# R Commander Menu Definitions # last modified 2016-07-19 by J. Fox # type menu/item operation/parent label command/menu activation install? menu fileMenu topMenu "" "" "" "" item fileMenu command "Change working directory..." Setwd "" "" item fileMenu separator "" "" "" "" item fileMenu command "Open script file..." loadLog "" "" item fileMenu command "Save script..." saveLog "" "" item fileMenu command "Save script as..." saveLogAs "" "" item fileMenu separator "" "" "" "getRcmdr('use.markdown') || getRcmdr('use.knitr')" item fileMenu command "Open R Markdown file..." loadRmd "" "getRcmdr('use.markdown')" item fileMenu command "Open knitr file..." loadRnw "" "getRcmdr('use.knitr')" item fileMenu command "Save R Markdown file..." saveRmd "" "getRcmdr('use.markdown')" item fileMenu command "Save knitr file..." saveRnw "" "getRcmdr('use.knitr')" item fileMenu command "Save R Markdown file as..." saveRmdAs "" "getRcmdr('use.markdown')" item fileMenu command "Save knitr file as..." saveRnwAs "" "getRcmdr('use.knitr')" item fileMenu separator "" "" "" "" item fileMenu command "Save output..." saveOutput "" "" item fileMenu command "Save output as..." saveOutputAs "" "" item fileMenu separator "" "" "" "" item fileMenu command "Save R workspace..." saveWorkspace "" "" item fileMenu command "Save R workspace as..." saveWorkspaceAs "" "" item fileMenu separator "" "" "" "" menu exitMenu fileMenu "" "" "" "" item exitMenu command "From Commander" CloseCommander "" "" item exitMenu command "From Commander and R" closeCommanderAndR "" "" item fileMenu cascade "Exit" exitMenu "" "" item topMenu cascade "File" fileMenu "" "" menu editMenu topMenu "" "" "" "" item editMenu command "Edit R Markdown document" editMarkdown "" "MarkdownP()" item editMenu command "Edit knitr document" editKnitr "" "knitrP()" item editMenu command "Remove last Markdown command block" removeLastRmdBlock "" "MarkdownP()" item editMenu command "Remove last knitr command block" removeLastRnwBlock "" "knitrP()" item editMenu separator "" "" "" "" item editMenu command "Cut" onCut "" "" item editMenu command "Copy" onCopy "" "" item editMenu command "Paste" onPaste "" "" item editMenu command "Delete" onDelete "" "" item editMenu separator "" "" "" "" item editMenu command "Find..." onFind "" "" item editMenu command "Select all" onSelectAll "" "" item editMenu separator "" "" "" "" item editMenu command "Undo" onUndo "" "" item editMenu command "Redo" onRedo "" "" item editMenu separator "" "" "" "" item editMenu command "Clear window" onClear "" "" item topMenu cascade "Edit" editMenu "" "" menu dataMenu topMenu "" "" "" "" item dataMenu command "New data set..." newDataSet "" "getRcmdr('editDataset.threshold') > 0" item dataMenu command "Load data set..." loadDataSet "" "" item dataMenu command "Merge data sets..." mergeDataSets "dataSetsP(2)" "packageAvailable('car') && packageAvailable('RcmdrMisc')" item dataMenu separator "" "" "" "" menu importMenu dataMenu "" "" "" "" item importMenu command "from text file, clipboard, or URL..." readDataSet "" "" item importMenu command "from SPSS data set..." importSPSS "" "packageAvailable('foreign')" item importMenu command "from SAS xport file..." importSAS "" "packageAvailable('foreign')" item importMenu command "from Minitab data set..." importMinitab "" "packageAvailable('foreign')" item importMenu command "from STATA data set..." importSTATA "" "packageAvailable('foreign')" # item importMenu command "from Excel, Access or dBase data set..." importRODBCtable "" "WindowsP() && packageAvailable('RODBC') && (.Platform$r_arch == 'i386')" # item importMenu command "from Excel file..." importExcel "" "packageAvailable('XLConnect') && (!WindowsP() | (.Platform$r_arch != 'i386')) && hasJava()" item importMenu command "from Excel file..." importExcel "" "packageAvailable('readxl')" item dataMenu cascade "Import data" importMenu "" "" menu packagesMenu dataMenu "" "" "" "" item packagesMenu command "List data sets in packages" listDataSetsInPackages "" "" item packagesMenu command "Read data set from an attached package..." readDataFromPackage "" "" item dataMenu cascade "Data in packages" packagesMenu "" "" menu activeMenu dataMenu "" "" "" "" item activeMenu command "View data..." viewData "activeDataSetP()" "" item activeMenu command "Select active data set..." selectActiveDataSet "dataSetsP()" "" item activeMenu command "Refresh active data set" refreshActiveDataSet "activeDataSetP()" "" item activeMenu command "Help on active data set (if available)" helpDataSet "activeDataSetP()" "" item activeMenu command "Variables in active data set" variablesDataSet "activeDataSetP()" "" item activeMenu command "Set case names..." setCaseNames "activeDataSetP()" "" item activeMenu command "Subset active data set..." subsetDataSet "activeDataSetP()" "" item activeMenu command "Sort active data set..." sortDataSet "activeDataSetP()" "" item activeMenu command "Aggregate variables in active data set..." Aggregate "activeDataSetP() && factorsP()" "" item activeMenu command "Remove row(s) from active data set..." RemoveRows "activeDataSetP()" "" item activeMenu command "Stack variables in active data set..." Stack "activeDataSetP() && numericP(2)" "" item activeMenu command "Remove cases with missing data..." filterNA "activeDataSetP()" "" item activeMenu command "Save active data set..." saveDataSet "activeDataSetP()" "" item activeMenu command "Export active data set..." exportDataSet "activeDataSetP()" "" item dataMenu cascade "Active data set" activeMenu "" "" menu variablesMenu dataMenu "" "" "" "" item variablesMenu command "Recode variables..." RecodeDialog "activeDataSetP()" "packageAvailable('car')" item variablesMenu command "Compute new variable..." Compute "activeDataSetP()" "" item variablesMenu command "Add observation numbers to data set" addObsNumbers "activeDataSetP()" "" item variablesMenu command "Standardize variables..." standardize "numericP()" "" item variablesMenu command "Convert numeric variables to factors..." numericToFactor "numericP()" "" item variablesMenu command "Bin numeric variable..." binVariable "numericP()" "packageAvailable('RcmdrMisc')" item variablesMenu command "Reorder factor levels..." reorderFactor "factorsP()" "" item variablesMenu command "Drop unused factor levels..." dropUnusedFactorLevels "factorsP()" "" item variablesMenu command "Define contrasts for a factor..." setContrasts "factorsP()" "" item variablesMenu command "Rename variables..." renameVariables "activeDataSetP()" "" item variablesMenu command "Delete variables from data set ..." deleteVariable "activeDataSetP()" "" item dataMenu cascade "Manage variables in active data set" variablesMenu "" "" item topMenu cascade "Data" dataMenu "" "" menu statisticsMenu topMenu "" "" "" "" menu summariesMenu statisticsMenu "" "" "" "" item summariesMenu command "Active data set" summarizeDataSet "activeDataSetP()" "" item summariesMenu command "Numerical summaries..." numericalSummaries "numericP()" "packageAvailable('RcmdrMisc') && packageAvailable('abind')" item summariesMenu command "Frequency distributions..." frequencyDistribution "factorsP()" "" item summariesMenu command "Count missing observations" countMissing "activeDataSetP()" "" item summariesMenu command "Table of statistics..." statisticsTable "numericP() && factorsP()" "" item summariesMenu command "Correlation matrix..." correlationMatrix "numericP(2)" "packageAvailable('RcmdrMisc')" item summariesMenu command "Correlation test..." correlationTest "numericP(2)" "packageAvailable('RcmdrMisc')" # item summariesMenu command "Shapiro-Wilk test of normality..." ShapiroTest "numericP()" "" item summariesMenu command "Test of normality..." normalityTest "numericP()" "packageAvailable('nortest')" menu tablesMenu statisticsMenu "" "" "" "" item tablesMenu command "Two-way table..." twoWayTable "factorsP(2)" "packageAvailable('RcmdrMisc') && packageAvailable('abind')" item tablesMenu command "Multi-way table..." multiWayTable "factorsP(3)" "packageAvailable('RcmdrMisc') && packageAvailable('abind')" item tablesMenu command "Enter and analyze two-way table..." enterTable "" "packageAvailable('RcmdrMisc') && packageAvailable('abind')" menu meansMenu statisticsMenu "" "" "" "" item meansMenu command "Single-sample t-test..." singleSampleTTest "numericP()" "" item meansMenu command "Independent samples t-test..." independentSamplesTTest "numericP() && twoLevelFactorsP()" "" item meansMenu command "Paired t-test..." pairedTTest "numericP(2)" "" item meansMenu command "One-way ANOVA..." oneWayAnova "numericP() && factorsP()" "packageAvailable('multcomp') && packageAvailable('abind')" item meansMenu command "Multi-way ANOVA..." multiWayAnova "numericP() && factorsP()" "" menu proportionsMenu statisticsMenu "" "" "" "" item proportionsMenu command "Single-sample proportion test..." singleProportionTest "twoLevelFactorsP()" "" item proportionsMenu command "Two-sample proportions test..." twoSampleProportionsTest "twoLevelFactorsP(2)" "packageAvailable('abind')" menu variancesMenu statisticsMenu "" "" "" "" item variancesMenu command "Two-variances F-test..." twoVariancesFTest "numericP() && twoLevelFactorsP()" "" item variancesMenu command "Bartlett's test..." BartlettTest "numericP() && factorsP()" "" item variancesMenu command "Levene's test..." LeveneTest "numericP() && factorsP()" "packageAvailable('car')" menu nonparametricMenu statisticsMenu "" "" "" "" item nonparametricMenu command "Two-sample Wilcoxon test..." twoSampleWilcoxonTest "numericP() && twoLevelFactorsP()" "" item nonparametricMenu command "Single-sample Wilcoxon test..." onesampleWilcoxonTest "numericP()" "" item nonparametricMenu command "Paired-samples Wilcoxon test..." pairedWilcoxonTest "numericP(2)" "" item nonparametricMenu command "Kruskal-Wallis test..." KruskalWallisTest "numericP() && factorsP()" "" item nonparametricMenu command "Friedman rank-sum test..." FriedmanTest "numericP(2)" "" menu dimensionalMenu statisticsMenu "" "" "" "" item dimensionalMenu command "Scale reliability..." Reliability "numericP(3)" "packageAvailable('RcmdrMisc')" item dimensionalMenu command "Principal-components analysis..." principalComponents "numericP(2)" "" item dimensionalMenu command "Factor analysis..." factorAnalysis "numericP(3)" "" item dimensionalMenu command "Confirmatory factor analysis..." CFA "numericP(3)" "packageAvailable('sem')" menu clusterMenu dimensionalMenu "" "" "" "" item clusterMenu command "k-means cluster analysis..." kmeansClustering "numericP()" "packageAvailable('RcmdrMisc')" item clusterMenu command "Hierarchical cluster analysis..." hierarchicalCluster "numericP()" "packageAvailable('RcmdrMisc')" item clusterMenu command "Summarize hierarchical clustering..." hclustSummary "hclustSolutionsP()" "packageAvailable('RcmdrMisc')" item clusterMenu command "Add hierarchical clustering to data set..." appendHclustGroup "hclustSolutionsP()" "packageAvailable('RcmdrMisc')" item dimensionalMenu cascade "Cluster analysis" clusterMenu "" "" menu statModelsMenu statisticsMenu "" "" "" "" item statModelsMenu command "Linear regression..." linearRegressionModel "numericP(2)" "" item statModelsMenu command "Linear model..." linearModel "numericP()" "" item statModelsMenu command "Generalized linear model..." generalizedLinearModel "activeDataSetP()" "" item statModelsMenu command "Multinomial logit model..." multinomialLogitModel "factorsP()" "packageAvailable('nnet')" item statModelsMenu command "Ordinal regression model..." ordinalRegressionModel "factorsP()" "packageAvailable('MASS')" item topMenu cascade "Statistics" statisticsMenu "" "" item statisticsMenu cascade "Summaries" summariesMenu "" "" item statisticsMenu cascade "Contingency tables" tablesMenu "" "packageAvailable('abind')" item statisticsMenu cascade "Means" meansMenu "" "" item statisticsMenu cascade "Proportions" proportionsMenu "" "" item statisticsMenu cascade "Variances" variancesMenu "" "" item statisticsMenu cascade "Nonparametric tests" nonparametricMenu "" "" item statisticsMenu cascade "Dimensional analysis" dimensionalMenu "" "" item statisticsMenu cascade "Fit models" statModelsMenu "" "" menu graphsMenu topMenu "" "" "" "" item graphsMenu command "Color palette..." setPalette "" "" item graphsMenu separator "" "" "" "" item graphsMenu command "Index plot..." indexPlot "numericP()" "packageAvailable('RcmdrMisc')" item graphsMenu command "Dot plot..." DotPlot "numericP()" "packageAvailable('RcmdrMisc')" item graphsMenu command "Histogram..." Histogram "numericP()" "packageAvailable('RcmdrMisc')" item graphsMenu command "Density estimate..." DensityPlot "numericP()" "" item graphsMenu command "Stem-and-leaf display..." stemAndLeaf "numericP()" "packageAvailable('aplpack')" item graphsMenu command "Boxplot..." boxPlot "numericP()" "" item graphsMenu command "Quantile-comparison plot..." QQPlot "numericP()" "packageAvailable('car')" item graphsMenu separator "" "" "" "" item graphsMenu command "Scatterplot..." scatterPlot "numericP(2)" "packageAvailable('car')" item graphsMenu command "Scatterplot matrix..." scatterPlotMatrix "numericP(3)" "packageAvailable('car')" item graphsMenu command "Line graph..." linePlot "numericP(2)" "packageAvailable('RcmdrMisc')" item graphsMenu command "XY conditioning plot..." Xyplot "numericP(2)" "" item graphsMenu command "Plot of means..." PlotMeans "numericP() && factorsP()" "packageAvailable('RcmdrMisc')" item graphsMenu command "Strip chart..." stripChart "numericP()" "" item graphsMenu separator "" "" "" "" item graphsMenu command "Bar graph..." barGraph "factorsP()" "" item graphsMenu command "Pie chart..." pieChart "factorsP()" "packageAvailable('colorspace')" item graphsMenu separator "" "" "" "" menu