Nothing
R/statistics-summaries-menu.R
In Rcmdr2: R Commander
Defines functions
summarizeDataSet
numericalSummaries
correlationTest
countMissing
# Statistics Menu dialogs
# last modified 2013-05-05 by J. Fox
# Summaries menu
summarizeDataSet <- function(){
nvar <- length(Variables())
.activeDataSet <- ActiveDataSet()
if (nvar > 10){
response <- RcmdrTkmessageBox(message=sprintf(gettextRcmdr("There are %d variables in the data set %s.\nDo you want to proceed?"), nvar, .activeDataSet),
icon="question", type="okcancel", default="cancel")
if ("cancel" == tclvalue(response)) {
tkfocus(CommanderWindow())
return()
}
}
doItAndPrint(paste("summary(", .activeDataSet, ")", sep=""))
}
numericalSummaries <- function(){ # dialog memory 2011-06-27 J. Fox
Library("abind")
Library("e1071")
defaults <- list(initial.x=NULL, initial.mean="1", initial.sd="1", initial.IQR="1", initial.cv="0",
initial.quantiles.variable="1",
initial.quantiles="0, .25, .5, .75, 1",
initial.skewness="0", initial.kurtosis="0", initial.type="2",
initial.group=NULL)
dialog.values <- getDialog("numericalSummaries", defaults)
initial.group <- dialog.values$initial.group
initializeDialog(title=gettextRcmdr("Numerical Summaries"))
notebook <- ttknotebook(top, width=600)
dataTab <- tkframe(top)
statisticsTab <- tkframe(top)
xBox <- variableListBox(dataTab, Numeric(), selectmode="multiple", title=gettextRcmdr("Variables (pick one or more)"),
initialSelection=varPosn(dialog.values$initial.x, "numeric"))
checkBoxes(window = statisticsTab, frame="checkBoxFrame", boxes=c("mean", "sd", "IQR", "cv"),
initialValues=c(dialog.values$initial.mean, dialog.values$initial.sd, dialog.values$initial.IQR, dialog.values$initial.cv),
labels=gettextRcmdr(c("Mean", "Standard Deviation", "Interquartile Range", "Coefficient of Variation")))
skFrame <- tkframe(statisticsTab)
checkBoxes(window = skFrame, frame="skCheckBoxFrame", boxes=c("skewness", "kurtosis"),
initialValues=c(dialog.values$initial.skewness, dialog.values$initial.kurtosis),
labels=gettextRcmdr(c("Skewness", "Kurtosis")))
radioButtons(window = skFrame, name="typeButtons", buttons=c("b1", "b2", "b3"), values=c("1", "2", "3"),
initialValue=dialog.values$initial.type,
labels=gettextRcmdr(c("Type 1", "Type 2", "Type 3")))
quantilesVariable <- tclVar(dialog.values$initial.quantiles.variable)
quantilesFrame <- tkframe(statisticsTab)
quantilesCheckBox <- tkcheckbutton(quantilesFrame, variable=quantilesVariable)
quantiles <- tclVar(dialog.values$initial.quantiles)
quantilesEntry <- ttkentry(quantilesFrame, width="20", textvariable=quantiles)
groupsBox(recall=numericalSummaries, label=gettextRcmdr("Summarize by:"),
initialLabel=if (is.null(initial.group)) gettextRcmdr("Summarize by groups")
else paste(gettextRcmdr("Summarize by:"), initial.group),
initialGroup=initial.group, window = dataTab)
onOK <- function(){
x <- getSelection(xBox)
quants <- tclvalue(quantiles)
meanVar <- tclvalue(meanVariable)
sdVar <- tclvalue(sdVariable)
IQRVar <- tclvalue(IQRVariable)
cvVar <- tclvalue(cvVariable)
quantsVar <- tclvalue(quantilesVariable)
skewnessVar <- tclvalue(skewnessVariable)
kurtosisVar <- tclvalue(kurtosisVariable)
typeVar <- tclvalue(typeButtonsVariable)
putDialog("numericalSummaries", list(
initial.x=x, initial.mean=meanVar, initial.sd=sdVar, initial.IQR=IQRVar, initial.cv=cvVar,
initial.quantiles.variable=quantsVar, initial.quantiles=quants,
initial.skewness=skewnessVar, initial.kurtosis=kurtosisVar, initial.type=typeVar,
initial.group=if (.groups != FALSE) .groups else NULL
))
if (length(x) == 0){
errorCondition(recall=numericalSummaries, message=gettextRcmdr("You must select a variable."))
return()
}
closeDialog()
quants <- paste("c(", gsub(",+", ",", gsub(" ", ",", quants)), ")", sep="")
.activeDataSet <- ActiveDataSet()
vars <- if (length(x) == 1) paste('"', x, '"', sep="")
else paste("c(", paste('"', x, '"', collapse=", ", sep=""), ")", sep="")
vars <- paste(.activeDataSet, "[,", vars, "]", sep="")
stats <- paste("c(",
paste(c('"mean"', '"sd"', '"IQR"', '"quantiles"', '"cv"', '"skewness"', '"kurtosis"')
[c(meanVar, sdVar, IQRVar, quantsVar, cvVar, skewnessVar, kurtosisVar) == 1],
collapse=", "), ")", sep="")
if (stats == "c()"){
errorCondition(recall=numericalSummaries, message=gettextRcmdr("No statistics selected."))
