Package: RVAideMemoire 0.9-83-7

RVAideMemoire: Testing and Plotting Procedures for Biostatistics

Contains miscellaneous functions useful in biostatistics, mostly univariate and multivariate testing procedures with a special emphasis on permutation tests. Many functions intend to simplify user's life by shortening existing procedures or by implementing plotting functions that can be used with as many methods from different packages as possible.

Authors:Maxime HERVE

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NEWS

# Install 'RVAideMemoire' in R:
install.packages('RVAideMemoire', repos = c('https://maximeherve.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

On CRAN:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

145 exports 8 stars 6.21 score 107 dependencies 191 mentions 442 scripts 3.2k downloads

Last updated 11 months agofrom:d39ecaa81d. Checks:OK: 3 NOTE: 2 WARNING: 2. Indexed: yes.

TargetResultDate
Doc / VignettesOKSep 01 2024
R-4.5-winNOTESep 01 2024
R-4.5-linuxNOTESep 01 2024
R-4.4-winOKSep 01 2024
R-4.4-macOKSep 01 2024
R-4.3-winWARNINGSep 01 2024
R-4.3-macWARNINGSep 01 2024

Exports:adonis.IIAnova.clmAnova.clmmback.emmeansback.lsmeansbootstrapbyf.histbyf.mqqnormbyf.mshapirobyf.normhistbyf.qqnormbyf.shapiroCDA.cvCDA.testcdf.discretechisq.bin.expchisq.bintestchisq.expchisq.multcompchisq.theo.bintestchisq.theo.multcompcochran.qtestcond.multinomcoord.projcor.2compcor.confcor.multcompcor.sparsecov.testcox.residcramercramer.testcvCvM.testDA.confusionDA.validDA.vardendro.gpDIABLO.cvDIABLO.testdummydunn.testelogisfc.multcompfisher.bintestfisher.multcompfp.testfriedman.rating.testG.bintestG.multcompG.testG.theo.multcompGPA.testind.contribkruskal.rating.testleast.rectloc.slplogis.fitlogis.noisemodmood.medtestmqqnormmshapiro.testmultinomial.multcompmultinomial.testmultinomial.theo.multcompmulttest.cormulttest.gpmulttest.gp.binMVA.anovaMVA.biplotMVA.cmvMVA.corMVA.corplotMVA.cvMVA.loadMVA.loadplotMVA.pairplotMVA.plotMVA.scoreplotMVA.scoresMVA.syntMVA.testMVA.trajplotOR.multinomord.rwoverdisp.glmerp.betapairwise.CDA.testpairwise.factorfitpairwise.G.testpairwise.mood.medtestpairwise.MVA.testpairwise.perm.manovapairwise.perm.t.testpairwise.perm.var.testpairwise.to.groupspairwise.var.testpairwise.wilcox.rating.testpcorpcor.testperm.anovaperm.bartlett.testperm.cor.testperm.t.testperm.var.testplot1comp.indplot1comp.varplotresidplotsurvivorsPLSDA.ncompPLSDA.testPLSDA.VIPprop.bin.multcompprop.multcompprop.multinomprop.multinom.testquasibinomial.QAICquasipoisson.QAICrating.emmeansrating.lsmeansrating.probreg.cis.corcircle2scat.crscat.mix.categoricalscat.mix.numericscatter.coa2seseq2spearman.cispearman.cor.multcompsplitfstandtest.multinomto.dudiuser.contwald.ptheo.multinom.testwald.ptheo.testwilcox.paired.multcompwilcox.paired.rating.multcompwilcox.rating.signtestwilcox.rating.testwilcox.signtestwmean

Dependencies:abindade4backportsbase64encbootbroombslibcachemcarcarDatacliclustercolorspacecowplotcpp11crosstalkDerivdigestdoBydplyrDTellipseemmeansestimabilityevaluateFactoMineRfansifarverfastmapflashClustfontawesomeFormulafsgenericsggplot2ggrepelgluegtablehighrhtmltoolshtmlwidgetshttpuvisobandjquerylibjsonliteknitrlabelinglaterlatticelazyevalleapslifecyclelme4magrittrMASSMatrixMatrixModelsmemoisemgcvmicrobenchmarkmimeminqamodelrmultcompViewmunsellmvtnormnlmenloptrnnetnumDerivpbkrtestpermutepillarpixmappkgconfigplspromisespspearmanpurrrquantregR6rappdirsRColorBrewerRcppRcppArmadilloRcppEigenrlangrmarkdownsassscalesscatterplot3dspSparseMstringistringrsurvivaltibbletidyrtidyselecttinytexutf8vctrsveganviridisLitewithrxfunyaml