ThreeDPlotMenu graphsMenu "" "" "" "packageAvailable('rgl')" item ThreeDPlotMenu command "3D scatterplot..." Scatter3D "numericP(3)" "packageAvailable('rgl')" item ThreeDPlotMenu command "Identify observations with mouse" Identify3D "rglLoaded() && 0 != rgl.cur() && !is.null(getRcmdr('Identify3d'))" "packageAvailable('rgl')" item ThreeDPlotMenu command "Save graph to file" saveRglGraph "rglLoaded() && 0 != rgl.cur()" "packageAvailable('rgl')" item graphsMenu cascade "3D graph" ThreeDPlotMenu "" "packageAvailable('rgl')" menu saveGraphsMenu graphsMenu "" "" "" "" item saveGraphsMenu command "as bitmap..." saveBitmap "dev.cur() != 1" "" item saveGraphsMenu command "as PDF/Postscript/EPS..." savePDF "dev.cur() != 1" "" item saveGraphsMenu command "3D RGL graph..." saveRglGraph "rglLoaded() && 0 != rgl.cur()" "packageAvailable('rgl')" item graphsMenu cascade "Save graph to file" saveGraphsMenu "" "" item topMenu cascade "Graphs" graphsMenu "" "" menu modelsMenu topMenu "" "" "" "" item modelsMenu command "Select active model..." selectActiveModel "modelsP()" "" item modelsMenu command "Summarize model" summarizeModel "activeModelP()" "" item modelsMenu command "Compare model coefficients..." compareCoefficients "modelsP(2)" "" item modelsMenu command "Add observation statistics to data..." addObservationStatistics "activeModelP()" "" item modelsMenu separator "" "" "" "" item modelsMenu command "Akaike Information Criterion (AIC)" aic "activeModelP()" "" item modelsMenu command "Bayesian Information Criterion (BIC)" bic "activeModelP()" "" item modelsMenu command "Stepwise model selection..." stepwiseRegression "aicP()" "packageAvailable('RcmdrMisc') && packageAvailable('MASS')" item modelsMenu command "Subset model selection..." subsetRegression "lmP()" "packageAvailable('leaps')" item modelsMenu separator "" "" "" "" item modelsMenu command "Confidence intervals..." confidenceIntervals "activeModelP()" "packageAvailable('MASS') && packageAvailable('abind')" item modelsMenu command "Bootstrap confidence intervals..." Bootstrap "activeModelP() && (glmP() || lmP())" "packageAvailable('boot')" item modelsMenu command "Delta method confidence interval..." DeltaMethodConfInt "activeModelP() && (!multinomP())" "" menu hypothesisMenu modelsMenu "" "" "" "" item modelsMenu cascade "Hypothesis tests" hypothesisMenu "" "" item hypothesisMenu command "ANOVA table..." anovaTable "activeModelP()" "packageAvailable('car')" item hypothesisMenu command "Compare two models..." compareModels "modelsP(2)" "" item hypothesisMenu command "Linear hypothesis..." testLinearHypothesis "activeModelP()" "packageAvailable('car')" item modelsMenu separator "" "" "" "" menu diagnosticsMenu modelsMenu "" "" "" "" item modelsMenu cascade "Numerical diagnostics" diagnosticsMenu "" "" item diagnosticsMenu command "Variance-inflation factors" VIF "(lmP() || glmP())" "packageAvailable('car')" item diagnosticsMenu command "Breusch-Pagan test for heteroscedasticity..." BreuschPaganTest "lmP()" "packageAvailable('lmtest')" item diagnosticsMenu command "Durbin-Watson test for autocorrelation..." DurbinWatsonTest "lmP()" "packageAvailable('lmtest')" item diagnosticsMenu command "RESET test for nonlinearity..." RESETtest "lmP()" "packageAvailable('lmtest')" item diagnosticsMenu command "Bonferroni outlier test" OutlierTest "(lmP() || glmP())" "packageAvailable('car')" menu modelsGraphsMenu modelsMenu "" "" "" "" item modelsMenu cascade "Graphs" modelsGraphsMenu "" "" item modelsGraphsMenu command "Basic diagnostic plots" plotModel "lmP() || glmP()" "" item modelsGraphsMenu command "Residual quantile-comparison plot..." residualQQPlot "lmP()" "packageAvailable('car')" item modelsGraphsMenu command "Component+residual plots" CRPlots "(lmP() || glmP())" "packageAvailable('car')" item modelsGraphsMenu command "Added-variable plots" AVPlots "(lmP() || glmP())" "packageAvailable('car')" item modelsGraphsMenu command "Influence plot" InfluencePlot "(lmP() || glmP())" "packageAvailable('car')" item modelsGraphsMenu command "Effect plots" effectPlots "(lmP() || glmP()) || polrP() || multinomP()" "packageAvailable('effects')" item topMenu cascade "Models" modelsMenu "" "" # Distributions menu distributionsMenu topMenu "" "" "" "" menu continuousMenu distributionsMenu "" "" "" "" menu discreteMenu distributionsMenu "" "" "" "" item distributionsMenu command "Set random number generator seed..." setRandomSeed "" "" # Normal distribution menu normalMenu continuousMenu "" "" "" "" item continuousMenu cascade "Normal distribution" normalMenu "" "" item normalMenu command "Normal