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Changelog#

0.109.0 (2024-04-10)#

New features#

  • The structsearch tool can now take an mfl string as search space

  • Allow list of lists of parameters in iovsearch options

  • Explicitly handle CMT columns for observations in the expression for F for NONMEM models

Changes#

  • Deafault to keeping eta on CL in iivsearch

Bugfixes#

  • Handle cases with covariates on MU when parsing phi-file with PHI columns

  • Fix issues with allometry and structural covariates for PKPD models in amd

  • Fix broken conversion to RxODE for models without ODE system

  • Fix handling of datasets with multiple DVIDs in ruvsearch and sructsearch for TMDD models

0.108.0 (2024-03-18)#

New features#

  • New simulation tool tools.run_simulations

  • Add reports with various plots for final model in all AMD subtools

  • Add VPC plot to AMD

  • Add functions modeling.add_predictions_residuals and modeling.remove_predictions_residuals

Changes#

  • Force positive definitiveness in retries tool

  • Make initial estimates in AMD mandatory

  • Add default search space for PKPD models

  • Remove TMDD models with less than 2 DVs

Bugfixes#

  • Correct extraction of CL/VC parameters in PSC metabolite models

  • Remove unused K-parameters from NONMEM code

  • Correct number of expected models in BIC calculation for bottom up algorithm in IIVSearch

  • Use input model results when updating initial estimates for first model in bottom up algorithm in IIVSearch

  • Add keep-option to bottom up algorithm in IIVSearch

0.107.0 (2024-03-04)#

New features#

  • Add bottom up algorithm in IIVSearch

  • Add modeling.set_dataset

  • Add AMD results plots for each DV

  • Add default search space for TMDD in AMD

  • Support EFIM as parameter uncertainty method

  • Allow specific (covariate, parameter) combinations as part of input for mechanistic covariates in AMD

Changes#

  • Use Pharmpy class Expr instead of sympy/symengine

  • Remove ModelfitResults attribute from Model

  • Change logic of IIVsearch algorithm argument, add correlation_algorithm argument

  • Ignore datainfo fallback in AMD (to avoid automatically filling in information not given by user)

  • Raise error instead of warn when expression is invalid in modeling.filter_dataset

  • Change strategy names in AMD (to “default” and “reevaluation”)

Bugfixes#

  • Keep IIV on all clearance parameters of central compartment in AMD

  • Fix bug in AMD for TMDD models where dir_name was not specified

  • Fix bug with naming of K-parameters in models with 9 compartments

  • Skip first order absorption with 1 transit (no depot) combination

  • Fix bug which caused added IOVs to be removed in covsearch when running AMD (edited)

0.106.0 (2024-01-11)#

New features#

  • Change to mBIC as default ranking function in modelsearch, iivsearch and iovsearch

  • Add modeling.get_central_volume_and_clearance

  • New option parameter_uncertainty_method to amd

  • New option ignore_datainfo_fallback to amd

  • Handle conversion to ETA/ETC for PHI/PHC in NONMEM phi files

Changes#

  • Remove the order option in amd and instead add strategy with “fixed” orders and options to subtools

Bugfixes#

  • Allow ~ in paths in write_csv

  • Have non-linear elimination models in default search space for amd TMDD models

  • Fix issue causing removed off-diagonal omegas being transformed into thetas

  • Fix issues in frem postprocessing when using mu-referencing

0.105.0 (2023-12-07)#

New features#

  • Add modeling.bin_observations

  • Add modeling.plot_dv_vs_pred

  • Add modeling.plot_abs_cwres_vs_ipred

  • Support strictness for thetas, omegas and sigmas separately

  • Support stagewise addition of covariates in amd

  • Support multiple DVs for TMDD models

  • Add retries tool

  • Use retries in the amd

Changes#

  • Always keep an iiv eta on clearence in amd

0.104.0 (2023-11-06)#

New features#

  • Add modeling.replace_non_random_rvs

  • Add option keep_index to modeling.get_observations to allow keeping the original dataset index