Readme and manuals

Help Manual

Help pageTopics
Testing and Plotting Procedures for BiostatisticsRVAideMemoire-package RVAideMemoire
Type II permutation MANOVA using distance matricesadonis.II
Anova Tables for Cumulative Link (Mixed) ModelsAnova.clm Anova.clmm
Back-transformation of EMMeansback.emmeans
Bootstrapbootstrap
Histogram for factor levelsbyf.hist
QQ-plot for factor levelsbyf.mqqnorm
Shapiro-Wilk test for factor levelsbyf.mshapiro
QQ-plot for factor levelsbyf.qqnorm
Shapiro-Wilk test for factor levelsbyf.shapiro
Cross validationCDA.cv
Significance test for CDACDA.test
Cumulative Distribution Function of a known discrete distributioncdf.discrete
Expected counts for comparison of response probabilities to given valueschisq.bin.exp
Pearson's Chi-squared test for binary variableschisq.bintest
Expected counts for comparison of proportions to given valueschisq.exp
Pairwise comparisons after a chi-squared goodness-of-fit testchisq.multcomp
Pearson's Chi-squared test for comparison of response probabilities to given valueschisq.theo.bintest
Pairwise comparisons after a chi-squared test for given probabilitieschisq.theo.multcomp
Cochran's Q testcochran.qtest
Condition number of the Hessian matrix of a multinomial log-linear modelcond.multinom
Coordinates of projected pointscoord.proj
Comparison of 2 Pearson's linear correlation coefficientscor.2comp
Equality of a Pearson's linear correlation coefficient to a given valuecor.conf
Comparison of several Pearson's linear correlation coefficientscor.multcomp
Significance test for the covariance between two datasetscov.test
Martingale residuals of a Cox modelcox.resid
Cramer's association coefficientcramer
Cramer's association coefficientcramer.test
Coefficient of variationcv
Dendrogram and number of groups to be chosendendro.gp
Deprecated functions in RVAideMemoire packageback.lsmeans byf.normhist cor.sparse CvM.test DA.confusion DA.valid DA.var dunn.test fc.multcomp friedman.rating.test kruskal.rating.test pairwise.manova pairwise.to.groups pairwise.wilcox.rating.test plot1comp.ind plot1comp.var PLSDA.ncomp PLSDA.test rating.lsmeans s.corcircle2 scat.mix.categorical scat.mix.numeric scatter.coa2 wilcox.paired.rating.multcomp wilcox.rating.signtest wilcox.rating.test
Cross validationDIABLO.cv
Significance test based on cross-validationDIABLO.test
Dummy responsesdummy
Empirical logistic transformationelogis
Fisher's exact test for binary variablesfisher.bintest
Pairwise comparisons using Fisher's exact testfisher.multcomp
Fligner-Policello testfp.test fp.test.default fp.test.formula
G-test for binary variablesG.bintest
Pairwise comparisons after a G-testG.multcomp
G-testG.test
Pairwise comparisons after a G-test for given probabilitiesG.theo.multcomp
Significance test for GPAGPA.test
Individual contributions in regressionind.contrib
Least rectangles linear regressionleast.rect
Slope of a hand-defined lineloc.slp
Graphical adujstment of a simple binary logistic regression to datalogis.fit
Creating a nls model for logistic regression from fitted values of a glm modellogis.noise
Modemod
Mood's median testmood.medtest mood.medtest.default mood.medtest.formula
Multivariate normality QQ-Plotmqqnorm
Shapiro-Wilk multivariate normality testmshapiro.test
Pairwise comparisons after an exact multinomial testmultinomial.multcomp
Exact multinomial testmultinomial.test
Pairwise comparisons after an exact multinomial test for given probabilitiesmultinomial.theo.multcomp
Univariate correlation test for multiple variablesmulttest.cor plot.multtest.cor
Univariate comparison of groups for multiple variablesmulttest.gp plot.multtest.gp