quantiles..." normalQuantiles "" "" item normalMenu command "Normal probabilities..." normalProbabilities "" "" item normalMenu command "Plot normal distribution..." normalDistributionPlot "" "packageAvailable('RcmdrMisc')" item normalMenu command "Sample from normal distribution..." normalDistributionSamples "" "" # t distribution menu tMenu continuousMenu "" "" "" "" item continuousMenu cascade "t distribution" tMenu "" "" item tMenu command "t quantiles..." tQuantiles "" "" item tMenu command "t probabilities..." tProbabilities "" "" item tMenu command "Plot t distribution..." tDistributionPlot "" "packageAvailable('RcmdrMisc')" item tMenu command "Sample from t distribution..." tDistributionSamples "" "" # Chi-square distribution menu chisqMenu continuousMenu "" "" "" "" item continuousMenu cascade "Chi-squared distribution" chisqMenu "" "" item chisqMenu command "Chi-squared quantiles..." chisqQuantiles "" "" item chisqMenu command "Chi-squared probabilities..." chisqProbabilities "" "" item chisqMenu command "Plot chi-squared distribution..." chisqDistributionPlot "" "packageAvailable('RcmdrMisc')" item chisqMenu command "Sample from chi-squared distribution..." chisqDistributionSamples "" "" # F distribution menu FMenu continuousMenu "" "" "" "" item continuousMenu cascade "F distribution" FMenu "" "" item FMenu command "F quantiles..." FQuantiles "" "" item FMenu command "F probabilities..." FProbabilities "" "" item FMenu command "Plot F distribution..." FDistributionPlot "" "packageAvailable('RcmdrMisc')" item FMenu command "Sample from F distribution..." FDistributionSamples "" "" # Exponential distribution menu exponentialMenu continuousMenu "" "" "" "" item continuousMenu cascade "Exponential distribution" exponentialMenu "" "" item exponentialMenu command "Exponential quantiles..." exponentialQuantiles "" "" item exponentialMenu command "Exponential probabilities..." exponentialProbabilities "" "" item exponentialMenu command "Plot exponential distribution..." exponentialDistributionPlot "" "packageAvailable('RcmdrMisc')" item exponentialMenu command "Sample from exponential distribution..." exponentialDistributionSamples "" "" # Uniform distribution menu uniformMenu continuousMenu "" "" "" "" item continuousMenu cascade "Uniform distribution" uniformMenu "" "" item uniformMenu command "Uniform quantiles..." uniformQuantiles "" "" item uniformMenu command "Uniform probabilities..." uniformProbabilities "" "" item uniformMenu command "Plot uniform distribution..." uniformDistributionPlot "" "packageAvailable('RcmdrMisc')" item uniformMenu command "Sample from uniform distribution..." uniformDistributionSamples "" "" # beta distribution menu betaMenu continuousMenu "" "" "" "" item continuousMenu cascade "Beta distribution" betaMenu "" "" item betaMenu command "Beta quantiles..." betaQuantiles "" "" item betaMenu command "Beta probabilities..." betaProbabilities "" "" item betaMenu command "Plot beta distribution..." betaDistributionPlot "" "packageAvailable('RcmdrMisc')" item betaMenu command "Sample from beta distribution..." betaDistributionSamples "" "" # Cauchy distribution menu CauchyMenu continuousMenu "" "" "" "" item continuousMenu cascade "Cauchy distribution" CauchyMenu "" "" item CauchyMenu command "Cauchy quantiles..." CauchyQuantiles "" "" item CauchyMenu command "Cauchy probabilities..." CauchyProbabilities "" "" item CauchyMenu command "Plot Cauchy distribution..." CauchyDistributionPlot "" "packageAvailable('RcmdrMisc')" item CauchyMenu command "Sample from Cauchy distribution..." CauchyDistributionSamples "" "" # Logistic distribution menu logisticMenu continuousMenu "" "" "" "" item continuousMenu cascade "Logistic distribution" logisticMenu "" "" item logisticMenu command "Logistic quantiles..." logisticQuantiles "" "" item logisticMenu command "Logistic probabilities..." logisticProbabilities "" "" item logisticMenu command "Plot logistic distribution..." logisticDistributionPlot "" "packageAvailable('RcmdrMisc')" item logisticMenu command "Sample from logistic distribution..." logisticDistributionSamples "" "" # Lognormal distribution menu lognormalMenu continuousMenu "" "" "" "" item continuousMenu cascade "Lognormal distribution" lognormalMenu "" "" item lognormalMenu command "Lognormal quantiles..." lognormalQuantiles "" "" item lognormalMenu command "Lognormal probabilities..." lognormalProbabilities "" "" item lognormalMenu command "Plot lognormal distribution..." lognormalDistributionPlot "" "packageAvailable('RcmdrMisc')" item lognormalMenu command "Sample from lognormal