Version 2.0 • pathfindR

updated the java active subnetwork search component and added the seedForRandom argument in active_snw_search()to ensure reproducibility. By default behavior, in run_pathfindR(), a seed is set for each iteration to produce reproducible results (#108)
as the example input/output data were renamed for convenience in ‘pathfindR.data’ v2.0, ‘pathfindR’ now depends on pathfindR.data (>= 2.0)
refactored/simplified run_pathfindR()
visualization enriched term diagrams are now NOT part of run_pathfindR()
default behavior of run_pathfindR() is now to run in a temporary directory. The user can still set output_dir to run in a specified directory and also produce HTML reports
in hierarchical_term_clustering(), update the sequence of number of clusters for which silhouette width is calculated for choosing the optimal number of clusters. This should speed up the function for cases with a large number of enriched terms
updated the relevant vignettes to reflect the implemented changes

fixed a minor issue in return_pin_path() where the PIN was not properly read (#157)

added the dir_for_report argument in the internal function create_HTML_report() to fix test issues on CRAN

Changelog 2.0