stan-dev/rstan — pull request #108 by bgoodri (2014-10-21 16:44:02+00:00)
Title: Enhance pairs

This branch generalizes the pairs() function which plots two-dimensional smoothed density functions in the upper and lower triangles for each pair of specified (or all if unspecified variables). Previously, there were very limited options for specifying which chains are plotted in each triangle, which are preserved, but now the argument is called ```condition``` instead of ```chain_id```. As documented, the ```condition``` argument now also accepts
* a scalar indicating what proportion of all chains to plot in the lower triangle with the rest in the upper triangle, which is useful for judging convergence
* a string among the column names of the get_sampler_params() which separates the draws according to whether they fall above or below the median of the designated string or in the case of n_divergent__ plots divergent draws in one triangle and non-divergent draws in the other
* a logical vector or matrix whose length is equal to the number of iterations times the number of chains such that the draws corresponding to TRUE are plotted in one triangle and those corresponding to FALSE are plotted in the other triangle

Also, there is a realistic example now that builds on the example in read_stan_csv