distribution..." lognormalDistributionSamples "" "" # Gamma distribution menu gammaMenu continuousMenu "" "" "" "" item continuousMenu cascade "Gamma distribution" gammaMenu "" "" item gammaMenu command "Gamma quantiles..." gammaQuantiles "" "" item gammaMenu command "Gamma probabilities..." gammaProbabilities "" "" item gammaMenu command "Plot gamma distribution..." gammaDistributionPlot "" "packageAvailable('RcmdrMisc')" item gammaMenu command "Sample from gamma distribution..." gammaDistributionSamples "" "" # Weibull distribution menu WeibullMenu continuousMenu "" "" "" "" item continuousMenu cascade "Weibull distribution" WeibullMenu "" "" item WeibullMenu command "Weibull quantiles..." WeibullQuantiles "" "" item WeibullMenu command "Weibull probabilities..." WeibullProbabilities "" "" item WeibullMenu command "Plot Weibull distribution..." WeibullDistributionPlot "" "packageAvailable('RcmdrMisc')" item WeibullMenu command "Sample from Weibull distribution..." WeibullDistributionSamples "" "" # Gumbel distribution menu GumbelMenu continuousMenu "" "" "" "" item continuousMenu cascade "Gumbel distribution" GumbelMenu "" "" item GumbelMenu command "Gumbel quantiles..." GumbelQuantiles "" "" item GumbelMenu command "Gumbel probabilities..." GumbelProbabilities "" "" item GumbelMenu command "Plot Gumbel distribution..." GumbelDistributionPlot "" "packageAvailable('RcmdrMisc')" item GumbelMenu command "Sample from Gumbel distribution..." GumbelDistributionSamples "" "" # Binomial distribution menu binomialMenu discreteMenu "" "" "" "" item discreteMenu cascade "Binomial distribution" binomialMenu "" "" item binomialMenu command "Binomial quantiles..." binomialQuantiles "" "" item binomialMenu command "Binomial tail probabilities..." binomialProbabilities "" "" item binomialMenu command "Binomial probabilities..." binomialMass "" "" item binomialMenu command "Plot binomial distribution..." binomialDistributionPlot "" "packageAvailable('RcmdrMisc')" item binomialMenu command "Sample from binomial distribution..." binomialDistributionSamples "" "" # Poisson distribution menu PoissonMenu discreteMenu "" "" "" "" item discreteMenu cascade "Poisson distribution" PoissonMenu "" "" item PoissonMenu command "Poisson quantiles..." PoissonQuantiles "" "" item PoissonMenu command "Poisson tail probabilities..." PoissonProbabilities "" "" item PoissonMenu command "Poisson probabilities..." PoissonMass "" "" item PoissonMenu command "Plot Poisson distribution..." PoissonDistributionPlot "" "packageAvailable('RcmdrMisc')" item PoissonMenu command "Sample from Poisson distribution..." PoissonDistributionSamples "" "" # Geometric distribution menu geometricMenu discreteMenu "" "" "" "" item discreteMenu cascade "Geometric distribution" geometricMenu "" "" item geometricMenu command "Geometric quantiles..." geomQuantiles "" "" item geometricMenu command "Geometric tail probabilities..." geomProbabilities "" "" item geometricMenu command "Geometric probabilities..." geomMass "" "" item geometricMenu command "Plot geometric distribution..." geomDistributionPlot "" "packageAvailable('RcmdrMisc')" item geometricMenu command "Sample from geometric distribution..." geomDistributionSamples "" "" # Hypergeometric distribution menu hyperMenu discreteMenu "" "" "" "" item discreteMenu cascade "Hypergeometric distribution" hyperMenu "" "" item hyperMenu command "Hypergeometric quantiles..." hyperQuantiles "" "" item hyperMenu command "Hypergeometric tail probabilities..." hyperProbabilities "" "" item hyperMenu command "Hypergeometric probabilities..." hyperMass "" "" item hyperMenu command "Plot hypergeometric distribution..." hyperDistributionPlot "" "packageAvailable('RcmdrMisc')" item hyperMenu command "Sample from hypergeometric distribution..." hyperDistributionSamples "" "" # Negative binomial distribution menu negbinomialMenu discreteMenu "" "" "" "" item discreteMenu cascade "Negative binomial distribution" negbinomialMenu "" "" item negbinomialMenu command "Negative binomial quantiles..." negbinomialQuantiles "" "" item negbinomialMenu command "Negative binomial tail probabilities..." negbinomialProbabilities "" "" item negbinomialMenu command "Negative binomial probabilities..." negbinomialMass "" "" item negbinomialMenu command "Plot negative binomial distribution..." negbinomialDistributionPlot "" "packageAvailable('RcmdrMisc')" item negbinomialMenu command "Sample from negative binomial distribution..." negbinomialDistributionSamples "" "" item distributionsMenu cascade "Continuous distributions" continuousMenu "" "" item