return()
}
type.text <- if (skewnessVar == 1 || kurtosisVar == 1) paste(', type="', typeVar, '"', sep="") else ""
command <- if (.groups != FALSE) {
grps <- paste(.activeDataSet, "$", .groups, sep="")
paste("numSummary(", vars, ", groups=", grps, ", statistics=", stats,
", quantiles=", quants, type.text, ")", sep="")
}
else paste("numSummary(", vars, ", statistics=", stats,
", quantiles=", quants, type.text, ")", sep="")
doItAndPrint(command)
tkfocus(CommanderWindow())
}
OKCancelHelp(helpSubject="numSummary", reset="numericalSummaries", apply ="numericalSummaries")
tkgrid(getFrame(xBox), sticky="nw")
tkadd(notebook, dataTab, text=gettextRcmdr("Data"), padding=6)
tkadd(notebook, statisticsTab, text=gettextRcmdr("Statistics"), padding=6)
tkgrid(checkBoxFrame, sticky="w")
tkgrid(ttklabel(statisticsTab, text=""))
tkgrid(skCheckBoxFrame, typeButtonsFrame, sticky="nw")
tkgrid(skFrame, sticky="w")
tkgrid(labelRcmdr(quantilesFrame, text=gettextRcmdr("Quantiles")), quantilesCheckBox,
labelRcmdr(quantilesFrame, text=gettextRcmdr(" quantiles:")), quantilesEntry, sticky="w")
tkgrid(ttklabel(statisticsTab, text=""))
tkgrid(quantilesFrame, sticky="w")
tkgrid(ttklabel(dataTab, text=""))
tkgrid(groupsFrame, sticky = "w", padx=6)
tkgrid(notebook, sticky="nsew")
tkgrid(buttonsFrame, sticky="w")
dialogSuffix(rows=7, columns=1)
}
frequencyDistribution <- function () {
defaults <- list (initial.x = NULL, initial.goodnessOfFit = "0")
dialog.values <- getDialog ("frequencyDistribution", defaults)
initializeDialog(title = gettextRcmdr("Frequency Distributions"))
xBox <- variableListBox(top, Factors(), selectmode = "multiple",
title = gettextRcmdr("Variables (pick one or more)"),
initialSelection = varPosn (dialog.values$initial.x, "factor"))
optionsFrame <- tkframe(top)
goodnessOfFitVariable <- tclVar(dialog.values$initial.goodnessOfFit)
goodnessOfFitCheckBox <- ttkcheckbutton(optionsFrame, variable = goodnessOfFitVariable)
onOK <- function() {
x <- getSelection(xBox)
if (length(x) == 0) {
errorCondition(recall = frequencyDistribution, message = gettextRcmdr("You must select a variable."))
return()
}
goodnessOfFit <- tclvalue(goodnessOfFitVariable)
putDialog ("frequencyDistribution", list (initial.x = x, initial.goodnessOfFit = goodnessOfFit))
if (length(x) > 1 && goodnessOfFit == "1") {
errorCondition(recall = frequencyDistribution, message = gettextRcmdr("Goodness-of-fit test not available when more than one variable is selected."))
return()
}
closeDialog()
.activeDataSet <- ActiveDataSet()
for (variable in x) {
command <- paste("table(", .activeDataSet, "$", variable,
")", sep = "")
# logger(paste(".Table <-", command))
# assign(".Table", justDoIt(command), envir = .GlobalEnv)
doItAndPrint(paste(".Table <-", command))
doItAndPrint(paste(".Table # counts for", variable))
doItAndPrint(paste("round(100*.Table/sum(.Table), 2) # percentages for",
variable))
}
env <- environment()
if (goodnessOfFit == 1) {
initializeDialog(subwin, title = gettextRcmdr("Goodness-of-Fit Test"))
hypothesisFrame <- tkframe(subwin)
levs <- eval(parse(text = paste("levels(", .activeDataSet,
"$", x, ")", sep = "")))
n.levs <- length(levs)
assign(".entry.1", tclVar(paste("1/", n.levs, sep = "")),
envir = env)
make.entries <- "labelRcmdr(hypothesisFrame, text='Hypothesized probabilities: ')"
make.lev.names <- "labelRcmdr(hypothesisFrame, text='Factor levels:')"
for (i in 1:n.levs) {
entry.varname <- paste(".entry.", i, sep = "")
assign(entry.varname, tclVar(paste("1/", n.levs,
sep = "")), envir = env)
make.entries <- paste(make.entries, ", ", "ttkentry(hypothesisFrame, width='5', textvariable=",
entry.varname, ")", sep = "")
make.lev.names <- paste(make.lev.names, ", labelRcmdr(hypothesisFrame, text='",
levs[i], "')", sep = "")
}
eval(parse(text = paste("tkgrid(", make.lev.names,
", sticky='w')", sep = "")), envir = env)
eval(parse(text = paste("tkgrid(", make.entries,
", stick='w')", sep = "")), envir = env)
tkgrid(hypothesisFrame, sticky = "w")
onOKsub <- function() {
probs <- rep(NA, n.levs)
for (i in 1:n.levs) {
entry.varname <- paste(".entry.", i, sep = "")
res <- try(entry <- eval(parse(text = eval(parse(text = paste("tclvalue(",
entry.varname, ")", sep = "")), envir = env))),
silent = TRUE)
if (class(res) == "try-error") {
errorCondition(subwin, message = gettextRcmdr("Invalid entry."))
return()
}
if (length(entry) == 0) {
errorCondition(subwin, message = gettextRcmdr("Missing entry."))
return()
}
opts <- options(warn = -1)
probs[i] <- as.numeric(entry)
options(opts)
}
probs <- na.omit(probs)
if (length(probs) != n.levs) {
errorCondition(subwin, message = sprintf(gettextRcmdr("Number of valid entries (%d)\nnot equal to number levels (%d)."),
length(probs), n.levs))
return()
}
if (any(probs < 0)) {
errorCondition(subwin, message = gettextRcmdr("Negative probabilities not allowed."))
