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

```
+ 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)
```

```
+ 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
```

```
+ 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)
```

```
+ 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
```

```
+ 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
```

```
+ 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.
```

```
+ 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)
```

```
+ 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)
```

```
+ 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.
```

```
+ 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".
```

```
+ 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
```