Metadata-Version: 1.2
Name: pharmpy-core
Version: 0.24.2
Summary: Pharmacometric modelling
Home-page: https://pharmpy.github.io
Author: Rikard Nordgren
Author-email: rikard.nordgren@farmaci.uu.se
License: GNU Lesser General Public License v3 (LGPLv3)
Project-URL: Bug Tracker, https://github.com/pharmpy/pharmpy/issues
Project-URL: Source Code, https://github.com/pharmpy/pharmpy
Description: 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.
        
        0.24.0 (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.
        
Keywords: pharmacometrics
Platform: UNKNOWN
Classifier: Development Status :: 4 - Beta
Classifier: Intended Audience :: Science/Research
Classifier: Intended Audience :: Developers
Classifier: License :: OSI Approved :: GNU Lesser General Public License v3 (LGPLv3)
Classifier: Operating System :: POSIX
Classifier: Operating System :: MacOS
Classifier: Operating System :: Unix
Classifier: Operating System :: Microsoft :: Windows
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 3 :: Only
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3.9
Classifier: Programming Language :: Python :: Implementation :: CPython
Classifier: Topic :: Scientific/Engineering
Requires-Python: >=3.6