return()
}
if (abs(sum(probs) - 1) > 0.001) {
Message(message = gettextRcmdr("Probabilities rescaled to sum to 1."),
type = "warning")
probs <- probs/sum(probs)
}
closeDialog(subwin)
command <- paste("c(", paste(probs, collapse = ","),
")", sep = "")
# logger(paste(".Probs <-", command))
# assign(".Probs", justDoIt(command), envir = .GlobalEnv)
doItAndPrint(paste(".Probs <-", command))
doItAndPrint("chisq.test(.Table, p=.Probs)")
logger("remove(.Probs)")
remove(.Probs, envir = .GlobalEnv)
}
subOKCancelHelp(subwin)
tkgrid(subButtonsFrame, sticky = "w")
dialogSuffix(subwin, rows = 2, columns = 1, onOK = onOKsub,
focus = subwin)
}
logger("remove(.Table)")
remove(.Table, envir = .GlobalEnv)
tkfocus(CommanderWindow())
}
OKCancelHelp(helpSubject = "table", reset = "frequencyDistribution")
tkgrid(getFrame(xBox), sticky = "nw")
tkgrid(labelRcmdr(optionsFrame, text = gettextRcmdr("Chi-square goodness-of-fit test (for one variable only)")),
goodnessOfFitCheckBox, sticky = "w")
tkgrid(optionsFrame, sticky = "w")
tkgrid(buttonsFrame, sticky = "w")
dialogSuffix(rows = 3, columns = 2)
}
statisticsTable <- function () {
defaults <- list (initial.group=NULL, initial.response=NULL, initial.statistic="mean", initial.other = "")
dialog.values <- getDialog ("statisticsTable", defaults)
initializeDialog(title = gettextRcmdr("Table of Statistics"))
variablesFrame <- tkframe(top)
groupBox <- variableListBox(variablesFrame, Factors(), selectmode = "multiple",
title = gettextRcmdr("Factors (pick one or more)"),
initialSelection = varPosn(dialog.values$initial.group,"factor"))
responseBox <- variableListBox(variablesFrame, Numeric(), selectmode = "multiple",
initialSelection = varPosn(dialog.values$initial.response, "numeric"),
title = gettextRcmdr("Response variables (pick one or more)"))
statFrame <- tkframe(top)
radioButtons(statFrame, name = "statistic", buttons = c("mean", "median", "sd", "IQR", "other"),
labels = gettextRcmdr(c("Mean", "Median", "Standard deviation", "Interquartile range", "Other (specify)")),
initialValue = dialog.values$initial.statistic,
title = gettextRcmdr("Statistic"))
otherVariable <- tclVar(dialog.values$initial.other)
otherEntry <- ttkentry(statFrame, width = "20", textvariable = otherVariable)
tkgrid(statisticFrame, labelRcmdr(statFrame, text =" "), otherEntry, sticky = "sw")
onOK <- function() {
groups <- getSelection(groupBox)
if (0 == length(groups)) {
errorCondition(recall = statisticsTable, message = gettextRcmdr("No factors selected."))
return()
}
responses <- getSelection(responseBox)
if (0 == length(responses)) {
errorCondition(recall = statisticsTable, message = gettextRcmdr("You must select a response variable."))
return()
}
stat <- statistic <- tclvalue(statisticVariable)
if (statistic == "other")
statistic <- tclvalue(otherVariable)
putDialog ("statisticsTable", list(initial.group=groups, initial.response=responses,
initial.statistic=stat, initial.other = if(stat == "other") statistic else ""))
closeDialog()
.activeDataSet <- ActiveDataSet()
groups.list <- paste(paste(groups, "=", .activeDataSet,
"$", groups, sep = ""), collapse = ", ")
for (response in responses) {
if (length(responses) > 1)
doItAndPrint(paste("# Table for ", response,
":", sep = ""))
doItAndPrint(paste("tapply(", .activeDataSet, "$",
response, ", list(", groups.list, "), ", statistic,
", na.rm=TRUE)", sep = ""))
}
tkfocus(CommanderWindow())
}
OKCancelHelp(helpSubject = "tapply", reset="statisticsTable", apply="statisticsTable")
tkgrid(getFrame(groupBox), labelRcmdr(variablesFrame, text = " "),
getFrame(responseBox), sticky = "nw")
tkgrid(variablesFrame, sticky = "w")
tkgrid(statFrame, sticky = "w")
tkgrid(buttonsFrame, sticky = "w")
dialogSuffix(rows = 3, columns = 1, focus = otherEntry)
}
correlationMatrix <- function (){
defaults <- list (initial.x = NULL, initial.correlations = "Pearson", initial.pvaluesVar="0", initial.use="complete")
dialog.values <- getDialog ("correlationMatrix", defaults)
initializeDialog(title = gettextRcmdr("Correlation Matrix"))
xBox <- variableListBox(top, Numeric(), selectmode = "multiple",
title = gettextRcmdr("Variables (pick two or more)"),
initialSelection = varPosn (dialog.values$initial.x, "numeric"))
radioButtons(name = "correlations", buttons = c("pearson",
"spearman", "partial"), values = c("Pearson", "Spearman",
"partial"), labels = gettextRcmdr(c("Pearson product-moment",
"Spearman rank-order", "Partial")), title = gettextRcmdr("Type of Correlations"),
initialValue = dialog.values$initial.correlations)
radioButtons(name = "use", buttons = c("complete", "pairwise.complete"),
labels = gettextRcmdr(c("Complete observations", "Pairwise-complete observations")), title = gettextRcmdr("Observations to Use"),
initialValue = dialog.values$initial.use)
pvaluesFrame <- tkframe(top)
pvaluesVar <- tclVar(dialog.values$initial.pvaluesVar)
pvaluesCheckbox <- ttkcheckbutton(pvaluesFrame, variable = pvaluesVar)
onOK <- function() {
correlations <- tclvalue(correlationsVariable)
use <- tclvalue(useVariable)
x <- getSelection(xBox)
pvalues <- tclvalue(pvaluesVar)
if (2 > length(x)) {
errorCondition(recall = correlationMatrix, message = gettextRcmdr("Fewer than 2 variables selected."))
return()
}
if ((correlations == "partial") && (3 > length(x))) {
errorCondition(recall = correlationMatrix, message = gettextRcmdr("Fewer than 3 variables selected\nfor partial correlations."))
