pharmpy-core 0.54.0

Pharmacometric modelling

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

Current features:

• A model abstraction as a foundation for higher level operations on models

• Functions for manipulation of models, e.g. changing model components like elimination or absorption

• Reading NONMEM models and results

• Running models and complex workflows (with NONMEM or to some extent nlmixr)

This is the team behind Pharmpy

0.54.0 (2022-03-08)

New features

• New IIV version of BIC in calculate_bic

• Use IIV BIC in iiv tool

• Add allometry step in amd tool

• Reduced stepwise algorithm in modelsearch

• Add cutoff option to predict_outliers etc

Bugfix

• Fix issue with failing to creating correct subblocks of fullblock of random variables

• Set index name to id-name in predict_outliers

0.53.0 (2022-03-04)

New features

• Add option to remove specific IOV random variables

• Support Python 3.10

• Add modeling.check_dataset

Changes

• modeling.calculate_bic: Count epsilons interacting with etas to random parameters

• Updated tensorflow models for prediction of outliers and influential individuals

• Only consider parameters with etas for covariate modelbuilding in amd

• Include AIC/BIC in modeling.summarize_modelfit_results

Bugfix

• Update solvers in estmethod-tool

• Handle Q-parameters when adding IIV on structural parameters in iiv-tool

• Only add IIV on MDT-parameter with add_mdt_iiv-option in modelsearch-tool

0.52.0 (2022-02-25)

New features

• Add covariate search to amd tool

0.51.0 (2022-02-24)

New features

• Add option to add IIV to start model in iiv-tool

• Add solver option in estmethod-tool

• Add option to add IIV only on MDT in modelsearch-tool

Changes

• modeling.calculate_bic can Calculate three different versions of the BIC

  default has switched to be a mixed effects version

• Remove etas instead of setting to 0 fix in iiv-tool

• Parse more errors and warnings in .lst-file

• Rename add_eta -> add_iivs, etas_as_fullblock -> iiv_as_fullblock, add_mdt_eta -> add_mdt_iiv in modelsearch

0.50.1 (2022-02-16)

Bugfix

• Handle long paths when fitting NONMEM model

0.50.0 (2022-02-16)

New features

• Add modeling.write_results

• Add modeling.print_fit_summary

• Add modeling.remove_loq_data

• Add first version of WIP scm wrapper

Changes

• Change in mfl in modelsearch such that transits that don’t keep depot will have additional transit

• Make it possible to set $DATA directly for NONMEM models (via datainfo.path) (#130)

0.49.0 (2022-02-10)

New features

• Add modeling.calculate_se_from_cov

• Add modeling.calculate_se_from_inf

• Add modeling.calculate_corr_from_cov

• Add modeling.calculate_cov_from_inf

• Add modeling.calculate_cov_from_corrse

• Add modeling.calculate_inf_from_cov

• Add modeling.calculate_inf_from_corrse

• Add modeling.calculate_corr_from_inf

• Add modeling.create_report

• Add modeling.check_high_correlations

• Add modeling.calculate_bic

• Add modeling.check_parameters_near_bounds

• Add option to choose search space in AMD-tool

Changes

• Use p-value instead of OFV cutoff in resmod

Bugfix

• Fix issue with no conversion to $DES for some models (#528)

0.48.0 (2022-02-04)

New features

• Parse estimation step runtime from NONMEM results file

Changes

• Force initial estimates when reading model file to be positive definite

Bugfixes

• Random block was not split properly in some cases when random variable was removed

• Add $COV correctly in NM-TRAN models (#457)

0.47.0 (2022-01-28)

• Add modeling.drop_columns

• Add modeling.drop_dropped_columns

• Add modeling.undrop_columns

• Add modeling.translate_nmtran_time

0.46.0 (2022-01-27)

• Add modeling.calculate_aic

• Add modeling.print_model_code

• Add modeling.has_michaelis_menten_elimination

• Add modeling.has_zero_order_elimination

• Add modeling.has_first_order_elimination

• Add modeling.has_mixed_mm_fo_elimination

• Add parent_model attribute to Model object

• Support non-linear elimination in search space in modelsearch tool

• Rename summary -> summary_tool in IIV and modelsearch tool, add summary_models

• Update modelsearch algorithm to only run 2C if previous model is 1C

• Fix bug in transformation order in features column of summary in modelsearch tool

0.45.0 (2022-01-21)

• Add timevarying models to resmod

0.44.0 (2022-01-20)

• Add modeling.create_symbol

• Add modeling.remove_unused_parameters_and_rvs

• Add modeling.mu_reference_model

• Add modeling.simplify_expression

• Add option keep_depot to modeling.set_transit_compartments

• Add CLI for estmethod tool

• Add attributes isample, niter, auto and keep_every_nth_iter to EstimationStep

• Remove stepwise algorithm in modelsearch tool

0.43.0 (2022-01-12)