  • Add path-option to tools.fit

  • Add function tools.is_strictness_fulfilled

  • Add strictness option to AMD and subtools

  • Add TMDD models to AMD

  • Add option for TMDD models in structsearch

  • MFL for COVSearch works the same way as for Modelsearch

Bugfixes#

  • Properly handle 0 FIX etas in calculate_bic

  • Fix crash when setting 0 transit compartments

  • Fix various bugs in TMDD models (including allometry)

0.103.0 (2023-10-12)#

Changes#

  • Update initial estimates in structsearch

  • Add option dv to modeling.get_individual_parameters

  • Add default search space for drug-metabolite models in AMD

Bugfixes#

  • Fix bug in calculate_bic where parameters were incorrectly set to fixed for PKPD and drug-metabolite models

  • Fix bug in COVSearch step numbering

  • Fix bug in COVSearch where the final_model was set incorrectly

  • Fix bug in COVSearch where p-value wasn’t displayed for backward models

0.102.0 (2023-09-28)#

New features#

  • Add modeling.plot_dv_vs_ipred

  • Add modeling.plot_cwres_vs_idv

  • Add modeling.add_indirect_effect

  • Add option for presystemic circulation for modeling.add_metabolite

  • Add bic for multiple testing in modeling.calculate_bic

  • Support PKPD models in the amd tool

  • Support Drug-metabolite models in the amd tool

  • Add first version of report for amd

  • Add PKPD models to MFL

  • Add modeling.filter_dataset

Changes#

  • Change default p-value in ruvsearch from 0.05 to 0.001

  • Change default p-values in covsearch from 0.05 and 0.01 to 0.01 and 0.001

  • Change the mfl for modelsearch to mean search space and not which transformations to do

  • Change the syntax for LAGTIME in the MFL

Bugfixes#

  • Allow ~ for home directory in read_modelfit_results

0.101.0 (2023-09-01)#

New features#

  • Add modeling.load_dataset and modeling.unload_dataset

  • Add @BIOAVAIL to MFL

  • Add support for iv-oral administration for amd tool

0.100.0 (2023-08-25)#

New features#

  • Support for M5, M6 and M7 methods for blq data

  • New symbols @PK and @PD in MFL

  • Internal support for multiple doses to one compartment

Changes#

  • Change the blqdv type to blq in datainfo

  • Better usage of BLQ and LLOQ columns for blq data

0.99.0 (2023-08-23)#

New features#

  • Add function modeling.set_reference_values

  • Add function modeling.set_lloq_data

  • Parse IV+oral models using CMT column

  • Specify DV in RUVSearch

  • Option to add logit IIV in add_iiv

  • New options for remove_loq_data

Changes#

  • Make Task and Workflow immutable

  • Ignore fixed IIVs/IOVs in IIVSearch and IOVSearch

Bugfixes#

  • Fix bug where epsilons where removed in remove_iiv

  • Fix bug in create_basic_pk_model to handle space separated datasets

0.98.0 (2023-07-21)#

New features#

  • Support for multiple doses

  • Add function modeling.add_bioavailability

  • Add function modeling.remove_bioavailability

  • Support for PKPD models in structsearch

  • Option to keep IIVs in IIVSearch

  • Option to test uncertainty methods in Estmethod

  • Autogenerate CMT column

Changes#

  • Rename BLQ flag datainfo typ to blqdv

0.97.0 (2023-06-28)#

New features#

  • Support BLQ transformations in RUVSearch

  • New tool structsearch and support for TMDD models

  • Add function modeling.set_direct_effect

  • Add function modeling.add_effect_compartment

Changes#

  • Reorganizing of modeling module

  • Support changing error model with BLQ transformation

  • Add max_iter option for RUVSearch

0.96.0 (2023-05-26)#

Changes#

  • Rename functions handling the precision matrix (was previously referring to information matrix which was an error)

