotTs" and "plotBoxes" use traditional R graphics and will not be +discussed further here. + +"plotLetters" uses 'grid' graphics, because it seems to provide more support +for controlling the side-by-side placement of "Letters" of possibly +different colors and widths. The "Letters" display will be positioned in +the "plot region" defined by fig and mar, assuming the entire device region +is 37 lines both wide and tall. Thus, the plot region is diff(fig[1:2])*37 +lines wide and diff(fig(1:2])*37 lines high. If, for example, fig = c(0.9, +1, 0, 1), this makes the plot region 3.7 lines wide. With the default +mar=c(5, 4, 4, 2)+0.1 lines, the "width" of the plot region is therefore 3.7 +- (4.1+2.1) = (-2.5) lines. "plotLetters" initially ignores this +contradictory negative width, and centers the plot at the midpoint of h0 = +fig[1]+mar[2]/37, h1 = fig[2]-mar[4]/37, v0 = fig[3]+mar[1]/37, and v1 = +fig[4]-mar[3]/37. The "Letters" for the different levels compared are +rescaled from at[, "center"] to fit inside At.rng = if(horizontal) c(h0, h1) +else c(v0, v1). With "n" levels compared and at.rng = range(at[, +"center"]), at[, "center"] is expanded to (at.rng+/-0.5) and rescaled to +match At.rng; if(diff(At.rng)<=0), an error message is issued. + +Meanwhile, the "Letters" are centered at the midpoint of W.rng = +if(horizontal) c(v0, v1) else v(h0, h1) [the opposite of At.rng]; the +argument "width" used by plotTs and plotBoxes is not used (and not even +accepted) by plotLetters. If(label.levels), these are positioned in the +midpoint of the right margin in the "W" direction. +} +\examples{ + +# Designed to be called from plot.multcompTs +# or plot.multcompLetters, NOT directly by users. +} +\seealso{ +\code{\link{plot.multcompTs}} \code{\link{plot.multcompLetters}} +\code{\link[grid]{gpar}} +} +\author{ +Spencer Graves +} +\keyword{aplot} +\keyword{internal} diff -Nru r-cran-multcompview-0.1-7/man/plot.multcompLetters.Rd r-cran-multcompview-0.1-8/man/plot.multcompLetters.Rd --- r-cran-multcompview-0.1-7/man/plot.multcompLetters.Rd 2015-07-31 15:43:44.000000000 +0000 +++ r-cran-multcompview-0.1-8/man/plot.multcompLetters.Rd 2019-12-19 13:30:24.000000000 +0000 @@ -1,151 +1,162 @@ -% Generated by roxygen2 (4.1.1): do not edit by hand -% Please edit documentation in R/plot.multcompLetters.R -\name{plot.multcompLetters} -\alias{plot.multcomp} -\alias{plot.multcompLetters} -\title{plot multcomp graphics} -\usage{ -\method{plot}{multcompLetters}(x, horizontal = FALSE, col = 1:6, - type = c("Letters", "boxes"), add = FALSE, at, width, fig = c(0, 1, 0, - 1), label.levels = if (add) NA else 0.05, label.groups = NA, ...) -} -\arguments{ -\item{x}{an object of class 'multcompTs' or 'multcompLetters'.} - -\item{horizontal}{A logical scalar indicating whether the list of items -compared reads left to right (horizontal = TRUE) or top to bottom -(horizontal = FALSE). If this multcomp graphic accompanies boxplots for -different levels or groups compared, the 'boxplot' argument 'horizontal' is -the negation of the multcomp plot 'horizontal' argument.} - -\item{col}{The color for each group of items or factor levels. The colors -will cross the different items or factor levels and will therefore have the -orientation specified via 'horizontal'. If the number of columns exceeds -length(col), col is recycled. For alternative choices for col, see "Color -Specification" in the \code{\link{par}} help page.} - -\item{type}{An alternative display for either multcompTs or multcompLetters -is 'boxes' (or rectangles). If type="boxes" with "multcompTs", the -"base(s)" of each "T" will be indicated by a triangle.} - -\item{add}{TRUE to add to an existing plot; FALSE to start a new plot. The -names of the factor levels or items compared will be plotted only if -add=FALSE.} - -\item{at}{A numeric vector or matrix or a list with components "at" and -"width". If a list, both components must be either a numeric vector or -matrix. The numeric vector "at" (whether the function argument or "at" -component of the "at" list) must be either a numeric vector or matrix giving -the locations where the "Ts" or "Letters" graphics should be drawn. -length(at) is 1, 2 or 3 times the number of the number of factor levels or -items compared. If length(at) is twice the number of levels or items -compared, it gives the range of the display for that level; the base of a -"T" will be at the midpoint. If length(at) is three times the number of -items compared, the intermediate number will be the center of the base of -the "T".} - -\item{width}{A numeric vector or matrix with as many rows as "Ts" or -"groups" and with up to three columns. With one column, it will be the -"center" of the plot range for that group. With two columns, they will -delimit the range. With three, they will provide "bottom", "center", and -"top" of the range for that set of grouping indicators. If "at" is a list, -the argument "width" is ignored and is taken from the list "at".} - -\item{fig}{A numerical vector of the form 'c(x1, x2, y1, y2)' giving the -coordinates of the figure region in the display region of the plot device, -as described on the \code{\link{par}} help page.} - -\item{label.levels}{NA for no labels or distance away from the plot for the -labels as a proportion of the plot range.} - -\item{label.groups}{NA for no labels or distance away from the plot for the -labels as a proportion of the plot range.} - -\item{...}{graphical parameters can be given as described on the -\code{\link{plot}} help page or for plot.multcompLetters as describe on the -\code{\link[grid]{gpar}} help page.} -} -\value{ -A list with two components: \item{at }{ A matrix with three columns -giving the middle and extremes of the display for each of the factor levels -or items compared. } \item{width }{ A matrix with as many rows as "Ts" or -comparitor levels and with two columns giving the plot range for that -comparitor level. } -} -\description{ -Plot graphic(s) for multcompTs or multcompLetters objects -} -\details{ -The requested graphic is either plotted by itself or added to an existing -plot as specified by the arguments. The placement can be controlled by -'fig' and 'at'. - -The fontsize and fontface of a plot of a multcompLetters object with 'type = -"Letters"' can be adjusted as describe on the \code{\link[grid]{gpar}} help -page. -} -\examples{ -## -## plot(multcompTs(...)) -## -dif4 <- c(.1, .02, .03, 1) -names(dif4) <- c("A-B", "A-C", "B-C", "A-D") -(mcT4 <- multcompTs(dif4)) -# Standard plot, base of "Ts" point left -mcT4.1 <- plot(mcT4, label.groups=0.05) -# Redo using "at" = list -plot(mcT4, label.groups=0.05, at=mcT4.1) -# Same plot with group labels closer to the figure -plot(mcT4, label.groups=0.02) - -# Base of "Ts" point right -plot(mcT4, label.groups=TRUE, orientation="r") -# Base of "Ts" point down -plot(mcT4, horizontal=TRUE, label.groups=0.05) -# Base of "Ts" point up -plot(mcT4, horizontal=TRUE, label.groups=0.05, - orientation="r") - -# Same 4 plots but with boxes & triangles, not Ts -plot(mcT4, label.groups=0.05, type="b") -plot(mcT4, label.groups=0.05, orientation="r", - type="b") -plot(mcT4, horizontal=TRUE, label.groups=0.05, - type="b") -plot(mcT4, horizontal=TRUE, label.groups=0.05, - orientation="r", type="b") - -## -## plot(multcompLetters(...)) -## -# ... using dif4 from above -(mcL4 <- multcompLetters(dif4, Letters=LETTERS)) -# Standard plot -\dontrun{ -# Requires (grid) -mcL4.1 <- plot(mcL4, label.groups=0.05) -# Redo using "at" = list -plot(mcL4, label.groups=0.05, at=mcL4.1) - -# With bold face and larger font -plot(mcL4, label.groups=0.05, - fontsize=28, fontface="bold") - -# Horizontal rather than vertical -plot(mcL4, horizontal=TRUE, label.groups=0.05) -} - -# Same as boxes rather than letters -plot(mcL4, label.groups=0.05, type="b") -plot(mcL4, horizontal=TRUE, label.groups=0.05, - type="b") -} -\author{ -Spencer Graves -} -\seealso{ -\code{\link{multcompTs}} \code{\link{multcompLetters}} -\code{\link{multcompBoxplot}} \code{\link[grid]{gpar}} -} -\keyword{aplot} - +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/plot.multcompLetters.R +\name{plot.multcompLetters} +\alias{plot.multcompLetters} +\alias{plot.multcomp} +\title{plot multcomp graphics} +\usage{ +\method{plot}{multcompLetters}( + x, + horizontal = FALSE, + col = 1:6, + type = c("Letters", "boxes"), + add = FALSE, + at, + width, + fig = c(0, 1, 0, 1), + label.levels = if (add) NA else 0.05, + label.groups = NA, + ... +) +} +\arguments{ +\item{x}{an object of class 'multcompTs' or 'multcompLetters'.} + +\item{horizontal}{A logical scalar indicating whether the list of items +compared reads left to right (horizontal = TRUE) or top to bottom +(horizontal = FALSE). If this multcomp graphic accompanies boxplots for +different levels or groups compared, the 'boxplot' argument 'horizontal' is +the negation of the multcomp plot 'horizontal' argument.} + +\item{col}{The color for each group of items or factor levels. The colors +will cross the different items or factor levels and will therefore have the +orientation specified via 'horizontal'. If the number of columns exceeds +length(col), col is recycled. For alternative choices for col, see "Color +Specification" in the \code{\link{par}} help page.} + +\item{type}{An alternative display for either multcompTs or multcompLetters +is 'boxes' (or rectangles). If type="boxes" with "multcompTs", the +"base(s)" of each "T" will be indicated by a triangle.} + +\item{add}{TRUE to add to an existing plot; FALSE to start a new plot. The +names of the factor levels or items compared will be plotted only if +add=FALSE.} + +\item{at}{A numeric vector or matrix or a list with components "at" and +"width". If a list, both components must be either a numeric vector or +matrix. The numeric vector "at" (whether the function argument or "at" +component of the "at" list) must be either a numeric vector or matrix giving +the locations where the "Ts" or "Letters" graphics should be drawn. +length(at) is 1, 2 or 3 times the number of the number of factor levels or +items compared. If length(at) is twice the number of levels or items +compared, it gives the range of the display for that level; the base of a +"T" will be at the midpoint. If length(at) is three times the number of +items compared, the intermediate number will be the center of the base of +the "T".} + +\item{width}{A numeric vector or matrix with as many rows as "Ts" or +"groups" and with up to three columns. With one column, it will be the +"center" of the plot range for that group. With two columns, they will +delimit the range. With three, they will provide "bottom", "center", and +"top" of the range for that set of grouping indicators. If "at" is a list, +the argument "width" is ignored and is taken from the list "at".} + +\item{fig}{A numerical vector of the form 'c(x1, x2, y1, y2)' giving the +coordinates of the figure region in the display region of the plot device, +as described on the \code{\link{par}} help page.} + +\item{label.levels}{NA for no labels or distance away from the plot for the +labels as a proportion of the plot range.} + +\item{label.groups}{NA for no labels or distance away from the plot for the +labels as a proportion of the plot range.} + +\item{...}{graphical parameters can be given as described on the +\code{\link{plot}} help page or for plot.multcompLetters as describe on the +\code{\link[grid]{gpar}} help page.} +} +\value{ +A list with two components: \item{at }{ A matrix with three columns +giving the middle and extremes of the display for each of the factor levels +or items compared. } \item{width }{ A matrix with as many rows as "Ts" or +comparitor levels and with two columns giving the plot range for that +comparitor level. } +} +\description{ +Plot graphic(s) for multcompTs or multcompLetters objects +} +\details{ +The requested graphic is either plotted by itself or added to an existing +plot as specified by the arguments. The placement can be controlled by +'fig' and 'at'. + +The fontsize and fontface of a plot of a multcompLetters object with 'type = +"Letters"' can be adjusted as describe on the \code{\link[grid]{gpar}} help +page. +} +\examples{ + +## +## plot(multcompTs(...)) +## +dif4 <- c(.1, .02, .03, 1) +names(dif4) <- c("A-B", "A-C", "B-C", "A-D") +(mcT4 <- multcompTs(dif4)) +# Standard plot, base of "Ts" point left +mcT4.1 <- plot(mcT4, label.groups=0.05) +# Redo using "at" = list +plot(mcT4, label.groups=0.05, at=mcT4.1) +# Same plot with group labels closer to the figure +plot(mcT4, label.groups=0.02) + +# Base of "Ts" point right +plot(mcT4, label.groups=TRUE, orientation="r") +# Base of "Ts" point down +plot(mcT4, horizontal=TRUE, label.groups=0.05) +# Base of "Ts" point up +plot(mcT4, horizontal=TRUE, label.groups=0.05, + orientation="r") + +# Same 4 plots but with boxes & triangles, not Ts +plot(mcT4, label.groups=0.05, type="b") +plot(mcT4, label.groups=0.05, orientation="r", + type="b") +plot(mcT4, horizontal=TRUE, label.groups=0.05, + type="b") +plot(mcT4, horizontal=TRUE, label.groups=0.05, + orientation="r", type="b") + +## +## plot(multcompLetters(...)) +## +# ... using dif4 from above +(mcL4 <- multcompLetters(dif4, Letters=LETTERS)) +# Standard plot +\dontrun{ +# Requires (grid) +mcL4.1 <- plot(mcL4, label.groups=0.05) +# Redo using "at" = list +plot(mcL4, label.groups=0.05, at=mcL4.1) + +# With bold face and larger font +plot(mcL4, label.groups=0.05, + fontsize=28, fontface="bold") + +# Horizontal rather than vertical +plot(mcL4, horizontal=TRUE, label.groups=0.05) +} + +# Same