return()
}
closeDialog()
putDialog ("correlationMatrix", list (initial.x=x, initial.correlations=correlations,
initial.pvaluesVar=pvalues, initial.use=use))
x <- paste("\"", x, "\"", sep = "")
.activeDataSet <- ActiveDataSet()
if (correlations == "Pearson") {
if (pvalues == 0) {
doItAndPrint(paste("cor(", .activeDataSet, "[,c(",
paste(x, collapse = ","), ")], use=\"", use, "\")",
sep = ""))
}
else {
Library("Hmisc")
doItAndPrint(paste("rcorr.adjust(", .activeDataSet,
"[,c(", paste(x, collapse = ","), ")], type=\"pearson\", use=\"", use, "\")",
sep = ""))
}
}
else if (correlations == "Spearman") {
if (pvalues == 0) {
doItAndPrint(paste("cor(", .activeDataSet, "[,c(",
paste(x, collapse = ","), ")], method=\"spearman\", use=\"", use, "\")",
sep = ""))
}
else {
Library("Hmisc")
doItAndPrint(paste("rcorr.adjust(", .activeDataSet,
"[,c(", paste(x, collapse = ","), ")], type=\"spearman\", use=\"", use, "\")",
sep = ""))
}
}
else if (pvalues == 0){
doItAndPrint(paste("partial.cor(", .activeDataSet,
"[,c(", paste(x, collapse = ","), ")], use=\"", use, "\")",
sep = ""))
}
else {
doItAndPrint(paste("partial.cor(", .activeDataSet,
"[,c(", paste(x, collapse = ","), ")], tests=TRUE, use=\"", use, "\")",
sep = ""))
}
tkfocus(CommanderWindow())
}
OKCancelHelp(helpSubject = "rcorr.adjust", reset="correlationMatrix", apply="correlationMatrix")
tkgrid(getFrame(xBox), sticky = "nw")
tkgrid(correlationsFrame, sticky = "w")
tkgrid(useFrame, sticky="w")
tkgrid(labelRcmdr(pvaluesFrame, text = gettextRcmdr("Pairwise p-values"), fg=getRcmdr("title.color")),
pvaluesCheckbox, sticky = "w")
tkgrid(pvaluesFrame, sticky = "w")
tkgrid(buttonsFrame, sticky = "w")
dialogSuffix(rows = 5, columns = 1)
}
# the following dialog contributed by Stefano Calza, modified by J. Fox
correlationTest <- function(){
defaults <- list(initial.x=NULL,initial.correlations="pearson",initial.alternative ="two.sided")
dialog.values <- getDialog("correlationTest", defaults)
initializeDialog(title=gettextRcmdr("Correlation Test"))
xBox <- variableListBox(top, Numeric(), selectmode="multiple", title=gettextRcmdr("Variables (pick two)"),initialSelection=varPosn(dialog.values$initial.x, "numeric"))
radioButtons(name="correlations", buttons=c("pearson", "spearman", "kendall"),
labels=gettextRcmdr(c("Pearson product-moment", "Spearman rank-order", "Kendall's tau")),
initialValue=dialog.values$initial.correlations,
title=gettextRcmdr("Type of Correlation"))
radioButtons(name="alternative", buttons=c("two.sided", "less", "greater"),
values=c("two.sided", "less", "greater"),
initialValue=dialog.values$initial.alternative,
labels=gettextRcmdr(c("Two-sided", "Correlation < 0", "Correlation > 0")),
title=gettextRcmdr("Alternative Hypothesis"))
onOK <- function(){
alternative <- as.character(tclvalue(alternativeVariable))
correlations <- as.character(tclvalue(correlationsVariable))
x <- getSelection(xBox)
putDialog("correlationTest", list(initial.alternative=alternative, initial.correlations=correlations, initial.x=x))
if (2 > length(x)) {
errorCondition(recall=correlationTest,
message=gettextRcmdr("Fewer than 2 variables selected."))
return()
}
if(2 < length(x)) {
errorCondition(recall=correlationTest,
message=gettextRcmdr("More than 2 variables selected."))
return()
}
closeDialog()
.activeDataSet <- ActiveDataSet()
command <- paste("cor.test(", .activeDataSet, "$", x[1], ", ", .activeDataSet, "$", x[2],
', alternative="', alternative, '", method="', correlations, '")', sep="")
doItAndPrint(command)
tkfocus(CommanderWindow())
}
OKCancelHelp(helpSubject="cor.test", reset="correlationTest", apply="correlationTest")
tkgrid(getFrame(xBox), sticky="nw")
tkgrid(labelRcmdr(top, text=""))
tkgrid(correlationsFrame,alternativeFrame, sticky="w")
tkgrid(buttonsFrame,columnspan=2,sticky="w")
dialogSuffix(rows=4, columns=1)
}
countMissing <- function(){
command <- paste("sapply(", activeDataSet(),
", function(x)(sum(is.na(x)))) # NA counts", sep="")
doItAndPrint(command)
invisible(NULL)
}
ShapiroTest <- function () {
defaults <- list (initial.var = NULL)
dialog.values <- getDialog ("ShapiroTest", defaults)
initializeDialog(title = gettextRcmdr("Shapiro-Wilk Test for Normality"))
variableBox <- variableListBox(top, Numeric(), title = gettextRcmdr("Variable (pick one)"),
initialSelection = varPosn (dialog.values$initial.var, "numeric"))
onOK <- function() {
var <- getSelection(variableBox)
putDialog ("ShapiroTest", list (initial.var = var))
if (length(var) == 0) {
errorCondition(recall = ShapiroTest, message = gettextRcmdr("You must select a variable."))
return()
}
closeDialog()
doItAndPrint(paste("shapiro.test(", ActiveDataSet(),
"$", var, ")", sep = ""))
tkfocus(CommanderWindow())
}
OKCancelHelp(helpSubject = "shapiro.test", reset = "ShapiroTest", apply = "ShapiroTest")
tkgrid(getFrame(variableBox), sticky = "nw")
tkgrid(buttonsFrame, sticky = "w")
dialogSuffix(rows = 2, columns = 1)
}
Try the Rcmdr2 package in your browser
Any scripts or data that you put into this service are public.