  • Remove saddle reset for default AMD model

  • Let LLQ column takes precedence over BLQ column

New features#

  • Add tools.load_example_modelfit_results

Bugfixes#

  • Fix bug where if-statements were reordered incorrectly

0.95.0 (2023-05-22)#

Changes#

  • ModelfitResults.ofv_iterations and ModelfitResults.parameter_estimates_iterations have NaN rows in failed runs

Bugfixes#

  • Fix bug causing changes in FIX from model1 to model4 to crash frem

  • Fix bug causing individual parameters in $ERROR to crash frem

  • create_report now does not assume that results.json already exists

  • ~ for $HOME is now supported in write_model and create_report

  • Fix bug where LLOQ value did not override column in dataset in transform_blq

  • Correct BLQ indicator column condition in transform_blq

  • Fix bug where modelfit results were not connected to model after a fit

0.94.0 (2023-04-26)#

New features#

  • Support parsing assignments other than DADT in $DES in NONMEM

  • Fix parsing of some complex ODE-systems in NONMEM

Changes#

  • Drop support for Python 3.8

Bugfixes#

  • Fix bug causing BIC calculation to fail for models having first order absorption and lag_time after going into zero order absorption

0.93.0 (2023-04-19)#

New features#

  • Add function modeling.get_zero_order_inputs

  • Add function modeling.set_zero_order_input

  • Add function modeling.set_tmdd

  • Added plugin to convert models to RxODE

  • Support conversion of more models to nlmixr

Changes#

  • modeling.generate_model_code was renamed to modeling.get_model_code since the code is not generated by this function

  • Do not use ADVAN7 because models that should work with ADVAN7 didn’t were found

Bugfixes#

  • Fix multiple bugs in parsing $TABLE headers

0.92.0 (2023-04-05)#

New features#

  • Add function modeling.is_linearized

  • Add function modeling.plot_transformed_eta_distributions

  • Add function modeling.create_config_template

  • Add function modeling.get_dv_symbol

  • Add function modeling.get_initial_conditions

  • Add function modeling.set_initial_condition

  • Add function modeling.transform_blq

Bugfixes#

  • Fix bug where $ABBR wasn’t added for etas

0.91.0 (2023-03-03)#

New features#

  • Add function modeling.create_basic_pk_model

  • Add function modeling.add_metabolite

  • Add function modeling.set_dvid

  • Add function modeling.has_weighted_error_model

Changes#

  • model.dependent_variable becomes model.dependent_variables

Bugfixes#

  • Fix regression causing DEFDOSE to sometimes be put on the wrong compartment

  • Fix ruvsearch crashing in case of bad modelfit_results (#1551)

0.90.0 (2023-02-24)#

New features#

  • Add function modeling.has_odes

  • Add function modeling.has_linear_odes

  • Add function modeling.has_linear_odes_with_real_eigenvalues

  • Add function modeling.is_real

  • Support for more types of models in the nlmixr plugin

  • Automatic selection between ADVAN5 and ADVAN7 for NONMEM models

Changes#

  • Remove modeling.copy_model

  • Support nlmixr2 instead of nlmixr for the nlmixr plugin

  • The Model class is now immutable

  • update_source is run by all transformation functions

0.89.0 (2023-01-26)#

New features#

  • Add function modeling.display_odes

  • Add support for Python 3.11

Changes#

  • Naming of parameters for NONMEM models reworked. Configuration options removed.