as boxes rather than letters +plot(mcL4, label.groups=0.05, type="b") +plot(mcL4, horizontal=TRUE, label.groups=0.05, + type="b") + +} +\seealso{ +\code{\link{multcompTs}} \code{\link{multcompLetters}} +\code{\link{multcompBoxplot}} \code{\link[grid]{gpar}} +} +\author{ +Spencer Graves +} +\keyword{aplot} diff -Nru r-cran-multcompview-0.1-7/man/plot.multcompTs.Rd r-cran-multcompview-0.1-8/man/plot.multcompTs.Rd --- r-cran-multcompview-0.1-7/man/plot.multcompTs.Rd 2015-07-31 15:43:44.000000000 +0000 +++ r-cran-multcompview-0.1-8/man/plot.multcompTs.Rd 2019-12-19 13:30:24.000000000 +0000 @@ -1,163 +1,175 @@ -% Generated by roxygen2 (4.1.1): do not edit by hand -% Please edit documentation in R/plot.multcompTs.R -\name{plot.multcompTs} -\alias{plot.multcompTs} -\title{plot multcomp graphics} -\usage{ -\method{plot}{multcompTs}(x, horizontal = FALSE, col = 1:6, type = c("Ts", - "boxes"), orientation = c("standard", "reverse"), add = FALSE, at, width, - fig = c(0, 1, 0, 1), lwd = 3, label.levels = if (add) NA else 0.05, - label.groups = NA, T.base = 0.4, ...) -} -\arguments{ -\item{x}{an object of class 'multcompTs' or 'multcompLetters'.} - -\item{horizontal}{A logical scalar indicating whether the list of items -compared reads left to right (horizontal = TRUE) or top to bottom -(horizontal = FALSE). If this multcomp graphic accompanies boxplots for -different levels or groups compared, the 'boxplot' argument 'horizontal' is -the negation of the multcomp plot 'horizontal' argument.} - -\item{col}{The color for each group of items or factor levels. The colors -will cross the different items or factor levels and will therefore have the -orientation specified via 'horizontal'. If the number of columns exceeds -length(col), col is recycled. For alternative choices for col, see "Color -Specification" in the \code{\link{par}} help page.} - -\item{type}{An alternative display for either multcompTs or multcompLetters -is 'boxes' (or rectangles). If type="boxes" with "multcompTs", the -"base(s)" of each "T" will be indicated by a triangle.} - -\item{orientation}{The "standard" orientation has the 'multcompTs' pointing -towards the names of the items or factor levels; with the "reverse" -orientation, the bases of the "Ts" point away. By default, the names are on -the left or below unless the mean of the relevant 'fig' range is less than -0.5.} - -\item{add}{TRUE to add to an existing plot; FALSE to start a new plot. The -names of the factor levels or items compared will be plotted only if -add=FALSE.} - -\item{at}{A numeric vector or matrix or a list with components "at" and -"width". If a list, both components must be either a numeric vector or -matrix. The numeric vector "at" (whether the function argument or "at" -component of the "at" list) must be either a numeric vector or matrix giving -the locations where the "Ts" or "Letters" graphics should be drawn. -length(at) is 1, 2 or 3 times the number of the number of factor levels or -items compared. If length(at) is twice the number of levels or items -compared, it gives the range of the display for that level; the base of a -"T" will be at the midpoint. If length(at) is three times the number of -items compared, the intermediate number will be the center of the base of -the "T".} - -\item{width}{A numeric vector or matrix with as many rows as "Ts" or -"groups" and with up to three columns. With one column, it will be the -"center" of the plot range for that group. With two columns, they will -delimit the range. With three, they will provide "bottom", "center", and -"top" of the range for that set of grouping indicators. If "at" is a list, -the argument "width" is ignored and is taken from the list "at".} - -\item{fig}{A numerical vector of the form 'c(x1, x2, y1, y2)' giving the -coordinates of the figure region in the display region of the plot device, -as described on the \code{\link{par}} help page.} - -\item{lwd}{width of line to connect elements of "T" graphics that might not -otherwise be connected.} - -\item{label.levels}{NA for no labels or distance away from the plot for the -labels as a proportion of the plot range.} - -\item{label.groups}{NA for no labels or distance away from the plot for the -labels as a proportion of the plot range.} - -\item{T.base}{A numeric scalar giving the proportion of the available space -devoted to the base of the Ts; used only when type="Ts".} - -\item{...}{graphical parameters can be given as described on the -\code{\link{plot}} help page or for plot.multcompLetters as describe on the -\code{\link[grid]{gpar}} help page.} -} -\value{ -A list with two components: \item{at }{ A matrix with three columns -giving the middle and extremes of the display for each of the factor levels -or items compared. } \item{width }{ A matrix with as many rows as "Ts" or -comparitor levels and with two columns giving the plot range for that -comparitor level. } -} -\description{ -Plot graphic(s) for multcompTs or multcompLetters objects -} -\details{ -The requested graphic is either plotted by itself or added to an existing -plot as specified by the arguments. The placement can be controlled by -'fig' and 'at'. - -The fontsize and fontface of a plot of a multcompLetters object with 'type = -"Letters"' can be adjusted as describe on the \code{\link[grid]{gpar}} help -page. -} -\examples{ -## -## plot(multcompTs(...)) -## -dif4 <- c(.1, .02, .03, 1) -names(dif4) <- c("A-B", "A-C", "B-C", "A-D") -(mcT4 <- multcompTs(dif4)) -# Standard plot, base of "Ts" point left -mcT4.1 <- plot(mcT4, label.groups=0.05) -# Redo using "at" = list -plot(mcT4, label.groups=0.05, at=mcT4.1) -# Same plot with group labels closer to the figure -plot(mcT4, label.groups=0.02) - -# Base of "Ts" point right -plot(mcT4, label.groups=TRUE, orientation="r") -# Base of "Ts" point down -plot(mcT4, horizontal=TRUE, label.groups=0.05) -# Base of "Ts" point up -plot(mcT4, horizontal=TRUE, label.groups=0.05, - orientation="r") - -# Same 4 plots but with boxes & triangles, not Ts -plot(mcT4, label.groups=0.05, type="b") -plot(mcT4, label.groups=0.05, orientation="r", - type="b") -plot(mcT4, horizontal=TRUE, label.groups=0.05, - type="b") -plot(mcT4, horizontal=TRUE, label.groups=0.05, - orientation="r", type="b") - -## -## plot(multcompLetters(...)) -## -# ... using dif4 from above -(mcL4 <- multcompLetters(dif4, Letters=LETTERS)) -# Standard plot -\dontrun{ -# Requires (grid) -mcL4.1 <- plot(mcL4, label.groups=0.05) -# Redo using "at" = list -plot(mcL4, label.groups=0.05, at=mcL4.1) - -# With bold face and larger font -plot(mcL4, label.groups=0.05, - fontsize=28, fontface="bold") - -# Horizontal rather than vertical -plot(mcL4, horizontal=TRUE, label.groups=0.05) -} - -# Same as boxes rather than letters -plot(mcL4, label.groups=0.05, type="b") -plot(mcL4, horizontal=TRUE, label.groups=0.05, - type="b") -} -\author{ -Spencer Graves -} -\seealso{ -\code{\link{multcompTs}} \code{\link{multcompLetters}} -\code{\link{multcompBoxplot}} \code{\link[grid]{gpar}} -} -\keyword{aplot} - +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/plot.multcompTs.R +\name{plot.multcompTs} +\alias{plot.multcompTs} +\title{plot multcomp graphics} +\usage{ +\method{plot}{multcompTs}( + x, + horizontal = FALSE, + col = 1:6, + type = c("Ts", "boxes"), + orientation = c("standard", "reverse"), + add = FALSE, + at, + width, + fig = c(0, 1, 0, 1), + lwd = 3, + label.levels = if (add) NA else 0.05, + label.groups = NA, + T.base = 0.4, + ... +) +} +\arguments{ +\item{x}{an object of class 'multcompTs' or 'multcompLetters'.