• Add modeling.bump_model_number

• Fix regression in detection of dv column when synonym was used

0.42.0 (2022-01-11)

• Add modeling.get_doseid

• Add modeling.get_unit_of

• Add modeling.get_concentration_parameters_from_data

• Add modeling.write_csv

• Add modeling.resample_data

• Add modeling.omit_data

• Add modeling.get_observation_expression

• Add modeling.get_individual_prediction_expression

• Add modeling.get_population_prediction_expression

• Add modeling.evaluate_individual_prediction

• Add modeling.evaluate_population_prediction

• Add modeling.calculate_eta_gradient_expression

• Add modeling.calculate_epsilon_gradient_expression

• Add modeling.evaluate_eta_gradient

• Add modeling.evaluate_epsilon_gradient

• Add modeling.evaluate_weighted_residuals

• Support for Python 3.7 dropped

0.41.0 (2021-12-21)

• Add modeling.get_individuals

• Add modeling.get_baselines

• Add modeling.get_covariate_baselines

• Add modeling.get_doses

• Add modeling.list_time_varying_covariates

• Add combined error model to resmod

• Add option to zero_protect to set_proportional_error_model

• Add tool estmeth to find optimal estimation method for a model

• Fix bug causing resmod models to be incorrect

• New model.datainfo object

0.40.0 (2021-12-16)

• Add modeling.add_allometry

0.39.0 (2021-12-15)

• Add AMD and IIV tool and respective functions run_amd and run_iiv

• Add function add_covariance_step and remove_covariance_step

• Add method insert_after to ModelStatements

• Add option to set limit or no limit for power_on_ruv theta

• Rename EstimationMethod to EstimationStep and add EstimationSteps class

• Parse eta and epsilon derivatives from $TABLE

• Fix bug where lag time is removed when changing to ZO or FO absorption

0.38.0 (2021-12-08)

• Add function to get path to user configuration file

• Add function to get missing DVs

• Add option to add IIV on structural parameters (as diagonal and block)

• Add guard for log(0) in proportional error for log data

• Avoid crash if plots cannot be created in CDD results

• Fix issue saving modelsearch results

• Fix bipp issues with etas outside of FREM matrix

0.37.1 (2021-11-26)

• Fix bug causing frem report to crash with #IDs > 5000

• Fix bug for shifted uncertainty in frem with bipp

0.37.0 (2021-11-24)

• First version of IIV-tool

• Rename set_lag_time to add_lag_time

• Include run type in summarize_modelfit_results

• Fix bug with force option in write_model

• Fix bug in parsing .ext-files with tables without header

• Fix bug with nested update_source crashing due to incorrect handling of diagonal records

• Fix bug with inserted IGNORE on comment lines

0.36.0 (2021-11-11)

• Add option to set_dtbs_error_model to fix parameters to 0 (i.e. get data on log-scale)

• Create model file when fitting a model that has no model file

• Fix bug where files are missing during e.g. modelsearch

• Fix crash when including a model with no results in summarize_modelfit_results

• Fix bug in Pharmr where integers where interpreted as floats

• Fix issue with extra IPRED on power_on_ruv model

0.35.0 (2021-11-02)

• Option to include all estimation steps in summarize_modelfit_results

• Use kwargs in set_estimation_step and add_estimation_step

• First version of logger (via model.modelfit_results.log)

0.34.3 (2021-10-28)

• Let parametrization of peripheral compartment rates be kept if volume parameter can be found in the expression for K.

• Fix bug causing crashes when parsing some lst-files due to mixed encodings.

0.34.2 (2021-10-26)

• Fix broken parallelization for tools (workflows)

• Fix bug causing parsing of some NM-TRAN datasets to set a column index

0.34.1 (2021-10-20)

• Fix issues with retrieving results after model runs

0.34.0 (2021-10-14)

• Remove the need for update_source. Instead use model.model_code or modelling.generate_model_code(model)

• str(model) can no longer be used to get the model_code

• Fix crash in model database when using copies of models

0.33.0 (2021-10-11)

• Add modeling.read_model_from_database

• Add modeling.print_model_symbols

• Add modeling.append_estimation_step_options

• Fix crash for $DES models with RATE in dataset

• Fix estimation status for evaluation steps to use latest estimation

0.32.0 (2021-09-28)

• Move plot_iofv_vs_iofv to modeling

• Add modeling.get_observations

• Add modeling.plot_individual_predictions

0.31.0 (2021-09-21)

