pharmpy-core 0.23.2

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.

0.23.2 (2021-04-28)

• Fix bug #177

0.23.1 (2021-04-28)

• Bugfixes

0.23.0 (2021-04-28)

• Add function modelling.evaluate_expression

• Some documentation for modelfit_results

• Reworked interface to RandomVariables and Parameters

• Bugfixes

0.22.0 (2021-03-29)

• Support COM(n) in NONMEM abbreviated code

• Fix stdin handling issue when running NONMEM from R

0.21.0 (2021-03-22)

• New function read_results in modeling

• Add method to convert ExplicitODESystem to CompartmentalSystem

• Support running NONMEM 7.3 and 7.5

• Bugfixes:

  • Allow protected functions in NONMEM abbreviated code

  • Fix bad rates when changing number of transit compartments (#123)

0.20.1 (2021-03-11)

• Fix regression for calling NONMEM

0.20.0 (2021-03-11)

• New function modeling.set_peripheral_compartments

• New tool Model Search

• New model attribute estimation_steps to read and change $ESTIMATION

• Bugfixes (#99, #118)

0.19.0 (2021-03-02)

• Add create_result to create results from PsN

• Add documentation for covariate effects

0.18.0 (2021-03-01)

• Add functions to fix and unfix values to a specified value

• Add documentation for using Pharmpy with NONMEM models

• New execution system for modelfit

• Support for single string input for transformations of etas and epsilons (e.g. add_iov)

• Various bugfixes, including running NONMEM via Pharmpy on Windows

0.17.0 (2021-02-15)

• Add function to split an eta from a block structure

• New names for covariance between etas in create_rv_block

• Clearer error messages when adding IOVs (if only one level of occasion) and for parameter_names config

0.16.0 (2021-02-08)

• Improve initial estimates for adding peripheral compartments

• Parameter names are set according to priority in config

• Avoid duplication of e.g. median/mean when having multiple covariate effects with the same covariate

• Change assignments when multiple covariate effects are applied to the same parameter to be combined in one line

• Do not change error model if it is the same error model transformation multiple times

• Add AggregatedModelfitResults

• Document scm results

0.15.0 (2021-02-01)

• Change parameter_names config option to be a list of prioritized methods

• Option to read names from $ABBR for NONMEM models

• Add option to give parameter names to methods.add_iiv

• Add calculation of elimination half-life to one comp models in modelfit_results.pk_parameters

• Document cdd results

• Add set_initial_estimates, set_name and copy_model to modeling

• Allow single str as input to add_iiv and add_iov

0.14.0 (2021-01-25)

• Support reading $DES-records

• Add individual_parameter_statistics to ModelfitResults

• Add pk_parameters to ModelfitResults

• Add add_iov to modeling

• Rename add_etas -> add_iiv

0.13.0 (2021-01-18)

• Change names of covariate effect parameters for add_covariate_effects

• Improve ordering of terms in created NONMEM expressions

• Add parameter_inits, base_parameter_change, parameter_variability and coefficients to frem_results

• Add SimevalResults class

• Add fit and read_model_from_string functions to modeling

• Add solver attribute to ODESystem to be able to select ODE-system solver. Currently ADVANs for NONMEM

• New method nonfixed_inits to ParameterSet

• Add residuals attribute to ModelfitResults

• Various bug fixes

• Migrate to github actions for continuous integration

0.12.0 (2020-12-18)

• Add modeling.update_inits, modeling.add_peripheral_compartment and modeling.remove_peripheral_compartment

• Update FREM documentation

• Switch to using modelled covariate values for baselines in FREM

• Add methods for retrieving doses and Cmax, Tmax, Cmin and Tmin from dataset

• Various bugfixes and support for more ADVAN/TRANS combinations

0.11.0 (2020-11-20)

• Method df.pharmpy.observations to extract observations from dataframe

• Add ColumnTypes EVENT and DOSE

• Add model.to_base_model to convert model to its raw base model form

• New functions in modeling: remove_iiv, zero_order_elimination, comined_mm_fo_elimination and add_parameter

• Split modeling.absorption_rate and error into multiple functions

• Add calculations of AIC and BIC to ModelfitResults

• Improved pretty printing

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.