} + +\item{horizontal}{A logical scalar indicating whether the list of items +compared reads left to right (horizontal = TRUE) or top to bottom +(horizontal = FALSE). If this multcomp graphic accompanies boxplots for +different levels or groups compared, the 'boxplot' argument 'horizontal' is +the negation of the multcomp plot 'horizontal' argument.} + +\item{col}{The color for each group of items or factor levels. The colors +will cross the different items or factor levels and will therefore have the +orientation specified via 'horizontal'. If the number of columns exceeds +length(col), col is recycled. For alternative choices for col, see "Color +Specification" in the \code{\link{par}} help page.} + +\item{type}{An alternative display for either multcompTs or multcompLetters +is 'boxes' (or rectangles). If type="boxes" with "multcompTs", the +"base(s)" of each "T" will be indicated by a triangle.} + +\item{orientation}{The "standard" orientation has the 'multcompTs' pointing +towards the names of the items or factor levels; with the "reverse" +orientation, the bases of the "Ts" point away. By default, the names are on +the left or below unless the mean of the relevant 'fig' range is less than +0.5.} + +\item{add}{TRUE to add to an existing plot; FALSE to start a new plot. The +names of the factor levels or items compared will be plotted only if +add=FALSE.} + +\item{at}{A numeric vector or matrix or a list with components "at" and +"width". If a list, both components must be either a numeric vector or +matrix. The numeric vector "at" (whether the function argument or "at" +component of the "at" list) must be either a numeric vector or matrix giving +the locations where the "Ts" or "Letters" graphics should be drawn. +length(at) is 1, 2 or 3 times the number of the number of factor levels or +items compared. If length(at) is twice the number of levels or items +compared, it gives the range of the display for that level; the base of a +"T" will be at the midpoint. If length(at) is three times the number of +items compared, the intermediate number will be the center of the base of +the "T".} + +\item{width}{A numeric vector or matrix with as many rows as "Ts" or +"groups" and with up to three columns. With one column, it will be the +"center" of the plot range for that group. With two columns, they will +delimit the range. With three, they will provide "bottom", "center", and +"top" of the range for that set of grouping indicators. If "at" is a list, +the argument "width" is ignored and is taken from the list "at".} + +\item{fig}{A numerical vector of the form 'c(x1, x2, y1, y2)' giving the +coordinates of the figure region in the display region of the plot device, +as described on the \code{\link{par}} help page.} + +\item{lwd}{width of line to connect elements of "T" graphics that might not +otherwise be connected.} + +\item{label.levels}{NA for no labels or distance away from the plot for the +labels as a proportion of the plot range.} + +\item{label.groups}{NA for no labels or distance away from the plot for the +labels as a proportion of the plot range.} + +\item{T.base}{A numeric scalar giving the proportion of the available space +devoted to the base of the Ts; used only when type="Ts".} + +\item{...}{graphical parameters can be given as described on the +\code{\link{plot}} help page or for plot.multcompLetters as describe on the +\code{\link[grid]{gpar}} help page.} +} +\value{ +A list with two components: \item{at }{ A matrix with three columns +giving the middle and extremes of the display for each of the factor levels +or items compared. } \item{width }{ A matrix with as many rows as "Ts" or +comparitor levels and with two columns giving the plot range for that +comparitor level. } +} +\description{ +Plot graphic(s) for multcompTs or multcompLetters objects +} +\details{ +The requested graphic is either plotted by itself or added to an existing +plot as specified by the arguments. The placement can be controlled by +'fig' and 'at'. + +The fontsize and fontface of a plot of a multcompLetters object with 'type = +"Letters"' can be adjusted as describe on the \code{\link[grid]{gpar}} help +page. +} +\examples{ + +## +## plot(multcompTs(...)) +## +dif4 <- c(.1, .02, .03, 1) +names(dif4) <- c("A-B", "A-C", "B-C", "A-D") +(mcT4 <- multcompTs(dif4)) +# Standard plot, base of "Ts" point left +mcT4.1 <- plot(mcT4, label.groups=0.05) +# Redo using "at" = list +plot(mcT4, label.groups=0.05, at=mcT4.1) +# Same plot with group labels closer to the figure +plot(mcT4, label.groups=0.02) + +# Base of "Ts" point right +plot(mcT4, label.groups=TRUE, orientation="r") +# Base of "Ts" point down +plot(mcT4, horizontal=TRUE, label.groups=0.05) +# Base of "Ts" point up +plot(mcT4, horizontal=TRUE, label.groups=0.05, + orientation="r") + +# Same 4 plots but with boxes & triangles, not Ts +plot(mcT4, label.groups=0.05, type="b") +plot(mcT4, label.groups=0.05, orientation="r", + type="b") +plot(mcT4, horizontal=TRUE, label.groups=0.05, + type="b") +plot(mcT4, horizontal=TRUE, label.groups=0.05, + orientation="r", type="b") + +## +## plot(multcompLetters(...)) +## +# ... using dif4 from above +(mcL4 <- multcompLetters(dif4, Letters=LETTERS)) +# Standard plot +\dontrun{ +# Requires (grid) +mcL4.1 <- plot(mcL4, label.groups=0.05) +# Redo using "at" = list +plot(mcL4, label.groups=0.05, at=mcL4.1) + +# With bold face and larger font +plot(mcL4, label.groups=0.05, + fontsize=28, fontface="bold") + +# Horizontal rather than vertical +plot(mcL4, horizontal=TRUE, label.groups=0.05) +} + +# Same as boxes rather than letters +plot(mcL4, label.groups=0.05, type="b") +plot(mcL4, horizontal=TRUE, label.groups=0.05, + type="b") +} +\seealso{ +\code{\link{multcompTs}} \code{\link{multcompLetters}} +\code{\link{multcompBoxplot}} \code{\link[grid]{gpar}} +} +\author{ +Spencer Graves +} +\keyword{aplot} diff -Nru r-cran-multcompview-0.1-7/man/plotTs.Rd r-cran-multcompview-0.1-8/man/plotTs.Rd --- r-cran-multcompview-0.1-7/man/plotTs.Rd 2015-07-31 15:43:44.000000000 +0000 +++ r-cran-multcompview-0.1-8/man/plotTs.Rd 2019-12-19 13:30:24.000000000 +0000 @@ -1,119 +1,132 @@ -% Generated by roxygen2 (4.1.1): do not edit by hand -% Please edit documentation in R/plotTs.R -\name{plotTs} -\alias{plotTs} -\title{plot multcomp displays} -\usage{ -plotTs(obj, at, width, horizontal, col, add, lwd, label.levels, label.groups, - T.base, orientation = "", ...) -} -\arguments{ -\item{obj}{a matrix describing which levels (rows) will be plotted with -which groups (columns). For plotTs and plotBoxes, obj is a matrix of -numbers from (-1, 0, 1). For plotLetters, obj is a logical matrix = TRUE if -that "letter" (group or column of obj) is to be plotted with that level (row -of obj).