Rcmdr2 documentation built on May 2, 2019, 6:49 p.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Defines functions summarizeDataSet numericalSummaries correlationTest countMissing
# Statistics Menu dialogs
# last modified 2013-05-05 by J. Fox
# Summaries menu
summarizeDataSet <- function(){
nvar <- length(Variables())
.activeDataSet <- ActiveDataSet()
if (nvar > 10){
response <- RcmdrTkmessageBox(message=sprintf(gettextRcmdr("There are %d variables in the data set %s.\nDo you want to proceed?"), nvar, .activeDataSet),
icon="question", type="okcancel", default="cancel")
if ("cancel" == tclvalue(response)) {
tkfocus(CommanderWindow())
return()
}
}
doItAndPrint(paste("summary(", .activeDataSet, ")", sep=""))
}
numericalSummaries <- function(){ # dialog memory 2011-06-27 J. Fox
Library("abind")
Library("e1071")
defaults <- list(initial.x=NULL, initial.mean="1", initial.sd="1", initial.IQR="1", initial.cv="0",
initial.quantiles.variable="1",
initial.quantiles="0, .25, .5, .75, 1",
initial.skewness="0", initial.kurtosis="0", initial.type="2",
initial.group=NULL)
dialog.values <- getDialog("numericalSummaries", defaults)
initial.group <- dialog.values$initial.group
initializeDialog(title=gettextRcmdr("Numerical Summaries"))
notebook <- ttknotebook(top, width=600)
dataTab <- tkframe(top)
statisticsTab <- tkframe(top)
xBox <- variableListBox(dataTab, Numeric(), selectmode="multiple", title=gettextRcmdr("Variables (pick one or more)"),
initialSelection=varPosn(dialog.values$initial.x, "numeric"))
checkBoxes(window = statisticsTab, frame="checkBoxFrame", boxes=c("mean", "sd", "IQR", "cv"),
initialValues=c(dialog.values$initial.mean, dialog.values$initial.sd, dialog.values$initial.IQR, dialog.values$initial.cv),
labels=gettextRcmdr(c("Mean", "Standard Deviation", "Interquartile Range", "Coefficient of Variation")))
skFrame <- tkframe(statisticsTab)
checkBoxes(window = skFrame, frame="skCheckBoxFrame", boxes=c("skewness", "kurtosis"),
initialValues=c(dialog.values$initial.skewness, dialog.values$initial.kurtosis),
labels=gettextRcmdr(c("Skewness", "Kurtosis")))
radioButtons(window = skFrame, name="typeButtons", buttons=c("b1", "b2", "b3"), values=c("1", "2", "3"),
initialValue=dialog.values$initial.type,
labels=gettextRcmdr(c("Type 1", "Type 2", "Type 3")))
quantilesVariable <- tclVar(dialog.values$initial.quantiles.variable)
quantilesFrame <- tkframe(statisticsTab)
quantilesCheckBox <- tkcheckbutton(quantilesFrame, variable=quantilesVariable)
quantiles <- tclVar(dialog.values$initial.quantiles)
quantilesEntry <- ttkentry(quantilesFrame, width="20", textvariable=quantiles)
groupsBox(recall=numericalSummaries, label=gettextRcmdr("Summarize by:"),
initialLabel=if (is.null(initial.group)) gettextRcmdr("Summarize by groups")
else paste(gettextRcmdr("Summarize by:"), initial.group),
initialGroup=initial.group, window = dataTab)
onOK <- function(){
x <- getSelection(xBox)
quants <- tclvalue(quantiles)
meanVar <- tclvalue(meanVariable)
sdVar <- tclvalue(sdVariable)
IQRVar <- tclvalue(IQRVariable)
cvVar <- tclvalue(cvVariable)
quantsVar <- tclvalue(quantilesVariable)
skewnessVar <- tclvalue(skewnessVariable)
kurtosisVar <- tclvalue(kurtosisVariable)
typeVar <- tclvalue(typeButtonsVariable)
putDialog("numericalSummaries", list(
initial.x=x, initial.mean=meanVar, initial.sd=sdVar, initial.IQR=IQRVar, initial.cv=cvVar,
initial.quantiles.variable=quantsVar, initial.quantiles=quants,
initial.skewness=skewnessVar, initial.kurtosis=kurtosisVar, initial.type=typeVar,
initial.group=if (.groups != FALSE) .groups else NULL
))
if (length(x) == 0){
errorCondition(recall=numericalSummaries, message=gettextRcmdr("You must select a variable."))
return()
}
closeDialog()
quants <- paste("c(", gsub(",+", ",", gsub(" ", ",", quants)), ")", sep="")
.activeDataSet <- ActiveDataSet()
vars <- if (length(x) == 1) paste('"', x, '"', sep="")
else paste("c(", paste('"', x, '"', collapse=", ", sep=""), ")", sep="")
vars <- paste(.activeDataSet, "[,", vars, "]", sep="")
stats <- paste("c(",
paste(c('"mean"', '"sd"', '"IQR"', '"quantiles"', '"cv"', '"skewness"', '"kurtosis"')
[c(meanVar, sdVar, IQRVar, quantsVar, cvVar, skewnessVar, kurtosisVar) == 1],
collapse=", "), ")", sep="")
if (stats == "c()"){
errorCondition(recall=numericalSummaries, message=gettextRcmdr("No statistics selected."))
