Improvements¶

• Added ability to process scripts in PARALLEL. This speeds up computation time for models with a large number of individuals and takes advantage of multi-core computers.
• Created POSTPROCESS section to allow filtering of data create by a PoPy model. For example with a Gen Script
• Added ability to process multiple files in a directory with one command using ‘*’ syntax, see Running multiple scripts, Checking multiple scripts, Format multiple scripts, Edit multiple scripts, Open multiple html files
• Speed improvements to core JOE algorithm, Standard Errors computation and plotting using Grph Script.
• MFit Script now outputs a summary of the fitting results for all populations to a single .csv file.
• Displaying the diagonal elements of f[X] variance matrices at each iteration. The off diagonal f[X] elements are only displayed at the end of fitting, due to space considerations.

Format Changes¶

• Simplified the structure of old ‘LEVEL_PARAMS’, replaced with EFFECTS which removes the redundant ‘split_field’ and ‘split_dict’ attributes.
• Renamed the ‘output_mode’ values in OUTPUT_SCRIPTS, using shorter names ‘gen_script_and_run’ -> ‘run’, ‘gen_script_only’ -> ‘create’, ‘no_output’ -> ‘none’.
• Renamed the ‘FINITE_DIFF’ method in COVARIANCE to ‘SANDWICH’.

Note scripts in v1.0.1 and v1.0.0 format can be automatically updated to v1.0.2 using the popy_format tool.

Bug Fixes¶

• Made float_format change format of all float values in output scripts and summary html outputs. Only applied to subset before.
• Fixed bug in iteration number when displaying ObjV over time Objective function at each iteration for simple PopPK example

Improvements¶

• The Standard Errors are now output in an easy to read format, instead of the whole hessian matrix.
• Changed the configuration file entry required to compute standard errors see COVARIANCE.
• Log files apart from the main log file are now stored in a ‘_log’ sub directory.
• The popy_run tool now asks the user if they want to proceed if the main log file already exist for a given script. Previously only the existence of the output folder was checked. The can still skip this check using the ‘-o’ option.

Bug Fixes¶

• Licence manager was giving a date error in North American time zones.
• Bug in configuration file parser for DERIVATIVES section when encountering round brackets (as opposed to expected curly brackets) in Dosing Functions.
• Documentation contents page indexing in PDF was incorrect.