NEWS

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mvMORPH 1.2.1 (2024-08-28)

• fix type for integer in C header file

mvMORPH 1.2.0 (2024-08-27)

• update tolerance value for mvgls tuning parameter search
  • changes to Fortran routines calls following CRAN policies
  • wrapper to BIC

mvMORPH 1.1.9 (2023-12-09)

• reverse change for zero branch lengths in "penalized" file. A typo was introduced. Now a check is performed first in the "mvgls" function.

mvMORPH 1.1.8 (2023-11-29)

• add the pcaShape and dfaShape functions
  • add wrapper "simulate()" to simulate from 'mvgls' or 'mvols' fit
  • fix error in "estim" for BM with trend
  • fix issues with zero branch lengths in the pruning algorithm used in 'mvgls'
  • fix typo on factor labels in DFA predictions
  • fix CRAN requests (typo on Rd file and arguments in error function in C code)

mvMORPH 1.1.7 (2023-03-13)

• fix error in handling pairwise glh tests with the "effectSize" function
  • fix error in mvols with EIC - no use of the pruning algorithm now
  • add ploting option for pairwise tests
  • add AIC extractor

mvMORPH 1.1.6 (2022-05-09)

• fix error in the estimation of GIC with "BMM" model in mvgls. Now the 'mvgls' function uses a more robust parameterization of BMM which ease the computation of GIC.
  • mvols function - wrapper to mvgls to fit OLS (or WLS) multivariate models (possibly regularized)

mvMORPH 1.1.5 (2022-05-02)

• mvqqplot (multivariate normality and outliers assessment - beta)
  • effectsize (multivariate measures of association - beta)
  • pairs.contrasts (build a matrix of pairwise contrasts)
  • pairwise.glh (performs multivariate pairwises tests)
  • predict.mvgls.dfa (predict option for DFA - beta)
  • manova.gls (implements now contrasts for repeated measures designs)
  • fix error in estim
  • add "ancestral" function to estimate ancestral states for mvgls objects

mvMORPH 1.1.4 (2021-03-17)

• model BMM in mvgls
  • "predict" function for mvgls
  • plot function for mvgls objects
  • dfa on gls fit (beta)
  • fix typo in mvSHIFT output print
  • fix error in estimation of OU with n-ultrametric trees in mvgls + new adjusted bounds for parameters search
  • fix typo in summary.mvgls print option in the calculation of the AIC.
  • handling of design matrices with deficient ranks in regressions

mvMORPH 1.1.3 (2020-06-12)

• CRAN request to remove the export statements for S3 classes
  • replace is.binary.tree to is.binary.phylo, the former being deprecated from "ape".
  • fix error in mvSHIFT. The wrong values were returned (but not printed) for "beta" in BMEB models.

mvMORPH 1.1.2 (2020-04-17)

• replaced "F" by "FALSE" in example files to follow CRAN policies
  • optimization of some diagonal matrices computations
  • bug fix in mvSIM (SHIFT model without simmap tree provided)

mvMORPH 1.1.1 (2020-01-08)

• update help pages of various functions
  • Bugs fixes for bounds in the parameter search in "mvgls", and missing values estimation in "estim" with OU1 model.
  • manova.gls: MANOVA methods and multivariate statistics based on ML (n<p) and PL (any p) model fit.
  • Phyllostomid dataset from Monteiro & Nogueira (2011)
  • EIC: function to compute the EIC score for both ML and PL techniques (class mvgls)

mvMORPH 1.1.0 (2018-08-04)

• mvgls: a multivariate GLS function based on ML (n<p) and PL (any p).
  • mvgls.pca: a function to perform PCA on serially correlated data.
  • GIC: function to compute the GIC score for both ML and PL techniques (class mvgls)
  • suite of functions to use with mvgls
  • Bug fix for "mvSIM" with sparse methods and speed-up for "BM1" model.
  • Typo fix in testLRT
  • Typo fix in weight-matrix-mvmorph.c (indexing of variable)
  • add options for the pruning algorithm.
  • fix error with NA values for the mvOU function.

mvMORPH 1.0.9 (2017-06-08)

• Registration of compiled codes
  • New pruning algorithm to compute the determinant and square root matrix
  • Bugs fixes in "estim" for ancestral state reconstructions with OU models and "smean=FALSE" option.
  • Bug fix for "estim" with univariate data.
  • Corrected bug in mvSIM.
  • Fix bug with matrix parametrization "equaldiagonal".
  • add the "svd" option for simulating traits in mvSIM.
  • Bug fix in "mvEB".

mvMORPH 1.0.8 (2016-10-25)

• Allows estimating the missing cases (NA)
  • Allows estimating trends
  • User defined constrained models and parameterizations
  • Return the log-likelihood function
  • Simulating traits on package vignette
  • Multivariate models for time-series (TS)
  • Partial implementation of a tests-suite