return()
}
type.text <- if (skewnessVar == 1 || kurtosisVar == 1) paste(', type="', typeVar, '"', sep="") else ""
command <- if (.groups != FALSE) {
grps <- paste(.activeDataSet, "$", .groups, sep="")
paste("numSummary(", vars, ", groups=", grps, ", statistics=", stats,
", quantiles=", quants, type.text, ")", sep="")
}
else paste("numSummary(", vars, ", statistics=", stats,
", quantiles=", quants, type.text, ")", sep="")
doItAndPrint(command)
tkfocus(CommanderWindow())
}
OKCancelHelp(helpSubject="numSummary", reset="numericalSummaries", apply ="numericalSummaries")
tkgrid(getFrame(xBox), sticky="nw")
tkadd(notebook, dataTab, text=gettextRcmdr("Data"), padding=6)
tkadd(notebook, statisticsTab, text=gettextRcmdr("Statistics"), padding=6)
tkgrid(checkBoxFrame, sticky="w")
tkgrid(ttklabel(statisticsTab, text=""))
tkgrid(skCheckBoxFrame, typeButtonsFrame, sticky="nw")
tkgrid(skFrame, sticky="w")
tkgrid(labelRcmdr(quantilesFrame, text=gettextRcmdr("Quantiles")), quantilesCheckBox,
labelRcmdr(quantilesFrame, text=gettextRcmdr(" quantiles:")), quantilesEntry, sticky="w")
tkgrid(ttklabel(statisticsTab, text=""))
tkgrid(quantilesFrame, sticky="w")
tkgrid(ttklabel(dataTab, text=""))
tkgrid(groupsFrame, sticky = "w", padx=6)
tkgrid(notebook, sticky="nsew")
tkgrid(buttonsFrame, sticky="w")
dialogSuffix(rows=7, columns=1)
}
frequencyDistribution <- function () {
defaults <- list (initial.x = NULL, initial.goodnessOfFit = "0")
dialog.values <- getDialog ("frequencyDistribution", defaults)
initializeDialog(title = gettextRcmdr("Frequency Distributions"))
xBox <- variableListBox(top, Factors(), selectmode = "multiple",
title = gettextRcmdr("Variables (pick one or more)"),
initialSelection = varPosn (dialog.values$initial.x, "factor"))
optionsFrame <- tkframe(top)
goodnessOfFitVariable <- tclVar(dialog.values$initial.goodnessOfFit)
goodnessOfFitCheckBox <- ttkcheckbutton(optionsFrame, variable = goodnessOfFitVariable)
onOK <- function() {
x <- getSelection(xBox)
if (length(x) == 0) {
errorCondition(recall = frequencyDistribution, message = gettextRcmdr("You must select a variable."))
return()
}
goodnessOfFit <- tclvalue(goodnessOfFitVariable)
putDialog ("frequencyDistribution", list (initial.x = x, initial.goodnessOfFit = goodnessOfFit))
if (length(x) > 1 && goodnessOfFit == "1") {
errorCondition(recall = frequencyDistribution, message = gettextRcmdr("Goodness-of-fit test not available when more than one variable is selected."))
return()
}
closeDialog()
.activeDataSet <- ActiveDataSet()
for (variable in x) {
command <- paste("table(", .activeDataSet, "$", variable,
")", sep = "")
# logger(paste(".Table <-", command))
# assign(".Table", justDoIt(command), envir = .GlobalEnv)
doItAndPrint(paste(".Table <-", command))
doItAndPrint(paste(".Table # counts for", variable))
doItAndPrint(paste("round(100*.Table/sum(.Table), 2) # percentages for",
variable))
}
env <- environment()
if (goodnessOfFit == 1) {
initializeDialog(subwin, title = gettextRcmdr("Goodness-of-Fit Test"))
hypothesisFrame <- tkframe(subwin)
levs <- eval(parse(text = paste("levels(", .activeDataSet,
"$", x, ")", sep = "")))
n.levs <- length(levs)
assign(".entry.1", tclVar(paste("1/", n.levs, sep = "")),
envir = env)
make.entries <- "labelRcmdr(hypothesisFrame, text='Hypothesized probabilities: ')"
make.lev.names <- "labelRcmdr(hypothesisFrame, text='Factor levels:')"
for (i in 1:n.levs) {
entry.varname <- paste(".entry.", i, sep = "")
assign(entry.varname, tclVar(paste("1/", n.levs,
sep = "")), envir = env)
make.entries <- paste(make.entries, ", ", "ttkentry(hypothesisFrame, width='5', textvariable=",
entry.varname, ")", sep = "")
make.lev.names <- paste(make.lev.names, ", labelRcmdr(hypothesisFrame, text='",
levs[i], "')", sep = "")
}
eval(parse(text = paste("tkgrid(", make.lev.names,
", sticky='w')", sep = "")), envir = env)
eval(parse(text = paste("tkgrid(", make.entries,
", stick='w')", sep = "")), envir = env)
tkgrid(hypothesisFrame, sticky = "w")
onOKsub <- function() {
probs <- rep(NA, n.levs)
for (i in 1:n.levs) {
entry.varname <- paste(".entry.", i, sep = "")
res <- try(entry <- eval(parse(text = eval(parse(text = paste("tclvalue(",
entry.varname, ")", sep = "")), envir = env))),
silent = TRUE)
if (class(res) == "try-error") {
errorCondition(subwin, message = gettextRcmdr("Invalid entry."))
return()
}
if (length(entry) == 0) {
errorCondition(subwin, message = gettextRcmdr("Missing entry."))
return()
}
opts <- options(warn = -1)
probs[i] <- as.numeric(entry)
options(opts)
}
probs <- na.omit(probs)
if (length(probs) != n.levs) {
errorCondition(subwin, message = sprintf(gettextRcmdr("Number of valid entries (%d)\nnot equal to number levels (%d)."),
length(probs), n.levs))
return()
}
if (any(probs < 0)) {
errorCondition(subwin, message = gettextRcmdr("Negative probabilities not allowed."))