} - -\item{at}{an array with one row for each level and 3 columns giving low, -middle and high levels for the display for that level.} - -\item{width}{an array with one row for each group of levels in the display -and 3 columns giving low, middle and high levels for the display for that -group.} - -\item{horizontal}{A logical scalar indicating whether the list of items -compared reads left to right (horizontal = TRUE) or top to bottom -(horizontal = FALSE). If this multcomp graphic accompanies boxplots for -different levels or groups compared, the 'boxplot' argument 'horizontal' is -the negation of the multcomp plot 'horizontal' argument.} - -\item{col}{The color for each group of items or factor levels. The colors -will cross the different items or factor levels and will therefore have the -orientation specified via 'horizontal'. If the number of columns exceeds -length(col), col is recycled. For alternative choices for col, see "Color -Specification" in the \code{\link{par}} help page.} - -\item{add}{TRUE to add to an existing plot; FALSE to start a new plot. The -names of the factor levels or items compared will be plotted only if -add=FALSE.} - -\item{lwd}{line width for the display outline.} - -\item{label.levels}{Distance from the plot region to print the names of the -levels as a proportion of the plot range; NA for no level labels.} - -\item{label.groups}{Distance from the plot region to print the names of the -groups as a proportion of the plot range; NA for no level labels.} - -\item{T.base}{A numeric scalar giving the proportion of the available space -devoted to the base of the Ts.} - -\item{orientation}{If 'reversed', the base(s) of each "T" or traingle -indicating the master level(s) of that "undifferentiated class" will point -right or up (depending on horizontal) rather than down or left.} - -\item{...}{graphical parameters can be given as described on the -\code{\link{plot}} help page or the \code{\link[grid]{gpar}} help page.} - -\item{font.family}{character string naming the font family used by -"plotLetters". This function plots the different "Letters" in different -colors by plotting one color at a time. It's currently not smart enough to -align the letters properly except by assuming a mono-spaced font.} - -\item{fig}{figure region = (x0, x1, y0, y1) as a proportion of the device -region.} - -\item{mar}{margin = (lower, left, upper, right) in lines.} -} -\value{ -"Done" -} -\description{ -Helper functions for plot.multcompTs and plot.multcompLetters. These not -intended to be called directly and are hidden in a namespace. You can use -'getAnywhere' to see them. -} -\details{ -The requested graphic is either plotted by itself or added to an existing -plot as specified by the arguments. - -"plotTs" and "plotBoxes" use traditional R graphics and will not be -discussed further here. - -"plotLetters" uses 'grid' graphics, because it seems to provide more support -for controlling the side-by-side placement of "Letters" of possibly -different colors and widths. The "Letters" display will be positioned in -the "plot region" defined by fig and mar, assuming the entire device region -is 37 lines both wide and tall. Thus, the plot region is diff(fig[1:2])*37 -lines wide and diff(fig(1:2])*37 lines high. If, for example, fig = c(0.9, -1, 0, 1), this makes the plot region 3.7 lines wide. With the default -mar=c(5, 4, 4, 2)+0.1 lines, the "width" of the plot region is therefore 3.7 -- (4.1+2.1) = (-2.5) lines. "plotLetters" initially ignores this -contradictory negative width, and centers the plot at the midpoint of h0 = -fig[1]+mar[2]/37, h1 = fig[2]-mar[4]/37, v0 = fig[3]+mar[1]/37, and v1 = -fig[4]-mar[3]/37. The "Letters" for the different levels compared are -rescaled from at[, "center"] to fit inside At.rng = if(horizontal) c(h0, h1) -else c(v0, v1). With "n" levels compared and at.rng = range(at[, -"center"]), at[, "center"] is expanded to (at.rng+/-0.5) and rescaled to -match At.rng; if(diff(At.rng)<=0), an error message is issued. - -Meanwhile, the "Letters" are centered at the midpoint of W.rng = -if(horizontal) c(v0, v1) else v(h0, h1) [the opposite of At.rng]; the -argument "width" used by plotTs and plotBoxes is not used (and not even -accepted) by plotLetters. If(label.levels), these are positioned in the -midpoint of the right margin in the "W" direction. -} -\examples{ -# Designed to be called from plot.multcompTs -# or plot.multcompLetters, NOT directly by users. -} -\author{ -Spencer Graves -} -\seealso{ -\code{\link{plot.multcompTs}} \code{\link{plot.multcompLetters}} -\code{\link[grid]{gpar}} -} -\keyword{aplot} -\keyword{internal} - +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/plotTs.R +\name{plotTs} +\alias{plotTs} +\title{plot multcomp displays} +\usage{ +plotTs( + obj, + at, + width, + horizontal, + col, + add, + lwd, + label.levels, + label.groups, + T.base, + orientation = "", + ... +) +} +\arguments{ +\item{obj}{a matrix describing which levels (rows) will be plotted with +which groups (columns). For plotTs and plotBoxes, obj is a matrix of +numbers from (-1, 0, 1). For plotLetters, obj is a logical matrix = TRUE if +that "letter" (group or column of obj) is to be plotted with that level (row +of obj).} + +\item{at}{an array with one row for each level and 3 columns giving low, +middle and high levels for the display for that level.} + +\item{width}{an array with one row for each group of levels in the display +and 3 columns giving low, middle and high levels for the display for that +group.} + +\item{horizontal}{A logical scalar indicating whether the list of items +compared reads left to right (horizontal = TRUE) or top to bottom +(horizontal = FALSE). If this multcomp graphic accompanies boxplots for +different levels or groups compared, the 'boxplot' argument 'horizontal' is +the negation of the multcomp plot 'horizontal' argument.