  • Only allow MFL as input to run_covsearch

  • Remove read_model_from_database from pharmpy.modeling

  • Merge ExplicitODESystem into CompartmentalSystem

0.88.0 (2022-12-21)#

New features#

  • Add algorithm exhaustive_only_eval to Estmethod tool

  • Add replace methods to Assignment, Compartment, Bolus and Infusion

Changes#

  • Rename algorithms in Estmethod tool: reduced -> exhaustive. exhaustive -> exhaustive_only_eval

  • Always add iteration 0 in ofv_iterations and parameter_estimates_iterations for eval models with FO/FOCE

0.87.0 (2022-12-14)#

Changes#

  • Allometry model will update initial estimates in allometry tool

  • Base model in IIVSearch tool will update initial estimates

  • Do not update initial estimates from model that did not minimize successfully (except rounding errors), this affects all AMD subtools

  • Rename derive to replace in some base classes

0.86.0 (2022-11-30)#

Changes#

  • Add description to proxy-models (#1314)

  • Input check covariates (#1355), allometric variable (#1378) occasion-column before running AMD

Bugfixes#

  • Fix typo in COVSearch that caused it to select model with highest OFV (#1377)

  • Ignore NaNs when selecting models in COVSearch (#1381)

  • Fix issue where initial estimate for KM (in MM-elimination) was set outside of NONMEM’s bounds (#1064)

  • Fix issue where individuals without observations were not filtered for general model objects (afd7707, #1139)

  • Fix issue where saddle reset was not added in start model for AMD (#1394)

0.85.0 (2022-11-18)#

Changes#

  • Covariates are defined in search space option in AMD-tool

  • Store name of final model instead of final model in AMD

  • Change methods and solvers option in estimation method tool: None means none should be tested

  • Add FORMAT option if length of IDs are too long (#1139)

  • Make Result classes immutable

Bugfixes#

  • Fix bug in results parsing where extracting whether parameters are fixed (#1117)

  • Add timeout-loop to wait for .lst-file when renaming

0.84.1 (2022-11-13)#

Changes#

  • Much faster parsing of NONMEM models

  • 4 times faster parsing of NONMEM phi files

Bug fixes#

  • Have correct F-statement in $ERROR for $DES NONMEM models

  • Read compartment names correctly when having both NCOMP and COMP in $MODEL of NONMEM models

0.84.0 (2022-11-09)#

New features#

  • Add modeling.deidentify_data

Changes#

  • Change CLI anonymize into deidentify

0.83.0 (2022-11-01)#

Changes#

  • Only test IOV on statements before ODE

Bug fixes#

  • Allow spaces in DADT definitions when parsing ODE

  • Fix issue where expression setter was used

  • Fix issue in IIVSearch where tool doesn’t continue to next step if there is a multivariate distribution

  • Input dataset into model constructor in convert model (fixes #1293)

  • Modelfit should not crash if .lst-file does not exist, warns if .lst and .ext-files do not exist (#1302, #1303)

0.82.0 (2022-10-24)#

Changes#

  • modeling.summarize_modelfit_results takes results objects instead of model objects

  • Do not include aic and bic in summarize_modelfit_results

0.81.1 (2022-10-24)#

Bug fixes#

  • Handle NM-TRAN datasets with one and two digit year in DATx column using default LAST20 (50)

0.81.0 (2022-10-21)#

New features#

  • Add tools.read_modelfit_results

Changes#

  • run_modelsearch, run_iovsearch, run_ruvsearch, run_allometry, run_covsearch, run_amd and run_iivsearch now need results as a separate input

Bug fixes#

  • Correct scaling for F in NOMEM models for ADVAN 2,4,5,7 and 12

0.80.0 (2022-10-19)#

Changes#

  • modeling.fit returns ModelfitResults instead of Model

  • Let zero_protect default to True for modeling.set_proportional_error_model

  • Faster parsing of NONMEM table files

Bug fixes#

  • Let bioavailability parameters be part of rhs of ode_system

  • Make sure initials are non-zero for absorption parameters

0.79.0 (2022-10-16)#

New features#

  • Relative paths in files, absolute paths in Python objects (#1180, fixes 887)

  • Validate tool inputs (#1162, fixes #1032)

