News

version 0.9-69-3 (14-05-2018)

• changes in help pages as requested by CRAN

version 0.9-69-2 (29-01-2018)

• cochran.qtest corrected for pairwise comparisons with identical groups (thanks to Duncan Hedderley)

version 0.9-69 (03-01-2018)

• OR.multinom and test.multinom corrected for two-level responses
• change from package 'lsmeans' to 'emmeans': back.lsmeans becomes back.emmeans, rating.lsmeans becomes rating.emmeans
• plotresid improved to deal more properly with "quasi" distributions in GLM(M)s

version 0.9-68 (21-08-2017)

• miscellaneous small improvements

version 0.9-66 (10-07-2017)

• argument thresh of MVA.corplot improved
• few linguistic improvements

version 0.9-65 (03-05-2017)

• MVA.synt extended to DIABLO
• MVA.scores, MVA.cor, MVA.load (hence MVA.plot) extended to DIABLO
• new function DIABLO.cv (cross validation for DIABLO)
• new function DIABLO.test (significance test for DIABLO)

version 0.9-64 (25-03-2017)

• plotresid extended to glmmPQL models
• new function pairwise.var.test (pairwise comparisons based on F-tests)
• new function pairwise.perm.var.test (pairwise comparisons based on permutational F-tests)

version 0.9-63 (24-02-2017)

• back.lsmeans corrected for log transformations, fourth-root transformation added
• MVA.plot adapted for GPA
• plotresid re-thought

version 0.9-62 (12-12-2016)

• se corrected for proportions

version 0.9-61 (31-10-2016)

• MVA.cv and MVA.cmv corrected for errors provoked by scaling with nearly constant variables

version 0.9-60 (20-08-2016)

• MVA.synt extended to MCA, mix analysis, GPA, 2B-PLS, CCorA, rCCorA, RGCCA, CIA and PCIA
• MVA.corplot extended to db-RDA
• new function stand (standardization of a data frame based on another data frame)
• intergroup variance removed from MVA.synt (not relevant)
• new function CDA.cv (cross validation for CDA)
• new predict methods for "CDA.cv" objects
• new function CDA.test (significance test for CDA)
• new function pairwise.CDA.test (pairwise comparisons for CDA)
• pairwise.factorfit corrected for CA and CCA computed with the vegan package
• new function to.dudi (conversion of some vegan analyses to ade4 format)
• MVA.scores (hence MVA.plot) extended to (Generalized) Procrustean superimposition
• MVA.cor (hence MVA.plot) extended to Generalized Procrustean superimposition
• new function GPA.test (significance test for GPA)
• new function cov.test (significance test for covariance)
• new function ord.rw (re-computation of an ordination using given row weights)

version 0.9-57 (14-07-2016)

• new function pairwise.factorfit (pairwise comparisons of groups displayed on a factorial map)
• MVA.anova extended to deal with partial CCA/RDA/db-RDA
• MVA.synt extended to db-RDA
• new argument 'correct' in chisq.bintest (continuity correction)
• new argument 'y' in se (standard error of a proportion)
• new function cdf.discrete (Cumulative Distribution Function of a known discrete distribution)
• prop.multinom corrected for 1-row matrices
• new function wald.ptheo.multinom.test (Wald tests for comparison of proportions to theoretical values)
• multinomial.test, multinomial.multcomp and multinomial.theo.multcomp accept factors as response
• new argument 'prop' in multinomial.theo.multcomp (results displayed as counts or proportions)
• new function dunn.test (Dunn's test)
• new function cramer (Cram�r's association coefficient between 2 nominal variables)
• new argument 'progress' in all function performing permutation tests (display of the progress bar)
• new argument 'scale' in MVA.cv, MVA.cmv and MVA.test (scaling)
• new function pairwise.MVA.test (pairwise comparisons based on cross (model) validation)
• new function cond.multinom (condition number of the Hessian matrix of a multinomial log-linear model)
• new function OR.multinom (odds ratios in multinomial regression)
• new function test.multinom (significance test in multinomial regression)

version 0.9-56 (06-06-2016)

• MVA.synt extended to COA, RDA, CCA
• new argument 'vars' in multtest.gp and plotting method optimized
• splitf, MVA.cv, MVA.cmv, MVA.test optimized

version 0.9-55 (23-04-2016)

• function multtest renamed multtest.gp
• new function multtest.cor (correlation test for multiple variables)
• new function loc.slp (slope of a hand-defined line)
• new function coord.proj (coordinates of projected points)
• functions MVA.scores, MVA.cor and MVA.load are now visible

version 0.9-54 (28-03-2016)

• small bugs corrected in MVA.plot
• new argument 'adj' in least.rect (correction of confidence intervals and p-values for multiple testing)
• new function spearman.cor.multcomp (computation of adjusted confidence interval of Spearman's correlation coefficients for multiple comparisons)
• small bug corrected in prop.multinom
• new function dummy (creation of dummy responses from a factor)

version 0.9-53 (28-02-2016)