} + +\item{col}{The color for each group of items or factor levels. The colors +will cross the different items or factor levels and will therefore have the +orientation specified via 'horizontal'. If the number of columns exceeds +length(col), col is recycled. For alternative choices for col, see "Color +Specification" in the \code{\link{par}} help page.} + +\item{add}{TRUE to add to an existing plot; FALSE to start a new plot. The +names of the factor levels or items compared will be plotted only if +add=FALSE.} + +\item{lwd}{line width for the display outline.} + +\item{label.levels}{Distance from the plot region to print the names of the +levels as a proportion of the plot range; NA for no level labels.} + +\item{label.groups}{Distance from the plot region to print the names of the +groups as a proportion of the plot range; NA for no level labels.} + +\item{T.base}{A numeric scalar giving the proportion of the available space +devoted to the base of the Ts.} + +\item{orientation}{If 'reversed', the base(s) of each "T" or traingle +indicating the master level(s) of that "undifferentiated class" will point +right or up (depending on horizontal) rather than down or left.} + +\item{...}{graphical parameters can be given as described on the +\code{\link{plot}} help page or the \code{\link[grid]{gpar}} help page.} + +\item{font.family}{character string naming the font family used by +"plotLetters". This function plots the different "Letters" in different +colors by plotting one color at a time. It's currently not smart enough to +align the letters properly except by assuming a mono-spaced font.} + +\item{fig}{figure region = (x0, x1, y0, y1) as a proportion of the device +region.} + +\item{mar}{margin = (lower, left, upper, right) in lines.} +} +\value{ +"Done" +} +\description{ +Helper functions for plot.multcompTs and plot.multcompLetters. These not +intended to be called directly and are hidden in a namespace. You can use +'getAnywhere' to see them. +} +\details{ +The requested graphic is either plotted by itself or added to an existing +plot as specified by the arguments. + +"plotTs" and "plotBoxes" use traditional R graphics and will not be +discussed further here. + +"plotLetters" uses 'grid' graphics, because it seems to provide more support +for controlling the side-by-side placement of "Letters" of possibly +different colors and widths. The "Letters" display will be positioned in +the "plot region" defined by fig and mar, assuming the entire device region +is 37 lines both wide and tall. Thus, the plot region is diff(fig[1:2])*37 +lines wide and diff(fig(1:2])*37 lines high. If, for example, fig = c(0.9, +1, 0, 1), this makes the plot region 3.7 lines wide. With the default +mar=c(5, 4, 4, 2)+0.1 lines, the "width" of the plot region is therefore 3.7 +- (4.1+2.1) = (-2.5) lines. "plotLetters" initially ignores this +contradictory negative width, and centers the plot at the midpoint of h0 = +fig[1]+mar[2]/37, h1 = fig[2]-mar[4]/37, v0 = fig[3]+mar[1]/37, and v1 = +fig[4]-mar[3]/37. The "Letters" for the different levels compared are +rescaled from at[, "center"] to fit inside At.rng = if(horizontal) c(h0, h1) +else c(v0, v1). With "n" levels compared and at.rng = range(at[, +"center"]), at[, "center"] is expanded to (at.rng+/-0.5) and rescaled to +match At.rng; if(diff(At.rng)<=0), an error message is issued. + +Meanwhile, the "Letters" are centered at the midpoint of W.rng = +if(horizontal) c(v0, v1) else v(h0, h1) [the opposite of At.rng]; the +argument "width" used by plotTs and plotBoxes is not used (and not even +accepted) by plotLetters. If(label.levels), these are positioned in the +midpoint of the right margin in the "W" direction. +} +\examples{ + +# Designed to be called from plot.multcompTs +# or plot.multcompLetters, NOT directly by users. + +} +\seealso{ +\code{\link{plot.multcompTs}} \code{\link{plot.multcompLetters}} +\code{\link[grid]{gpar}} +} +\author{ +Spencer Graves +} +\keyword{aplot} +\keyword{internal} diff -Nru r-cran-multcompview-0.1-7/man/print.multcompLetters.Rd r-cran-multcompview-0.1-8/man/print.multcompLetters.Rd --- r-cran-multcompview-0.1-7/man/print.multcompLetters.Rd 2015-07-31 15:43:44.000000000 +0000 +++ r-cran-multcompview-0.1-8/man/print.multcompLetters.Rd 2019-12-19 13:30:24.000000000 +0000 @@ -1,45 +1,46 @@ -% Generated by roxygen2 (4.1.1): do not edit by hand -% Please edit documentation in R/print.multcompLetters.R -\name{print.multcompLetters} -\alias{print.multcompLetters} -\title{print a multcompLetters object} -\usage{ -\method{print}{multcompLetters}(x, all = FALSE, ...) -} -\arguments{ -\item{x}{an object of class 'multcompLetters'} - -\item{all}{FALSE to print only the character vector representations of the -'multcompLetters' comparison summary; TRUE to print also the matrix -representation.} - -\item{...}{Other optional print parameters as described on the -\code{\link{print}} help page.} -} -\value{ -x\$Letters = the named, character vector representation of the -'multcompLetters' evaluation of the distance relationships -} -\description{ -print method for an object of class 'multcompLetters'. -} -\details{ -Prints only the Letters component of the 'multcompLetters' list unless -all=TRUE. -} -\examples{ -dif3 <- c(FALSE, FALSE, TRUE) -names(dif3) <- c("A-B", "A-C", "B-C") -dif3L <- multcompLetters(dif3) -dif3L -print(dif3L) -print(dif3L, TRUE) -} -\author{ -Spencer Graves -} -\seealso{ -\code{\link{multcompLetters}} -} -\keyword{dplot} - +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/print.multcompLetters.R +\name{print.multcompLetters} +\alias{print.multcompLetters} +\title{print a multcompLetters object} +\usage{ +\method{print}{multcompLetters}(x, all = FALSE, ...) +} +\arguments{ +\item{x}{an object of class 'multcompLetters'} + +\item{all}{FALSE to print only the character vector representations of the +'multcompLetters' comparison summary; TRUE to print also the matrix +representation.} + +\item{...}{Other optional print parameters as described on the +\code{\link{print}} help page.} +} +\value{ +x\$Letters = the named, character vector representation of the +'multcompLetters' evaluation of the distance relationships +} +\description{ +print method for an object of class 'multcompLetters'. +} +\details{ +Prints only the Letters component of the 'multcompLetters' list unless +all=TRUE. +} +\examples{ + +dif3 <- c(FALSE, FALSE, TRUE) +names(dif3) <- c("A-B", "A-C", "B-C") +dif3L <- multcompLetters(dif3) +dif3L +print(dif3L) +print(dif3L, TRUE) + +} +\seealso{ +\code{\link{multcompLetters}} +} +\author{ +Spencer Graves +} +\keyword{dplot} diff -Nru r-cran-multcompview-0.1-7/man/vec2mat2.Rd r-cran-multcompview-0.1-8/man/vec2mat2.Rd --- r-cran-multcompview-0.1-7/man/vec2mat2.Rd 2015-07-31 15:43:44.000000000 +0000 +++ r-cran-multcompview-0.1-8/man/vec2mat2.Rd 2019-12-19 13:30:24.000000000 +0000 @@ -1,53 +1,54 @@ -% Generated by roxygen2 (4.1.1): do not edit by hand -% Please edit documentation in R/vec2mat2.R -\name{vec2mat2} -\alias{vec2mat2} -\title{Convert a vector of hyphenated names into a character matrix.