  • Add allow_nested flag to add_covariate_effect (#1004)

  • Add has_covariate_effect and remove_covariate_effect (#1004)

  • Generalize get_rv_parameters (#1181)

  • 9fd701521 Store input models in tool database

  • Replace best_model with final_model_name and retrieve_final_model

  • a7fbcbfe2 Handle results and databases as input to retrieve_models

  • Add modeling.update_initial_individual_estimates function

Changes#

  • Include input model as step 0 in summary_models for AMD tools

  • Rename all AMD tool candidates such that modelsearch_candidate1 -> modelsearch_run1

  • Add columns for number of parameters and delta parameters in summary_tool for AMD tools

  • Only include chosen models in AMD summary_tool

  • New names and description for COVSearch candidates

  • Modify COVSearch summary_tool to include information from the steps-table, remove ranking

  • New candidate descriptions in IOVSearch

  • Add multiindex to RUVSearch which include step/iteration, remove ranking.

  • Add algorithm column to IIVSearch summary_tool, remove algorithm from candidate name

  • Compare final model in IIVSearch to input model, return input if worse

  • Generalize detection of existing effects in add_covariate_effect (#1004)

  • calculate_bic and calculate_aic will need the -2LL as input instead of modelfit_results

  • calculate_eta_shrinkage needs the explicit arguments parameter_estimates and individual_estimates

  • calculate_individual_shrinkage needs the explicit arguments parameter_estimates and individual_estimates_covariance

  • check_parameters_near_bounds needs the parameter estimates given in the arguments

  • check_high_correlations needs the correlation matrix as an explicit argument

  • plot_iofv_vs_iofv takes two iofv series instead of two models as input

  • plot_individual_predictions takes the predictions dataframe as input

  • create_joint_distribution takes an option individual_estimates argument and does not use modelfit_results directly

  • evaluate_expression to get parameter estimates from optional argument instead of from modelfit_results

  • evaluate_population_prediction will not take parameter estimates from modelfit_results

  • evaluate_individual_prediction will not take parameter estimates from modelfit_results

  • evaluate_eta_gradient will not take parameter estimates from modelfit_results

  • evaluate_epsilon_gradient will not take parameter estimates from modelfit_results

  • evaluate_weighted_residuals will not take parameter estimates from modelfit_results

  • sample_parameters_from_covariance_matrix will need parameter_estimates and covariance_matrix as explicit arguments

  • sample_parameters_uniformly will need parameter_esimtates as explicit arguments

  • sample_individual_estimates will need individual_estimates and individual_estimates_covariance as explicit arguments

  • calculate_individual_parameter_statistics and calculate_pk_parameters_statistics will need parameter estimates and covariance matrix

  • update_inits need explicit estimates as argument and does not use modelfit_results

  • update_inits does not update initial individual estimates

  • Move predict_* functions from modeling to pharmpy.tools

  • Move summarize_individuals and summarize_individuals_count_table to pharmpy.tools

  • Move print_fit_summary to pharmpy.tools

  • Move write_results to pharmpy.tools

  • Move summarize_errors to pharmpy.tools

  • Move rank_models to pharmpy.tools

  • Move summarize_modelfit_results to pharmpy.tools

  • Speedup parsing of NONMEM results

Bug fixes#

  • 297a64041 Handle individual_ofv is None in dofv (fixes #1101)

  • 57fc4fee8 Fix adding categorical covariate effects (#1004)

0.78.0 (2022-09-20)#

Changes#

  • fd417aaf Always return a new model in convert_model

  • d5458e36 Raise KeyError in LocalModelDirectory#retrieve_model (instead of FileNotFoundError)

  • 1193bd39 Remove unused pharmpy.symbols submodule

Bugfixes#

  • bb96a13c Fix update_parameters when parameters are added

  • 0ca786c5 Fix backward search of covsearch

  • dd056da3 Fix for models with bioavailability parameters

  • 915bc9c7 Fix get_config_path output when config file is disabled

  • 82b32278 Remove some unwanted debug printing

  • 1131a610 Fix issue in PsN SCM results parsing

  • ebfafb45 Assign ODE as compartmental system to variable (#1173)