• Move parameter_sampling-functions into modeling module

• Add run_tool function to modeling

• Add predict_outliers, predict_influential_individuals and predict_influential_outliers functions to modeling

• Update API documentation (e.g. add examples, and improved index)

0.30.0 (2021-09-06)

• Add modeling.load_example_model

• Move eta_shrinkage results method to modeling.calculate_eta_shrinkage

• Add first version of resmod tool

• Update documentation (including API reference)

• Rename summarize_models to summarize_modelfit_results

• Fix bug related in running NONMEM on Windows via Rstudio

0.29.0 (2021-08-25)

• Rename zero_order_absorption to set_zero_order_absorption

• Rename first_order_absorption to set_first_order_absorption

• Rename bolus_absorption to set_bolus_absorption

• Rename seq_zo_fo_absorption to set_seq_zo_fo_absorption

• Rename have_zero_order_absorption to has_zero_order_absorption

• Rename power_on_ruv to set_power_on_ruv

• Rename add_lag_time to set_lag_time

• Move individual_shrinkage results method to modeling.calculate_individual_shrinkage

0.28.0 (2021-08-24)

• Move method individual_parameter_statistics from Results to a function in modeling and rename to calculate_individual_parameter_statistics

• Move method pk_parameters from Results to a function in modeling and rename to calculate_pk_parameters_statistics

• Rename create_rv_block to create_joint_distribution

• Rename split_rv_block to split_joint_distribution

• New default option force=True for write_model

• Rename ninds to get_number_of_individuals

• Rename nobs to get_number_of_observations

• Rename nobsi to get_number_of_observations_per_individual

• Rename remove_error to remove_error_model

• Rename additive_error to set_additive_error_model

• Rename proportional_error to set_proportional_error_model

• Rename combined_error to set_combined_error_model

• Rename has_additive_error to has_additive_error_model

• Rename has_proportional_error to has_proportional_error_model

• Rename has_combined_error to has_combined_error_model

• Rename theta_as_stdev to use_thetas_for_error_stdev

• Rename set_dtbs_error to set_dtbs_error_model

• Rename boxcox to transform_etas_boxcox

• Rename tdist to transform_etas_tdist

• Rename john_draper to transform_etas_john_draper

• Rename iiv_on_ruv to set_iiv_on_ruv

• Rename add_parameter to add_individual_parameter

• Rename first_order_elimination to set_first_order_elimination

• Rename zero_order_elimination to set_zero_order_elimination

• Rename michaelis_menten_elimination to set_michaelis_menten_elimination

• Rename mixed_mm_fo_elimination to mixed_mm_fo_elimination

• Function summarize_models to create a summary of models

• Parse total runtime

• Revert to dask distributed

0.27.0 (2021-08-09)

• Use dask threaded for Windows, allow configuration of dispatcher type

• Filter out individuals without observations in .phi-file

0.26.1 (2021-08-04)

• Correct residual calculation in simeval

• Correct how laplace estimation method is written

0.26.0 (2021-07-13)

• Add functions to set, add, and remove estimation step

• Add supported estimation methods (ITS, LAPLACE, IMPMAP, IMP, SAEM)

• When updating estimation step, old options are kept

0.25.1 (2021-07-08)

• Read site path if user path doesn’t exist (previously read user path)

• Change return type of covariates to a list for easier handling in R

0.25.0 (2021-06-24)

• Add modeling.ninds, nobs and nobsi to get number of individuals and observations of dataset

• Add reading results for resmod and crossval

• Add structural bias, simeval and resmod results to qa results

• Update index of cdd case_results to plain numbers

• Support line continuation (&) in NM-TRAN code

• Fix error in calculation of sdcorr form of parameter estimates

• Fix crash of cdd results retrieval

• Various fixes for running NONMEM models

0.24.0 (2021-05-25)

• Added theta_as_stdev, set_weighted_error_model and set_dtbs_error

• Error models can be added with log transformed DV using data_trans option

• Added model attributes data_transformation and observation_transformation

• Protected functions in NM-TRAN translated to Piecewise. Should now give the same result as when evalutated by NONMEM.

• Bugfixes for frem, scm and bootstrap results generation

• Rename model attribute dependent_variable_symbol to dependent_variable

• Added simplify method on Parameter class to simplify expressions given parameter constraints

0.23.4 (2021-05-03)

• 10-100 times Speedup of modeling.evaluate_expression

0.23.3 (2021-04-29)

• Documentation fix for pharmr release

• Handle implicit ELSE clauses for NM-TRAN IF

0.23.2 (2021-04-28)

• Fix bug #177

0.23.1 (2021-04-28)

• Bugfixes

0.23.0 (2021-04-28)

• Add function modeling.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.