} -\usage{ -vec2mat2(x, sep = "-") -} -\arguments{ -\item{x}{Vector of hyphenated names} - -\item{sep}{"strsplit" character to apply to names(x).} -} -\value{ -A character matrix with rownames = x and with the character string -preceeding the "sep" character in the first column and the character string -following the "sep" character in the second column. -} -\description{ -Convert a vector of hyphenated names into a character matrix with 2 columns -containing the names split in each row. -} -\details{ -If each element of x does not contain exactly 1 "sep" character, an error is -issued. -} -\examples{ -vec2mat2(c("a-b", "a-c", "b-c")) - -vec2mat2(c("a-b", "b-a")) - -\dontshow{ -(tst3 <- substring(try( - vec2mat2(c("a", "b-a", "b-c"))), 1, 20) -=="Error in vec2mat2(c(") -# Error: name without a sep character - -(tst4 <- substring(try( - vec2mat2(c("a-c", "b-a", "b-c-d"))), 1, 20) -=="Error in vec2mat2(c(") -# Error: multiple hyphens (sep characters) - -} -} -\author{ -Spencer Graves -} -\seealso{ -\code{\link{vec2mat}} \code{\link{multcompLetters}} -} -\keyword{array} -\keyword{manip} - +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/vec2mat2.R +\name{vec2mat2} +\alias{vec2mat2} +\title{Convert a vector of hyphenated names into a character matrix.} +\usage{ +vec2mat2(x, sep = "-") +} +\arguments{ +\item{x}{Vector of hyphenated names} + +\item{sep}{"strsplit" character to apply to names(x).} +} +\value{ +A character matrix with rownames = x and with the character string +preceeding the "sep" character in the first column and the character string +following the "sep" character in the second column. +} +\description{ +Convert a vector of hyphenated names into a character matrix with 2 columns +containing the names split in each row. +} +\details{ +If each element of x does not contain exactly 1 "sep" character, an error is +issued. +} +\examples{ + +vec2mat2(c("a-b", "a-c", "b-c")) + +vec2mat2(c("a-b", "b-a")) + +\dontshow{ +(tst3 <- substring(try( + vec2mat2(c("a", "b-a", "b-c"))), 1, 20) +=="Error in vec2mat2(c(") +# Error: name without a sep character + +(tst4 <- substring(try( + vec2mat2(c("a-c", "b-a", "b-c-d"))), 1, 20) +=="Error in vec2mat2(c(") +# Error: multiple hyphens (sep characters) + +} + +} +\seealso{ +\code{\link{vec2mat}} \code{\link{multcompLetters}} +} +\author{ +Spencer Graves +} +\keyword{array} +\keyword{manip} diff -Nru r-cran-multcompview-0.1-7/man/vec2mat.Rd r-cran-multcompview-0.1-8/man/vec2mat.Rd --- r-cran-multcompview-0.1-7/man/vec2mat.Rd 2015-07-31 15:43:44.000000000 +0000 +++ r-cran-multcompview-0.1-8/man/vec2mat.Rd 2019-12-19 13:30:24.000000000 +0000 @@ -1,81 +1,82 @@ -% Generated by roxygen2 (4.1.1): do not edit by hand -% Please edit documentation in R/vec2mat.R -\name{vec2mat} -\alias{vec2mat} -\title{Convert a vector with hyphenated names into a matrix.} -\usage{ -vec2mat(x, sep = "-") -} -\arguments{ -\item{x}{Either (1) a vector with hyphenated names indicating pairs of -factor levels, groups or items that are and are not significantly different -or (2) a matrix indicating same. If x is already a matrix, it is checked -for symmetry. NAs are not allowed.} - -\item{sep}{"strsplit" character to apply to names(x).} -} -\value{ -A symmetrix matrix of the same class as the input with names -obtained from unique(strsplit(names(x))). All nonspecified elements will be -1 if class(x) is numeric, FALSE if logical and "" if character. Used by the -functions 'multcompLetters' and 'multcompTs'. -} -\description{ -Convert a vector with hypehnated names into a symmetric matrix with names -obtained from vect2mat2(names(x)). -} -\details{ -x must have names each of which contains exactly one hyphen; if not, vec2mat -issues an error message. If the same comparison is present multiple times, -the last value is used; no check is made for duplicates. -} -\examples{ -dif3 <- c(FALSE, FALSE, TRUE) -names(dif3) <- c("a-b", "a-c", "b-c") -vec2mat(dif3) - -dif3. <- 1:3 -names(dif3.) <- c("a-b", "a-c", "b-c") -vec2mat(dif3.) - -dif.ch <- c("this",'is','it') -names(dif.ch) <- c("a-b", "a-c", "b-c") -vec2mat(dif.ch) - -vec2mat(array(1, dim=c(2,2))) -\dontshow{ - try(vec2mat(array(1:24, dim=2:4)))# must be 2-d - try(vec2mat(array(1:6, dim=2:3)))# must be square - try(vec2mat(array(1:4, dim=c(2,2))))# must be symmetric - try(vec2mat(array(1, dim=c(2,2)))) # diag should be 0 - try(vec2mat(array(TRUE, dim=c(2,2)))) # diag should be FALSE - try(vec2mat(array("a", dim=c(2,2)))) # diag should be "" - - try(vec2mat(c(1:3, NA))) # NAs not allowed - try(vec2mat(1:3))# Error: No names - - errVec2 <- 1:3 - names(errVec2) <- c("a", "b-a", "b-c") - try(vec2mat(errVec2))# Error: missing hyphen (sep character) - - errVec3 <- 1:3 - names(errVec3) <- c("a-c", "b-a", "b-c-d") - try(vec2mat(errVec3)) -# Error: multiple hyphens (sep characters) - - dif4 <- 1:4 - names(dif4) <- c("a-b", "a-c", "b-c", "b-a") -# Both "b-a" and "a-b" specified; -# use the latest. - vec2mat(dif4) -} -} -\author{ -Spencer Graves -} -\seealso{ -\code{\link{multcompLetters}} \code{\link{multcompTs}} -} -\keyword{array} -\keyword{manip} - +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/vec2mat.R +\name{vec2mat} +\alias{vec2mat} +\title{Convert a vector with hyphenated names into a matrix.} +\usage{ +vec2mat(x, sep = "-") +} +\arguments{ +\item{x}{Either (1) a vector with hyphenated names indicating pairs of +factor levels, groups or items that are and are not significantly different +or (2) a matrix indicating same. If x is already a matrix, it is checked +for symmetry. NAs are not allowed.} + +\item{sep}{"strsplit" character to apply to names(x).