version 0.9-74 (04-01-2020)
- MVA.plot now uses the same default scale for x and y axes
- pairwise.perm.manova can now return F values and R2 values
- new functions multtest.gp.bin (and associated plotting method) for univariate comparison of groups for multiple binary variables
- CvM.test removed (the cramer.test function of the package cramer does the same job)
- new argument 'col' in byf.hist
version 0.9-73 (26-03-2019)
- new argument 'type.DA' in predict.MVA.cv and predict.MVA.cmv (probability for the most probable class or for each class)
- new argument 'type' in predict.CDA.cv (probability for the most probable class or for each class)
version 0.9-72 (10-02-2019)
- MVA.cv and MVA.cmv improved to return individual prediction probabilities
- MVA.cor corrected for PCIA and CIA based on at least one mix analysis
- MVA.scores, MVA.cor and MVA.load improved to return more than 2 axes
- fourth-root transformation added to multtest.gp
version 0.9-71 (10-01-2019)
- least.rect() corrected for >2 levels (printing error)
- MVA.cv and MVA.cmv improved to return confusion matrices
version 0.9-70 (05-11-2018)
- dunn.test removed (the dunnTest function of the package FSA does the same job)
- pairwise.to.groups removed (not very useful)
- package dependencies changed to follow migration of mixOmics from CRAN to Bioconductor
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 (Cramér'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