• small bugs corrected in MVA.synt
• new function multtest (univariate comparison of groups for multiple variables)

version 0.9-52 (15-11-2015)

• small bugs corrected in MVA.plot

version 0.9-51 (17-10-2015)

• small bugs corrected in MVA.plot
• plotresid rewritten, new support for gls models
• new arguments xlab and ylab in byf.hist

version 0.9-50 (08-08-2015)

• wald.ptheo.test now deals with overdispersion
• new function prop.multinom (computation of proportions and SE based on a multinomial log-linear model)
• new function wmean (weighted arithmetic mean)
• plot1comp.ind, plot1comp.var, s.corcircle2, scat.mix.categorical, scat.mix.numeric and scatter.coa2 removed (the MVA.plot function of this package does the same job and is more generic)
• new function splitf (random splitting of data frame, respecting the relative proportions of levels of a factor)
• new function MVA.cmv (cross model validation)
• new function MVA.cv (cross validation)
• DA.confusion and DA.valid removed (the MVA.cmv and MVA.cv functions of this package do the same job and are more generic)
• new predict methods for "MVA.cv" and "MVA.cmv" objects
• new function MVA.test (significance test based on cross (model) validation)
• PLSDA.test removed (the MVA.test function of this package does the same job and is more generic)
• PLSDA.ncomp removed (not really useful and the mvr function of the 'pls' package does nearly the same job)
• new function MVA.plot (various plots for multivariate analyses)
• cor.sparse removed (the MVA.plot function of this package does the same job and is more generic)
• LDA.format not exported anymore (the MVA.plot function of this package does the same job and is more generic)
• new arguments 'ord' and 'decreasing' in back.lsmeans
• new function MVA.anova (wrapper to anova.cca of the 'vegan' package but for type II tests)
• perm.t.test corrected for the computation of p-values (underestimated in some particular cases when using a two tailed test)
• MVA.synt rewritten

version 0.9-45 (13-03-2015)

• histograms with density polygons improved
• G.test, G.multcomp and G.theo.multcomp modified to deal with 0 values (but warning that it should not be done)
• new functions multinomial.test, multinomial.multcomp and multinomial.theo.multcomp (exact multinomial goodness-of-fit test and pairwise comparisons)
• chisq.bintest splitted into chisq.bintest and fisher.bintest (chi-square and Fisher's exact tests for comparing response probabilities)
• new function G.bintest (G test for comparing response probabilities)
• new functions chisq.theo.bintest, chisq.bin.exp and prop.bin.multcomp (comparison of response probabilities to theoretical values)
• new function fp.test (Fligner-Policello test)
• new function CvM.test (two-sample Cramer-von Mises test)
• new method for perm.t.test
• new method for perm.var.test
• new functions pcor and pcor.test (equivalents to cor and cor.test for (semi-)partial correlation)
• new function pairwise.to.groups (conversion of a pairwise-comparison matrix to letters showing significantly different factor levels)
• "mlm" models are now dealt properly by plotresid
• pairwise.manova removed (dealt in a much powerful manner by the 'lsmeans' package)
• new function pairwise.perm.manova (pairwise comparisons using permutational MANOVAs)
• wald.ptheo.test accepts 2-column matrices as response
• new function adonis.II (wrapper to adonis of the 'vegan' package but for type II tests)
• new predict method for "coadisc" objects (Correspondence Discriminant Analysis performed with discrimin.coa from 'ade4')
• DA.valid and DA.confusion can now handle "coadisc" objects (Correspondence Discriminant Analysis performed with discrimin.coa from 'ade4')
• new arguments arrows in s.corcircle2
• new function scat.cr ("correlation" of variables to axes in MCA or mix analyses)
• MVA.synt extended to NSCA
• wilcox.signtest now computes the confidence interval of the Hodges-Lehmann estimator (and this estimator)
• new functions mood.medtest (Mood's median test) and pairwise.mood.medtest
• new function prop.multinom.test (pairwise comparisons of proportions based on multinomial log-linear models)
• wilcox.rating.signtest, wilcox.rating.test, kruskal.rating.test, friedman.rating.test, pairwise.wilcox.rating.test and wilcox.paired.rating.multcomp removed (these tests can be problematic with ratings, CLMs (package 'ordinal') are much better)
• new function back.lsmeans (back-transformation of LSMeans and SE interval)

version 0.9-41 (15-11-2014)

• lsm.basis.clm and lsm.basis.clmm removed (now dealt in a much powerful manner by the 'lsmeans' package)
• DA.var removed (the MVA.synt function of this package does the same job and is more generic)
• fc.multcomp removed (comparison of slopes dealt in a much powerful manner by the 'lsmeans' package)
• plot1comp.ind rewritten to display a more easy-to-interpret graph
• byf.normhist removed (not very useful and nearly same thing now done by byf.hist)
• MVA.synt extended to MCA and mixed analyses

Reference manual