} +} +\value{ +A symmetrix matrix of the same class as the input with names +obtained from unique(strsplit(names(x))). All nonspecified elements will be +1 if class(x) is numeric, FALSE if logical and "" if character. Used by the +functions 'multcompLetters' and 'multcompTs'. +} +\description{ +Convert a vector with hypehnated names into a symmetric matrix with names +obtained from vect2mat2(names(x)). +} +\details{ +x must have names each of which contains exactly one hyphen; if not, vec2mat +issues an error message. If the same comparison is present multiple times, +the last value is used; no check is made for duplicates. +} +\examples{ + +dif3 <- c(FALSE, FALSE, TRUE) +names(dif3) <- c("a-b", "a-c", "b-c") +vec2mat(dif3) + +dif3. <- 1:3 +names(dif3.) <- c("a-b", "a-c", "b-c") +vec2mat(dif3.) + +dif.ch <- c("this",'is','it') +names(dif.ch) <- c("a-b", "a-c", "b-c") +vec2mat(dif.ch) + +vec2mat(array(1, dim=c(2,2))) +\dontshow{ + try(vec2mat(array(1:24, dim=2:4)))# must be 2-d + try(vec2mat(array(1:6, dim=2:3)))# must be square + try(vec2mat(array(1:4, dim=c(2,2))))# must be symmetric + try(vec2mat(array(1, dim=c(2,2)))) # diag should be 0 + try(vec2mat(array(TRUE, dim=c(2,2)))) # diag should be FALSE + try(vec2mat(array("a", dim=c(2,2)))) # diag should be "" + + try(vec2mat(c(1:3, NA))) # NAs not allowed + try(vec2mat(1:3))# Error: No names + + errVec2 <- 1:3 + names(errVec2) <- c("a", "b-a", "b-c") + try(vec2mat(errVec2))# Error: missing hyphen (sep character) + + errVec3 <- 1:3 + names(errVec3) <- c("a-c", "b-a", "b-c-d") + try(vec2mat(errVec3)) +# Error: multiple hyphens (sep characters) + + dif4 <- 1:4 + names(dif4) <- c("a-b", "a-c", "b-c", "b-a") +# Both "b-a" and "a-b" specified; +# use the latest. + vec2mat(dif4) +} + +} +\seealso{ +\code{\link{multcompLetters}} \code{\link{multcompTs}} +} +\author{ +Spencer Graves +} +\keyword{array} +\keyword{manip} diff -Nru r-cran-multcompview-0.1-7/MD5 r-cran-multcompview-0.1-8/MD5 --- r-cran-multcompview-0.1-7/MD5 2015-07-31 16:40:25.000000000 +0000 +++ r-cran-multcompview-0.1-8/MD5 2019-12-19 16:50:10.000000000 +0000 @@ -1,12 +1,12 @@ -e7d59e42274e38b4e62eab138f7a7057 *DESCRIPTION -525686948fa773b3ded8faecf3fd8c14 *NAMESPACE -9e892290a67dc7ba156b89ed1fd3378d *R/extract_p.R +57870005938880b4af04bcf00e988563 *DESCRIPTION +fe3a985aaf21c61ebd12a1a672dc7b0c *NAMESPACE +bd4d65ed8b2d08484f9d8d7cc5599fe6 *R/extract_p.R 7839b75a96f51f8e5fc0ab68a9469a2f *R/multcompBoxplot.R -63b8743a2910b8a619bda0261d631928 *R/multcompLetters.R +eb2dbbcd2c3434d24dd97d97451b2116 *R/multcompLetters.R f3ffb29139de0ed5b35da51b0e687c63 *R/multcompLetters2.R bf30220ebd681e3deb713bb4009e22ed *R/multcompLetters3.R dd820f0694cf2639612bc3497763cc7c *R/multcompLetters4.R -58e73921f82c3d3feb24baaddd1c55d6 *R/multcompTs.R +9fab5b5f01ce62015c5f26a83dd2495a *R/multcompTs.R 9f07fb4a79a01096315506947ed5ad67 *R/multcompView-package.R 48100771a2a07ec401182761e6ff5727 *R/plot.multcompLetters.R 281b0cc9d01a1d930814bb2af9e97766 *R/plot.multcompTs.R @@ -17,19 +17,16 @@ 086f28eec6c8ac73faaa8ae27b1fed0a *R/vec2mat.R 0ff72033af477590aabd8a7011d9d134 *R/vec2mat2.R 23161c7eb305fec411df18388de0d35c *README -136df18f755cd1559ce3bfa4eb1fc403 *inst/doc/VisualizingPairedComparisons.doc -5474edcadd8b09248c9de2bbe788b896 *inst/doc/VisualizingPairedComparisons.pdf -99e065698cd88f0670721300c526a068 *inst/doc/VisualizingPairedComparisons.ppt -32d2991bedc10c803afca5bfb38616ad *man/extract_p.Rd -31ef13c7208dfa1325756e63eb8d5703 *man/multcompBoxplot.Rd -288f6b17e0312d0197fc276a6cd52da0 *man/multcompLetters.Rd -b2adc141dce77884ec72b3a4f9da6c36 *man/multcompTs.Rd -d3f0cdfa6776ed67356bdddbaf4a210a *man/multcompView-package.Rd -a215f6f8f9b6025fc4fed20421b87401 *man/plot.multcompLetters.Rd -67928f7e42a419783b5ed846def38888 *man/plot.multcompTs.Rd -7cc8d84e3208072e9e9701fed3a99443 *man/plotBoxes.Rd -dcf57c02faecfe6452c03de3e2d914c4 *man/plotLetters.Rd -d4db58971f2187423dda92dcd96d3e54 *man/plotTs.Rd -08704262dec2b81859ad0df11b2239aa *man/print.multcompLetters.Rd -5b2ec590a411a5b7031569c5d6d96948 *man/vec2mat.Rd -32aa09cce02d26d6652dec4351604bc9 *man/vec2mat2.Rd +387a662ff5b6165ac8910e85dd167b36 *man/extract_p.Rd +61a076d59321f642c6b6fe31ad934512 *man/multcompBoxplot.Rd +f3476be7fcbbcd0c9d93760c0084ee53 *man/multcompLetters.Rd +e1944ae39e56f7c07997a96ece23d6eb *man/multcompTs.Rd +b2211496a0d0a17f909c6f800cf0e710 *man/multcompView-package.Rd +5a474fd951474eed50b6fd932ac2fae9 *man/plot.multcompLetters.Rd +66280f1f6d511b0628d27bb9021b3566 *man/plot.multcompTs.Rd +4070cab23be67264c1782f2110d442de *man/plotBoxes.Rd +c9900dd4f7c8414fc09e68598669e9db *man/plotLetters.Rd +89bf718442353a79aa61c0dc80751b00 *man/plotTs.Rd +9fae0e7f4c06f42b589e72da097d6e56 *man/print.multcompLetters.Rd +432de67071e93b36eaa91549a6a0c7cd *man/vec2mat.Rd +853089e248d1b3fa16a70e3e60b36750 *man/vec2mat2.Rd diff -Nru r-cran-multcompview-0.1-7/NAMESPACE r-cran-multcompview-0.1-8/NAMESPACE --- r-cran-multcompview-0.1-7/NAMESPACE 2015-07-31 15:43:44.000000000 +0000 +++ r-cran-multcompview-0.1-8/NAMESPACE 2019-12-19 13:54:55.000000000 +0000 @@ -1,4 +1,4 @@ -# Generated by roxygen2 (4.1.1): do not edit by hand +# Generated by roxygen2: do not edit by hand S3method(extract_p,TukeyHSD) S3method(extract_p,default) diff -Nru r-cran-multcompview-0.1-7/R/extract_p.R r-cran-multcompview-0.1-8/R/extract_p.R --- r-cran-multcompview-0.1-7/R/extract_p.R 2015-07-31 15:43:44.000000000 +0000 +++ r-cran-multcompview-0.1-8/R/extract_p.R 2019-12-12 18:58:16.000000000 +0000 @@ -23,8 +23,9 @@ #' #' extract_p(exp_tukey) #' -#' require(pgirmess) +#' if(require(pgirmess)){ #' extract_p(kruskalmc(y ~ treatments, data = experiment)) +#' } #' #' "extract_p" <- function(x) { @@ -42,7 +43,7 @@ } #' @export -#' @describeIn extract_p +#' @describeIn extract_p extract p values from a TukeyHSD object extract_p.TukeyHSD <- function(x) { x <- lapply(x, extract_p.default) diff -Nru r-cran-multcompview-0.1-7/R/multcompLetters.R r-cran-multcompview-0.1-8/R/multcompLetters.R --- r-cran-multcompview-0.1-7/R/multcompLetters.R 2015-07-31 15:43:44.000000000 +0000 +++ r-cran-multcompview-0.1-8/R/multcompLetters.R 2019-12-10 19:22:21.000000000 +0000 @@ -179,7 +179,7 @@ ## 1. Covert to logical ## x.is <- deparse(substitute(x)) - if(class(x)=="dist")x <- as.matrix(x) + if(any(class(x)=="dist"))x <- as.matrix(x) if(!is.logical(x)) x <- do.call(compare, list(x, threshold)) ## @@ -381,7 +381,8 @@ } #' @export -#' @describeIn multcompLetters +#' @describeIn multcompLetters create a compact letters display and order the +#' letters "multcompLetters3" <- function (z, y , x, data, ...) { y.z <- tapply(data[, y], data[, z], @@ -398,7 +399,7 @@ multcompLetters(value, ...) } #' @export -#' @describeIn multcompLetters +#' @describeIn multcompLetters create a compact letters display using a aov object #' "multcompLetters4" <- function (object, comp, ...) { diff -Nru r-cran-multcompview-0.1-7/R/multcompTs.R r-cran-multcompview-0.1-8/R/multcompTs.R --- r-cran-multcompview-0.1-7/R/multcompTs.R 2015-07-31 15:43:44.000000000 +0000 +++ r-cran-multcompview-0.1-8/R/multcompTs.R 2019-12-19 13:30:17.000000000 +0000 @@ -49,8 +49,8 @@ #' 47) #' #' Spencer Graves and Hans-Peter Piepho (2006) "Simple Visualizations of Paired -#' Comparisons", \url{dir(system.file('doc', package='multcompView'), -#' pattern='\.pdf$', full.name=TRUE)} +#' Comparisons", \href{../doc/VisualizingPairedComparisons.pdf}{\code{vignette("VisualizingPairedComparisons", package = "multcompView")}} +#' #' @keywords dplot #' @export #' @examples @@ -121,7 +121,7 @@ ## ## 1. Covert to logical ## - if(class(x)=="dist")x <- as.matrix(x) + if(any(class(x) == "dist"))x <- as.matrix(x) if(!is.logical(x)) x <- do.call(compare, list(x, threshold)) ##