distributionsMenu cascade "Discrete distributions" discreteMenu "" "" item topMenu cascade "Distributions" distributionsMenu "" "" menu toolsMenu topMenu "" "" "" "" item toolsMenu command "Load package(s)..." loadPackages "" "" item toolsMenu command "Load Rcmdr plug-in(s)..." loadPlugins "length(listPlugins()) > 0" "" item toolsMenu command "Options..." Options "" "" item toolsMenu command "Save Rcmdr options..." saveOptions "" "" item toolsMenu command "Manage Mac OS X app nap for R.app..." appNap "" "RappP() && mavericksP()" item toolsMenu command "Install auxiliary software..." installSoftware "" "any(!unlist(getRcmdr('capabilities')))" item topMenu cascade "Tools" toolsMenu "" "" menu helpMenu topMenu "" "" "" "" item helpMenu command "Commander help" helpCommander "" "" item helpMenu command "Introduction to the R Commander" browseManual "" "" item helpMenu command "Introduction to the R Commander (English version)" browseEnglishManual "" "manualTranslationP()" item helpMenu command "R Commander website" browseRcmdrWebsite "" "" item helpMenu command "About Rcmdr" helpAboutCommander "" "" item helpMenu separator "" "" "" "" item helpMenu command "Help on active data set (if available)" helpDataSet "activeDataSetP()" "" item helpMenu separator "" "" "" "" item helpMenu command "Start R help system" startHelp "" "" item helpMenu command "R website" browseRWebsite "" "" item helpMenu command "Using R Markdown" browseRMarkdown "" "" item topMenu cascade "Help" helpMenu "" "" # Biodiversity analysis (R. Kindt, World Agroforestry Centre) # MAR 2016 menu biodivMenu topMenu "" "" "" "" menu communMenu biodivMenu "" "" "" "" item communMenu command "Select community data set..." selectCommunityDataSet "dataSetsP()" "" item communMenu command "Import datasets from Excel..." importfromExcelGUI "" "" item communMenu command "Import datasets from Excel2007..." importfromExcel2007GUI "" "" item communMenu command "Import datasets from Access..." importfromAccessGUI "" "" item communMenu command "Import datasets from Access2007..." importfromAccess2007GUI "" "" item communMenu command "Make community data set..." makecommunityGUI "activeDataSetP()" "" item communMenu command "View community data set" viewcommunity "communityDataSetP()" "" item communMenu command "Edit community data set" editcommunity "communityDataSetP()" "" item communMenu command "Check data sets" checkdatasets "activeDataSetP() && communityDataSetP()" "" item communMenu command "Same sites for community/environmental..." samesitesGUI "activeDataSetP() && communityDataSetP()" "" item communMenu command "Replace NA with 0" replaceNAs "communityDataSetP()" "" item communMenu command "Remove species with zero total abundance..." removezeroes "communityDataSetP()" "" item communMenu command "Remove NA from environmental data set..." removeNAGUI "activeDataSetP() && communityDataSetP()" "" item communMenu command "Transform community matrix..." disttransGUI "communityDataSetP()" "" item communMenu command "Vegemite community table" vegemite.table "communityDataSetP()" "" item communMenu command "Tabasco community table plot" tabasco.table "communityDataSetP()" "" item communMenu command "Beals smoothing" beals.smoothing "communityDataSetP()" "" item communMenu command "Indicator power" ind.power "communityDataSetP()" "" item communMenu command "Nestedness checks" nested.checks "communityDataSetP()" "" menu enviroMenu biodivMenu "" "" "" "" item enviroMenu command "Select environmental data set..." selectActiveDataSet "dataSetsP()" "" item enviroMenu command "View environmental data set" viewenvironmental "activeDataSetP()" "" item enviroMenu command "Edit environmental data set" editenvironmental "activeDataSetP()" "" item enviroMenu command "Summary..." envirosummaryGUI "activeDataSetP()" "" item enviroMenu command "Box Cox transformation..." boxcoxGUI "activeDataSetP()" "" menu diversityMenu biodivMenu "" "" "" "" item diversityMenu command "Species accumulation curves..." accumGUI "activeDataSetP() && communityDataSetP()" "" item diversityMenu command "Diversity indices..." diversityGUI "activeDataSetP() && communityDataSetP()" "" item diversityMenu command "Add diversity variables to data set" diversityvars "activeDataSetP() && communityDataSetP()" "" item diversityMenu command "Rank abundance..." rankabunGUI "activeDataSetP() && communityDataSetP()" "" item diversityMenu command "Renyi profile..." renyiGUI "activeDataSetP() && communityDataSetP()" "" menu countsMenu biodivMenu "" "" "" "" item countsMenu command "Species abundance as response..." countGUI "activeDataSetP() && communityDataSetP()" "" item countsMenu command "Species presence-absence as response..." presabsGUI "activeDataSetP() && communityDataSetP()" "" item countsMenu command "Set up diversity as response" diversityresponse "activeDataSetP() && communityDataSetP()" "" menu ordinMenu biodivMenu "" "" "" "" item ordinMenu command "Calculate distance matrix..." distmatrixGUI "communityDataSetP()" "" item ordinMenu command "Unconstrained ordination..." unconordiGUI "activeDataSetP() && communityDataSetP()" "" item ordinMenu command "Constrained ordination..." conordiGUI "activeDataSetP() && communityDataSetP()" "" item ordinMenu command "Clustering..." clusterGUI "activeDataSetP() && communityDataSetP()" "" item ordinMenu command "Compare distance matrices..." mantelGUI "activeDataSetP() && communityDataSetP()" "" menu ensMenu biodivMenu "" "" "" "" item ensMenu command "Getting started" ens.start "" "" item ensMenu command "Species Distribution Modelling with R" dismo.pdf "" "" item ensMenu command "Change working directory..." ens.directory "" "" item ensMenu command "Save R workspace as..." saveWorkspaceAs "" "" menu stackMenu ensMenu "" "" "" "" item stackMenu command "Select calibration stack..." stack.select.GUI "stack.listP()" "" item stackMenu command "View calibration stack" viewstack "stack.focalP()" "" item stackMenu command "Create stack of raster layers..." stack.create.GUI "" "" item stackMenu command "Update list of available stacks..." update.stacklist.menu "" "" item stackMenu command "Change files to raster grd format..." ens.grd.menu "" "" item stackMenu command "Delete layers from calibration stack..." stack.delete.GUI "stack.focalP()" "" item stackMenu command "Rename layers for calibration stack..." stack.rename.GUI "stack.focalP()" "" item stackMenu command "Identify factors for calibration stack..." stack.factors.GUI "stack.focalP()" "" item stackMenu command "Identify dummies for calibration stack..." stack.dummies.GUI "stack.focalP()" "" menu presMenu ensMenu "" "" "" "" item presMenu command "Select presence data set..." presence.select.GUI "dataSetsP()" "" item presMenu command "View selected presence data set" viewpresence "presence.focalP()" "" item presMenu command "Select data set to create presence data..." selectActiveDataSet "dataSetsP()" "" item presMenu command "Create species presence data set..." make.presence.GUI "activeDataSetP()" "" menu absMenu ensMenu "" "" "" "" item absMenu command "Select absence data set..." absence.select.GUI "dataSetsP()" "" item absMenu command "View selected absence data set" viewabsence "absence.focalP()" "" item absMenu command "Select focal stack of raster layers..." stack.select.GUI "stack.listP()" "" item absMenu command "Select focal presence data set..." presence.select.GUI "dataSetsP()" "" item absMenu command "Create species absence data set..." make.absence.GUI "stack.focalP() && presence.focalP()" "" menu calibMenu ensMenu "" "" "" "" item calibMenu command "Ensemble suitability modelling..." batch.GUI "" "" item calibMenu command "Plot suitability maps..." ensemble.plot.GUI "stack.focalP() && presence.focalP() && absence.focalP()" "" item calibMenu command "Select ensemble models..." model.select.menu "" "" item calibMenu command "Evaluation strips..." eval.strip.GUI "stack.listP() && ensmodelsP()" "" item calibMenu command "Predict ensembles..." ens.predict.GUI "stack.listP() && ensmodelsP()" "" menu helpbioMenu biodivMenu "" "" "" "" item helpbioMenu command "Help about BiodiversityR" helpBiodiversityR "" "" item helpbioMenu command "Citations for loaded packages" allcitations "" "" item helpbioMenu command "Go to website for BiodiversityR" browseTDAwebsite "" "" item helpbioMenu command "Tree Diversity Analysis PDF (7.7 MB)" browseTDAmanual "" "" item topMenu cascade "BiodiversityR" biodivMenu "" "" item biodivMenu cascade "Community matrix" communMenu "" "" item biodivMenu cascade "Environmental matrix" enviroMenu "" "" item biodivMenu cascade "Analysis of diversity" diversityMenu "" "" item biodivMenu cascade "Analysis of species as response" countsMenu "" "" item biodivMenu cascade "Analysis of ecological distance" ordinMenu "" "" item biodivMenu cascade "Ensemble suitability modelling" ensMenu "" "" item ensMenu cascade "Stacks of environmental layers" stackMenu "" "" item ensMenu cascade "Presence data set" presMenu "" "" item ensMenu cascade "Absence data set" absMenu "" "" item ensMenu cascade "Ensemble suitability modeling" calibMenu "" "" item biodivMenu cascade "Help about BiodiversityR" helpbioMenu "" ""