return()
}
if (abs(sum(probs) - 1) > 0.001) {
Message(message = gettextRcmdr("Probabilities rescaled to sum to 1."),
type = "warning")
probs <- probs/sum(probs)
}
closeDialog(subwin)
command <- paste("c(", paste(probs, collapse = ","),
")", sep = "")
# logger(paste(".Probs <-", command))
# assign(".Probs", justDoIt(command), envir = .GlobalEnv)
doItAndPrint(paste(".Probs <-", command))
doItAndPrint("chisq.test(.Table, p=.Probs)")
logger("remove(.Probs)")
remove(.Probs, envir = .GlobalEnv)
}
subOKCancelHelp(subwin)
tkgrid(subButtonsFrame, sticky = "w")
dialogSuffix(subwin, rows = 2, columns = 1, onOK = onOKsub,
focus = subwin)
}
logger("remove(.Table)")
remove(.Table, envir = .GlobalEnv)
tkfocus(CommanderWindow())
}
OKCancelHelp(helpSubject = "table", reset = "frequencyDistribution")
tkgrid(getFrame(xBox), sticky = "nw")
tkgrid(labelRcmdr(optionsFrame, text = gettextRcmdr("Chi-square goodness-of-fit test (for one variable only)")),
goodnessOfFitCheckBox, sticky = "w")
tkgrid(optionsFrame, sticky = "w")
tkgrid(buttonsFrame, sticky = "w")
dialogSuffix(rows = 3, columns = 2)
}
statisticsTable <- function () {
defaults <- list (initial.group=NULL, initial.response=NULL, initial.statistic="mean", initial.other = "")
dialog.values <- getDialog ("statisticsTable", defaults)
initializeDialog(title = gettextRcmdr("Table of Statistics"))
variablesFrame <- tkframe(top)
groupBox <- variableListBox(variablesFrame, Factors(), selectmode = "multiple",
title = gettextRcmdr("Factors (pick one or more)"),
initialSelection = varPosn(dialog.values$initial.group,"factor"))
responseBox <- variableListBox(variablesFrame, Numeric(), selectmode = "multiple",
initialSelection = varPosn(dialog.values$initial.response, "numeric"),
title = gettextRcmdr("Response variables (pick one or more)"))
statFrame <- tkframe(top)
radioButtons(statFrame, name = "statistic", buttons = c("mean", "median", "sd", "IQR", "other"),
labels = gettextRcmdr(c("Mean", "Median", "Standard deviation", "Interquartile range", "Other (specify)")),
initialValue = dialog.values$initial.statistic,
title = gettextRcmdr("Statistic"))
otherVariable <- tclVar(dialog.values$initial.other)
otherEntry <- ttkentry(statFrame, width = "20", textvariable = otherVariable)
tkgrid(statisticFrame, labelRcmdr(statFrame, text =" "), otherEntry, sticky = "sw")
onOK <- function() {
groups <- getSelection(groupBox)
if (0 == length(groups)) {
errorCondition(recall = statisticsTable, message = gettextRcmdr("No factors selected."))
return()
}
responses <- getSelection(responseBox)
if (0 == length(responses)) {
errorCondition(recall = statisticsTable, message = gettextRcmdr("You must select a response variable."))
return()
}
stat <- statistic <- tclvalue(statisticVariable)
if (statistic == "other")
statistic <- tclvalue(otherVariable)
putDialog ("statisticsTable", list(initial.group=groups, initial.response=responses,
initial.statistic=stat, initial.other = if(stat == "other") statistic else ""))
closeDialog()
.activeDataSet <- ActiveDataSet()
groups.list <- paste(paste(groups, "=", .activeDataSet,
"$", groups, sep = ""), collapse = ", ")
for (response in responses) {
if (length(responses) > 1)
doItAndPrint(paste("# Table for ", response,
":", sep = ""))
doItAndPrint(paste("tapply(", .activeDataSet, "$",
response, ", list(", groups.list, "), ", statistic,
", na.rm=TRUE)", sep = ""))
}
tkfocus(CommanderWindow())
}
OKCancelHelp(helpSubject = "tapply", reset="statisticsTable", apply="statisticsTable")
tkgrid(getFrame(groupBox), labelRcmdr(variablesFrame, text = " "),
getFrame(responseBox), sticky = "nw")
tkgrid(variablesFrame, sticky = "w")
tkgrid(statFrame, sticky = "w")
tkgrid(buttonsFrame, sticky = "w")
dialogSuffix(rows = 3, columns = 1, focus = otherEntry)
}
correlationMatrix <- function (){
defaults <- list (initial.x = NULL, initial.correlations = "Pearson", initial.pvaluesVar="0", initial.use="complete")
dialog.values <- getDialog ("correlationMatrix", defaults)
initializeDialog(title = gettextRcmdr("Correlation Matrix"))
xBox <- variableListBox(top, Numeric(), selectmode = "multiple",
title = gettextRcmdr("Variables (pick two or more)"),
initialSelection = varPosn (dialog.values$initial.x, "numeric"))
radioButtons(name = "correlations", buttons = c("pearson",
"spearman", "partial"), values = c("Pearson", "Spearman",
"partial"), labels = gettextRcmdr(c("Pearson product-moment",
"Spearman rank-order", "Partial")), title = gettextRcmdr("Type of Correlations"),
initialValue = dialog.values$initial.correlations)
radioButtons(name = "use", buttons = c("complete", "pairwise.complete"),
labels = gettextRcmdr(c("Complete observations", "Pairwise-complete observations")), title = gettextRcmdr("Observations to Use"),
initialValue = dialog.values$initial.use)
pvaluesFrame <- tkframe(top)
pvaluesVar <- tclVar(dialog.values$initial.pvaluesVar)
pvaluesCheckbox <- ttkcheckbutton(pvaluesFrame, variable = pvaluesVar)
onOK <- function() {
correlations <- tclvalue(correlationsVariable)
use <- tclvalue(useVariable)
x <- getSelection(xBox)
pvalues <- tclvalue(pvaluesVar)
if (2 > length(x)) {
errorCondition(recall = correlationMatrix, message = gettextRcmdr("Fewer than 2 variables selected."))
return()
}
if ((correlations == "partial") && (3 > length(x))) {
errorCondition(recall = correlationMatrix, message = gettextRcmdr("Fewer than 3 variables selected\nfor partial correlations."))
