pharmpy-core 0.10.0

Pharmacometric modelling

Pharmpy is a library for pharmacometrics. It can be used as a regular python package, in R via reticulate or via its built in command line interface.

Pharmpy is architectured to be able to handle different types of model formats and data formats and exposes a model agnostic API.

Current features:

• Parsing of many parts of a NONMEM model file

• Parsing of NONMEM result files

• CLI supporting dataset filtering, resampling, anonymization and viewing

Pharmpy is developed by the Uppsala University Pharmacometrics group.

0.10.0 (2020-11-16)

• modeling.create_rv_block

• modeling.michaelis_menten_elimination

• modeling.set_transit_compartments

• First version of modelfit method

• Add first version of bootstrap method

• Add parameter estimates histograms to bootstrap report

• Add automatic update of $SIZES PD when writing/updating NONMEM model

• Additions to QAResults

• NMTRanParseError replaced with ModelSyntaxError

• Multiple bugfixes to frem and scm result calculations

0.9.0 (2020-10-26)

• Add error_model function to the modeling module

• Added more standard models for modeling.add_etas

• Improve BootstrapResults

• Add plots to bootstrap

• Add support for the PHARMPYCONFIGPATH environment variable

• Add QAResults and LinearizeResults classes

• Bugfixes for some Windows specific issues

0.8.0 (2020-10-08)

• Add basic modeling functions to the modeling module

• modeling.add_etas

• Improved bootstrap results generation and additional plots

• Bugfix: Labelled OMEGAS could sometimes get wrong symbol names

0.7.0 (2020-09-28)

• Add method reset_indices in Results to flatten multiindices. Useful from R.

• absorption_rate can also set sequential zero first absorption

• New functionsadd_lag_time and remove_lag_time in modeling

• Add basic functions fix/unfix_parameter, update_source and read_model to modeling API

• Updated reading of NONMEM results

• Bugfixes in add_covariate_effects and absorption_rate

• Fix crash in FREM results if no log option could be found in meta.yaml

0.6.0 (2020-09-18)

• Add eta transformations: boxcox, t-dist and John Draper

• Add results cdd and scm to CLI

• Add different views for scm results

• Add support for taking parameter names from comment in NONMEM model

• Remove assumptions for symbols

• Add modeling.absorption_rate to set 0th or first order absorption

• Add update of $TABLE numbers

0.5.0 (2020-09-04)

• Many bugfixes and improvements to NONMEM code record parser

• Add calculation of symbolic and numeric eta and eps gradients, population and individulal prediction and wres for PRED models

• Add option to use comments in NONMEM parameter records as names for parameters

• Reading of ODE systems from NONMEM non-$DES models

• Calculation of compartmental matrix and ODE system

• New module ‘modeling’

• Function in modeling and CLI to change ADVAN implicit compartmental models to explicit $DES

• Function in modeling and CLI to add covariate effects

• Functions for reading cdd and scm results from PsN runs

• Many API updates

• Extended CLI documentation

0.4.0 (2020-07-24)

• Add categorical covariates to covariate effects plot in FREM

• Better support for reading NONMEM code statements (PK and PRED)

• Support for updating NONMEM code statements (PK and PRED)

• Bugfixes for CLI

0.3.0 (2020-06-16)

• New CLI command ‘data append’

• Parameter names is now the index in Parameters.summary()

• FREM postprocessing

• Standardized results.yaml and results.csv

0.2.0 (2020-03-27)

First release

0.1.0 (2018-07-22)

Initial library development/testing directory structure.