0.77.0 (2022-09-08)#

Changes#

  • fb070ee1 Return input model if allometry model fails (#1049)

0.76.1 (2022-09-06)#

Bugfixes#

  • Fix issue with adding allometry to models with MM elimination

  • Make pyreadr an optional dependency, making Pharmpy easier to install on Mac M1

0.76.0 (2022-09-05)#

New features#

  • Add modeling.get_evid to get or create evid from a model

  • Add modeling.get_cmt to get or create a cmt column from a model

  • New column type: “rate”

Changes#

  • Rename “resmod” tool to “ruvsearch”

  • Return only DataFrame in modeling.rank_models

  • Fall back to rank value if model fails in modeling.rank_models (fix #916)

  • Rename “strictness” to “errors_allowed” in modeling.rank_models

  • Only allow “rounding errors” by amd, iivsearch, iovsearch, modelsearch and covsearch (fix #1055)

  • Add attibute significant_digits to ModelfitResults

Bugfixes#

  • Serialize modelfit results #1092

  • Exlude “unreportable number of significant digits” in modeling.rank_models (fix #1076)

0.75.0 (2022-08-10)#

New features#

  • SCM forward search followed by backward search in covsearch (#988)

Changes#

  • Change initial estimates of IIV parameters of start model in AMD tool (1c65359)

  • Change default order of subtools in AMD tool (42fe72f)

Bugfixes#

  • Make NONMEM column renaming work in more cases (#1001)

  • Fix issue when search spaces which lead to uneven branch length in reduced stepwise algorithm (#694)

  • Fix issue with error record not numbering amounts properly with non-linear elimination (#708)

  • Fix issue with comments being removed in omega blocks (#790, #974)

  • Fix ranking issue when candidate models do not produce an OFV (#1017)

  • Fix issue with reading datasets in AMD with RATE column (#989)

0.74.0 (2022-07-18)#

Changes#

  • Rename pharmpy.parameter to pharmpy.parameters (71f4cf23)

  • Merge COVsearch DSL into MFL (#932, #973)

  • Add ZO absorption to default search space in AMD (cfc09bad)

Bugfixes#

  • Make run_amd work in more cases (#975)

  • Make run_iovsearch work in more cases (#917, #977)

  • Make remove_iov work in more cases (#917)

  • Make get_pk_parameters/run_covsearch work in more cases (#908)

  • Make NONMEM .mod parsing work in more cases (#917, #975, #977)

  • Make NONMEM .mod updating work in more cases (fd564168)

  • Make NONMEM dataset column dropping work in more cases (088a046a)

  • Make ODES updates work in more cases (c76fa476, 430f1d2e)

0.73.0 (2022-06-21)#

New features#

  • Add covsearch tool

  • Add function tools.retrieve_models to read in models from a tool database

  • Add functions modeling.get_individual_parameters, modeling.get_pk_parameters, modeling.get_rv_parameter, and modeling.has_random_effect

Changes#

  • Include covsearch tool in AMD

  • Add results for AMD tool

  • Move fit, run_tool, run_amd, and all tool wrappers from modeling module to tool module

  • Rename ‘diagonal’ -> ‘add_diagonal’ in iiv strategy option for iivsearch and modelsearch tool

  • Include column for selection criteria in rank_models

0.72.0 (2022-06-08)#

New features#

  • Add iovsearch tool

  • Add function modeling.summarize_errors to get a summary dataframe of parsed errors from result files

  • Add modeling.make_declarative

  • Add modeling.cleanup_model

  • Add modeling.greekify_model

Changes#

  • Use ‘no_add’, ‘diagonal’, ‘fullblock’, or ‘absorption_delay’ instead of numbers for iiv_strategy in iivsearch and modelsearch-tool