return()
}
closeDialog()
putDialog ("correlationMatrix", list (initial.x=x, initial.correlations=correlations,
initial.pvaluesVar=pvalues, initial.use=use))
x <- paste("\"", x, "\"", sep = "")
.activeDataSet <- ActiveDataSet()
if (correlations == "Pearson") {
if (pvalues == 0) {
doItAndPrint(paste("cor(", .activeDataSet, "[,c(",
paste(x, collapse = ","), ")], use=\"", use, "\")",
sep = ""))
}
else {
Library("Hmisc")
doItAndPrint(paste("rcorr.adjust(", .activeDataSet,
"[,c(", paste(x, collapse = ","), ")], type=\"pearson\", use=\"", use, "\")",
sep = ""))
}
}
else if (correlations == "Spearman") {
if (pvalues == 0) {
doItAndPrint(paste("cor(", .activeDataSet, "[,c(",
paste(x, collapse = ","), ")], method=\"spearman\", use=\"", use, "\")",
sep = ""))
}
else {
Library("Hmisc")
doItAndPrint(paste("rcorr.adjust(", .activeDataSet,
"[,c(", paste(x, collapse = ","), ")], type=\"spearman\", use=\"", use, "\")",
sep = ""))
}
}
else if (pvalues == 0){
doItAndPrint(paste("partial.cor(", .activeDataSet,
"[,c(", paste(x, collapse = ","), ")], use=\"", use, "\")",
sep = ""))
}
else {
doItAndPrint(paste("partial.cor(", .activeDataSet,
"[,c(", paste(x, collapse = ","), ")], tests=TRUE, use=\"", use, "\")",
sep = ""))
}
tkfocus(CommanderWindow())
}
OKCancelHelp(helpSubject = "rcorr.adjust", reset="correlationMatrix", apply="correlationMatrix")
tkgrid(getFrame(xBox), sticky = "nw")
tkgrid(correlationsFrame, sticky = "w")
tkgrid(useFrame, sticky="w")
tkgrid(labelRcmdr(pvaluesFrame, text = gettextRcmdr("Pairwise p-values"), fg=getRcmdr("title.color")),
pvaluesCheckbox, sticky = "w")
tkgrid(pvaluesFrame, sticky = "w")
tkgrid(buttonsFrame, sticky = "w")
dialogSuffix(rows = 5, columns = 1)
}
# the following dialog contributed by Stefano Calza, modified by J. Fox
correlationTest <- function(){
defaults <- list(initial.x=NULL,initial.correlations="pearson",initial.alternative ="two.sided")
dialog.values <- getDialog("correlationTest", defaults)
initializeDialog(title=gettextRcmdr("Correlation Test"))
xBox <- variableListBox(top, Numeric(), selectmode="multiple", title=gettextRcmdr("Variables (pick two)"),initialSelection=varPosn(dialog.values$initial.x, "numeric"))
radioButtons(name="correlations", buttons=c("pearson", "spearman", "kendall"),
labels=gettextRcmdr(c("Pearson product-moment", "Spearman rank-order", "Kendall's tau")),
initialValue=dialog.values$initial.correlations,
title=gettextRcmdr("Type of Correlation"))
radioButtons(name="alternative", buttons=c("two.sided", "less", "greater"),
values=c("two.sided", "less", "greater"),
initialValue=dialog.values$initial.alternative,
labels=gettextRcmdr(c("Two-sided", "Correlation < 0", "Correlation > 0")),
title=gettextRcmdr("Alternative Hypothesis"))
onOK <- function(){
alternative <- as.character(tclvalue(alternativeVariable))
correlations <- as.character(tclvalue(correlationsVariable))
x <- getSelection(xBox)
putDialog("correlationTest", list(initial.alternative=alternative, initial.correlations=correlations, initial.x=x))
if (2 > length(x)) {
errorCondition(recall=correlationTest,
message=gettextRcmdr("Fewer than 2 variables selected."))
return()
}
if(2 < length(x)) {
errorCondition(recall=correlationTest,
message=gettextRcmdr("More than 2 variables selected."))
return()
}
closeDialog()
.activeDataSet <- ActiveDataSet()
command <- paste("cor.test(", .activeDataSet, "$", x[1], ", ", .activeDataSet, "$", x[2],
', alternative="', alternative, '", method="', correlations, '")', sep="")
doItAndPrint(command)
tkfocus(CommanderWindow())
}
OKCancelHelp(helpSubject="cor.test", reset="correlationTest", apply="correlationTest")
tkgrid(getFrame(xBox), sticky="nw")
tkgrid(labelRcmdr(top, text=""))
tkgrid(correlationsFrame,alternativeFrame, sticky="w")
tkgrid(buttonsFrame,columnspan=2,sticky="w")
dialogSuffix(rows=4, columns=1)
}
countMissing <- function(){
command <- paste("sapply(", activeDataSet(),
", function(x)(sum(is.na(x)))) # NA counts", sep="")
doItAndPrint(command)
invisible(NULL)
}
ShapiroTest <- function () {
defaults <- list (initial.var = NULL)
dialog.values <- getDialog ("ShapiroTest", defaults)
initializeDialog(title = gettextRcmdr("Shapiro-Wilk Test for Normality"))
variableBox <- variableListBox(top, Numeric(), title = gettextRcmdr("Variable (pick one)"),
initialSelection = varPosn (dialog.values$initial.var, "numeric"))
onOK <- function() {
var <- getSelection(variableBox)
putDialog ("ShapiroTest", list (initial.var = var))
if (length(var) == 0) {
errorCondition(recall = ShapiroTest, message = gettextRcmdr("You must select a variable."))
return()
}
closeDialog()
doItAndPrint(paste("shapiro.test(", ActiveDataSet(),
"$", var, ")", sep = ""))
tkfocus(CommanderWindow())
}
OKCancelHelp(helpSubject = "shapiro.test", reset = "ShapiroTest", apply = "ShapiroTest")
tkgrid(getFrame(variableBox), sticky = "nw")
tkgrid(buttonsFrame, sticky = "w")
dialogSuffix(rows = 2, columns = 1)
}
Try the Rcmdr2 package in your browser
Any scripts or data that you put into this service are public.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.