Univariate comparison of groups for multiple binary variablesmulttest.gp.bin plot.multtest.gp.bin
Type II permutation test for constrained multivariate analysesMVA.anova
Biplot of multivariate analysesMVA.biplot
Cross model validationMVA.cmv
Correlations of multivariate analysesMVA.cor
Correlation circle of multivariate analysesMVA.corplot
Cross validationMVA.cv
Loadings of multivariate analysesMVA.load
Loading plot of multivariate analysesMVA.loadplot
Paired plot of multivariate analysesMVA.pairplot
Plotting of multivariate analysesMVA.plot
Score plot of multivariate analysesMVA.scoreplot
Scores of multivariate analysesMVA.scores
Synthesis quality of multivariate analysesMVA.synt
Significance test based on cross (model) validationMVA.test
Trajectory plot of multivariate analysesMVA.trajplot
Odds-ratio (multinomial regression)OR.multinom
Re-computation of an ordination using given row weightsord.rw
Estimation of overdispersion with 'glmer' modelsoverdisp.glmer
Rescaling of a [0,1] variable into the (0,1) interval (and vice-versa)p.beta
Pairwise comparisons for CDApairwise.CDA.test
Pairwise comparisons of groups displayed on a factorial mappairwise.factorfit
Pairwise comparisons for proportions using G-testspairwise.G.test
Pairwise Mood's median testspairwise.mood.medtest
Pairwise permutation tests based on cross (model) validationpairwise.MVA.test
Pairwise permutation MANOVAspairwise.perm.manova
Pairwise permutation t testspairwise.perm.t.test
Pairwise permutation F testspairwise.perm.var.test
Pairwise F testspairwise.var.test
(Semi-)Partial correlationpcor
Tests for (semi-)partial association/correlation between paired samplespcor.test
Permutation Analysis of Varianceperm.anova
Permutation Bartlett's test of homogeneity of variancesperm.bartlett.test
Permutation Pearson's correlation testperm.cor.test
Permutation Student's t-testperm.t.test perm.t.test.default perm.t.test.formula
Permutation F test to compare two variancesperm.var.test perm.var.test.default perm.var.test.formula
Simple analysis of model residualsplotresid
Survivor curveplotsurvivors
Variable Importance in the Projection (VIP)PLSDA.VIP
Predict method for cross-validated CDA submodelspredict.CDA.cv
Predict method for CDApredict.coadisc
Predict method for cross-validated submodelspredict.MVA.cmv predict.MVA.cv
Pairwise comparisons after a test for given probabilitiesprop.bin.multcomp
Pairwise comparisons after a test for given proportionsprop.multcomp
Proportions and standard errorsprop.multinom
Wald tests for comparison of proportionsprop.multinom.test
QAIC(c) calculation with GLMs of the quasi- familyquasibinomial.QAIC quasipoisson.QAIC
EMMeans for Cumulative Link (Mixed) Modelsrating.emmeans
Observed rating frequenciesrating.prob
Confidence intervals of a simple linear regressionreg.ci
"Correlation" of variables to axes in MCA or mix analysesscat.cr
Standard errorse
Sequence generationseq2
Confidence interval of a Spearman's rank correlation coefficientspearman.ci
Comparison of several Spearman's rank correlation coefficientsspearman.cor.multcomp
Divide into groups respecting relative proportionssplitf
Standardization of a data frame based on another data framestand
Significance tests of coefficients (multinomial regression)test.multinom
Synthesis quality of multivariate analysesto.dudi
User defined contrasts for EMMeansuser.cont
Wald tests for comparison of proportions to theoretical valueswald.ptheo.multinom.test
Wald test for comparison of a proportion to a theoretical valuewald.ptheo.test
Non parametric pairwise comparisons for paired datawilcox.paired.multcomp
Wilcoxon sign testwilcox.signtest wilcox.signtest.default wilcox.signtest.formula
Weighted arithmetic meanwmean