  • Add results and documentation for allometry tool

  • Add error summaries to iivsearch, modelsearch, resmod, and allometry tools

  • Add algorithm argument in estmethod tool (‘exhaustive’ and ‘reduced’)

Bugfixes#

  • Handle etas after ODEs in iivsearch-tool

0.71.0 (2022-05-24)#

New features#

  • Add functions find_clearance_parameters and find_volume_parameters

Changes#

  • Rename candidate models in estmethod tool

Bugfixes#

  • Add upper limit to VP parameter in modelsearch tool

  • Fix issue with matrices not being considered positive semidefinite but considered positive definite

0.70.1 (2022-05-17)#

Bugfixes#

  • Require pandas 1.4 or newer for multiindex joins. (Fixes #820)

0.70.0 (2022-05-13)#

New features#

  • New tool allometry added

  • Add modeling.summarize_individuals_count_table

  • Add modeling.calculate_ucp_scale

  • Add modeling.calculate_parameters_from_ucp

  • Add description attribute to model objects

  • Add wrappers for iivsearch and modelsearch tools (run_iivsearch and run_modelsearch)

  • Add documentation for iivsearch tool

Changes#

  • resmod can now iterate and add multiple residual error models

  • Automatically generate R examples in a seprate tab in documentation

  • Merge iiv functions into one iivsearch algorithm (‘brute_force’)

  • Use parameter names instead of eta names in iivsearch tool features

Bugfixes#

  • Make sure dropping of DATE columns in NONMEM models are handled correctly

  • Solve issue with sporadic crashes because of a database race condition

  • Solve issue with sporadic crashes caused by race in lazy parsing of NONMEM records

  • Fix issues with converting some piecewise functions to NONMEM code correctly

  • Fix issue with generating candidate models for iivsearch tool

  • Fix issue with duplicate candidate models in iivsearch tool (#745)

0.69.0 (2022-04-29)#

New features#

  • Add 1st and 3rd quantiles of residual to simeval results

Changes#

  • Rename mfl -> search_space in modelsearch and amd

  • Use BIC as default ranking function in modelsearch

  • Start model in modelsearch is not fitted

  • Update modelsearch documentation

Bugfixes#

  • Fix bad odes when adding two peripheral compartments to model with MM elimination

  • Fix bug in block splitting in IIV-tool (fixes #745)

0.68.0 (2022-04-27)#

Bugfixes#

  • Fix bad odes when adding peripheral compartment to model with MM elimination (fixes #710)

0.67.0 (2022-04-25)#

New features#

  • Add modeling.get_thetas, modeling.get_omegas and modeling.get_sigmas

  • Add configuration option for NONMEM license file path

Bugfixes#

  • Correct parsing of ADVAN=ADVANx in $SUBROUTINES in NONMEM models

  • Fix issue with duplicated TAD in $INPUT after add_time_after_dose

  • Fix issue with not being able to use models with assignments in $DES in estmethod tool

  • Set an upper limit for intercompartmental clearances in the modelsearch tool (fixes #695)

0.66.0 (2022-04-20)#

Bugfixes#

  • Fix NONMEM model parsing issue causing ADVAN not to change for models with DEFOBS in $MODEL

0.65.0 (2022-04-14)#

New features#

  • Add option in add_iiv and add_pk_iiv to choose initial estimate

Changes#

  • Replace different iiv-options in IIV-tool with iiv_strategy

  • Use 0.01 as initial estimate for added IIVs in modelsearch tool

Bugfixes#

  • Add K-parameters in NONMEM model when changing to general linear (GL) solvers

0.64.0 (2022-04-12)#

New features#

  • Add modeling.solve_ode_system

  • Add documentation for .datainfo file

  • Add iofv plot to linearize results

  • Store tool meta data in metadata.json

Changes#

  • New options for modelsearch tool: switch order of mfl and algorithm, replace different iiv-options with iiv_strategy

