Fixing test-errors on r-patched-solaris-x86 and notes on r-devel-linux-x86_64-fedora-clang.
Fixed memory errors reported by ASAN and valgrind.
Improved default values for the parameter sigmae.
POUMM 1.3 Unreleased
Parallel likelihood calculation: (tested on Linux using Intel complier v16.0.0).
Added possibility to specify known measurement standard error for each tip of the tree. (see ?POUMM).
Added a bivariate densplot of the posterior samples displaying a pairs-plot, i.e. a matrix of plots with marginal densities at the diagonal, scatter plots on the lower triangle and correlation on the upper (see ?plot.summary.POUMM); possibility to change the color-palette used in the plot with color-blindness friendly default colors.
New default parameter settings: now the ML-limits (parUpper and parLower) as well as the priors for the parameters alpha and sigma are scaled according to the length of the tree (tMean) and the empirical variance of the trait (zVar) (see ?specifyPOUMM). Please note that the default parameter settings may change in future releases.
Improved ML-fit: now the optimization is run 50 times starting from different points in the search region. The ML-fit is still kept deterministic, i.e. consecutive runs should find the same optimum.
Fixed a dependency on the adaptMCMC package (now added as an import).