0.63.0 (2022-04-07)#

New features#

  • Support ~ as HOME in file paths input by users

  • Add modeling.read_dataset_from_datainfo

  • Store unique datasets for tool runs

Bugfixes#

  • Fix problem with TAD calculation for datasets with ADDL

  • Handle LinAlgError when updating initial estimates in modelsearch (#656)

0.62.0 (2022-04-04)#

New feature#

  • Store unique datasets in models/.datasets

Changes#

  • New name for final model in resmod

Bugfixes#

  • Use NaN in summary_individuals if tflite cannot be used

0.61.1 (2022-03-31)#

Bugfixes#

  • Fix time after dose calculation for steady state dosing

  • Fix issue where create_joint_distribution could create matrices that are not positively definite (#649)

  • Keep IIV from MAT in MDT when adding a transit (#654)

0.61.0 (2022-03-29)#

New features#

  • Add modeling.summarize_individuals

Changes#

  • Change initial estimates for QP1/QP2 ratio to 0.1/0.9

Bugfixes#

  • Handle ADDL columns for add_time_after_dose

0.59.0 (2022-03-25)#

New features#

  • Add modeling.expand_additional_doses

0.58.4 (2022-03-24)#

Bugfixes#

  • Fix issue with start model not being selected if no candidates are better in IIV- and modelsearch-tool

  • Fix issue with ranking models by dBIC in IIV-tool

0.58.1 (2022-03-22)#

Bugfixes#

  • Fix ordering of TAD values for dose at some time as observation

  • Fix TAD values for datasets with reset time event

  • Handle models with no covariates for predict_outliers and predict_influential_individuals

0.58.0 (2022-03-22)#

New features#

  • Add modeling.add_pk_iiv to add iiv to all pk parameters of a model

Changes#

  • Change cutoff for zero protection in proportional error ModelSyntaxError

  • Change to checking for positive semidefiniteness instead of only positive definiteness when validating omegas

Bugfixes#

  • Fix BIC-mixed calculation to not count thetas related to non-random etas (0 FIX) towards random parameters

  • Read 0 FIX diagonal etas as random variables

0.57.0 (2022-03-21)#

Bugfixes#

  • Keep thetas/etas when going across absorption transformations (#588, #625)

  • Fix missing ALAG-parameter in non-linear elimination (#578)

  • Fix issue with added VC1-parameter when adding transits to non-linear elimination (#577)

  • Fix missing D1-parameter and RATE-column when adding zero order absorption to non-linear elimination (#578)

  • Only do update_inits if start model was successful in IIV-tool (#632)

  • Fix issue where etas where added to KA/K-parameters instead of MAT/MDT (#636)

0.56.0 (2022-03-17)#

Changes#

  • Remove ZO elimination from the default search space in model search

  • Do not apply resmod mode if no change on the full model

Bugfixes#

  • Fix bad calculation of number of observations for datasets with both EVID and MDV

  • Properly handle observations and dose at same time for time after dose calculation

  • Handle DATE column for time after dose calculation

  • Handle NONMEM models with no ETAs

0.55.0 (2022-03-16)#

New features#

  • Option in modeling.update_inits to move estimates that are close to boundary

Changes#

  • Set different initial estimates of clearance for peripherals (#590)

Bugfixes#

  • Fix issue with duplicated features with IIV-options in modelsearch-tool

  • Fix issue where $MODEL was not added when setting ODE solver to GL or GL_REAL

  • Fix issue where reduced_stepwise failed for certain search spaces (#616)

  • Fix issue with reading in sampled_iofv in simeval

  • Use the same time varying cutoff for resmod models and best model

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

Bugfixes#

  • 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

Bugfixes#

  • 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)#

Bugfixes#

  • 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

Bugfixes#

  • 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 modeling.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.

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