- Support parsing assignments other than DADT in $DES in NONMEM
- Fix parsing of some complex ODE-systems in NONMEM
- Drop support for Python 3.8
- Fix bug causing BIC calculation to fail for models having first order absorption and lag_time after going into zero order absorption
- 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
modeling.generate_model_codewas renamed tomodeling.get_model_codesince the code is not generated by this function- Do not use ADVAN7 because models that should work with ADVAN7 didn't were found
- Fix multiple bugs in parsing $TABLE headers
- 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
- Fix bug where $ABBR wasn't added for etas
- Add function
modeling.create_basic_pk_model - Add function
modeling.add_metabolite - Add function
modeling.set_dvid - Add function
modeling.has_weighted_error_model
model.dependent_variablebecomesmodel.dependent_variables
- Fix regression causing DEFDOSE to sometimes be put on the wrong compartment
- Fix ruvsearch crashing in case of bad modelfit_results (#1551)
- 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
- 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
- Add function
modeling.display_odes - Add support for Python 3.11
- Naming of parameters for NONMEM models reworked. Configuration options removed.
- Only allow MFL as input to
run_covsearch - Remove
read_model_from_databasefrompharmpy.modeling - Merge
ExplicitODESystemintoCompartmentalSystem
- Add algorithm exhaustive_only_eval to Estmethod tool
- Add replace methods to Assignment, Compartment, Bolus and Infusion
- 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
- 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
- Add description to proxy-models (#1314)
- Input check covariates (#1355), allometric variable (#1378) occasion-column before running AMD
- 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)
- 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
- Fix bug in results parsing where extracting whether parameters are fixed (#1117)
- Add timeout-loop to wait for .lst-file when renaming
- Much faster parsing of NONMEM models
- 4 times faster parsing of NONMEM phi files
- 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
- Add modeling.deidentify_data
- Change CLI anonymize into deidentify
- Only test IOV on statements before ODE
- 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)
- modeling.summarize_modelfit_results takes results objects instead of model objects
- Do not include aic and bic in summarize_modelfit_results
- Handle NM-TRAN datasets with one and two digit year in DATx column using default LAST20 (50)
- Add tools.read_modelfit_results
- run_modelsearch, run_iovsearch, run_ruvsearch, run_allometry, run_covsearch, run_amd and run_iivsearch now need results as a separate input
- Correct scaling for F in NOMEM models for ADVAN 2,4,5,7 and 12
- 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
- Let bioavailability parameters be part of rhs of ode_system
- Make sure initials are non-zero for absorption parameters
- 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
- 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
- 297a64041 Handle individual_ofv is None in dofv (fixes #1101)
- 57fc4fee8 Fix adding categorical covariate effects (#1004)
- 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
- 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)
- fb070ee1 Return input model if allometry model fails (#1049)
- Fix issue with adding allometry to models with MM elimination
- Make pyreadr an optional dependency, making Pharmpy easier to install on Mac M1
- 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"
- 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
- Serialize modelfit results #1092
- Exlude "unreportable number of significant digits" in modeling.rank_models (fix #1076)
- SCM forward search followed by backward search in covsearch (#988)
- Change initial estimates of IIV parameters of start model in AMD tool (1c65359)
- Change default order of subtools in AMD tool (42fe72f)
- 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)
- Rename pharmpy.parameter to pharmpy.parameters (71f4cf23)
- Merge COVsearch DSL into MFL (#932, #973)
- Add ZO absorption to default search space in AMD (cfc09bad)
- 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)
- 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
- 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
- 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
- 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')
- Handle etas after ODEs in iivsearch-tool
- Add functions find_clearance_parameters and find_volume_parameters
- Rename candidate models in estmethod tool
- Add upper limit to VP parameter in modelsearch tool
- Fix issue with matrices not being considered positive semidefinite but considered positive definite
- Require pandas 1.4 or newer for multiindex joins. (Fixes #820)
- 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
- 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
- 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)
- Add 1st and 3rd quantiles of residual to simeval results
- 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
- Fix bad odes when adding two peripheral compartments to model with MM elimination
- Fix bug in block splitting in IIV-tool (fixes #745)
- Fix bad odes when adding peripheral compartment to model with MM elimination (fixes #710)
- Add modeling.get_thetas, modeling.get_omegas and modeling.get_sigmas
- Add configuration option for NONMEM license file path
- 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)
- Fix NONMEM model parsing issue causing ADVAN not to change for models with DEFOBS in $MODEL
- Add option in add_iiv and add_pk_iiv to choose initial estimate
- Replace different iiv-options in IIV-tool with iiv_strategy
- Use 0.01 as initial estimate for added IIVs in modelsearch tool
- Add K-parameters in NONMEM model when changing to general linear (GL) solvers
- Add modeling.solve_ode_system
- Add documentation for .datainfo file
- Add iofv plot to linearize results
- Store tool meta data in metadata.json
- New options for modelsearch tool: switch order of mfl and algorithm, replace different iiv-options with iiv_strategy
- Support ~ as HOME in file paths input by users
- Add modeling.read_dataset_from_datainfo
- Store unique datasets for tool runs
- Fix problem with TAD calculation for datasets with ADDL
- Handle LinAlgError when updating initial estimates in modelsearch (#656)
- Store unique datasets in models/.datasets
- New name for final model in resmod
- Use NaN in summary_individuals if tflite cannot be used
- 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)
- Add modeling.summarize_individuals
- Change initial estimates for QP1/QP2 ratio to 0.1/0.9
- Handle ADDL columns for add_time_after_dose
- Add modeling.expand_additional_doses
- 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
- 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
- Add modeling.add_pk_iiv to add iiv to all pk parameters of a model
- Change cutoff for zero protection in proportional error ModelSyntaxError
- Change to checking for positive semidefiniteness instead of only positive definiteness when validating omegas
- 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
- 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)
- Remove ZO elimination from the default search space in model search
- Do not apply resmod mode if no change on the full model
- 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
- Option in modeling.update_inits to move estimates that are close to boundary
- Set different initial estimates of clearance for peripherals (#590)
- 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
- 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
- Fix issue with failing to creating correct subblocks of fullblock of random variables
- Set index name to id-name in predict_outliers
- Add option to remove specific IOV random variables
- Support Python 3.10
- Add modeling.check_dataset
- 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
- 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
- Add covariate search to amd tool
- 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
- modeling.calculate_bic can Calculate three different versions of the BICdefault 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
- Handle long paths when fitting NONMEM model
- Add modeling.write_results
- Add modeling.print_fit_summary
- Add modeling.remove_loq_data
- Add first version of WIP scm wrapper
- 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)
- 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
- Use p-value instead of OFV cutoff in resmod
- Fix issue with no conversion to $DES for some models (#528)
- Parse estimation step runtime from NONMEM results file
- Force initial estimates when reading model file to be positive definite
- Random block was not split properly in some cases when random variable was removed
- Add $COV correctly in NM-TRAN models (#457)
- Add modeling.drop_columns
- Add modeling.drop_dropped_columns
- Add modeling.undrop_columns
- Add modeling.translate_nmtran_time
- 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
- Add timevarying models to resmod
- 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
- Add modeling.bump_model_number
- Fix regression in detection of dv column when synonym was used
- 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
- 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
- Add modeling.add_allometry
- 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
- 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
- Fix bug causing frem report to crash with #IDs > 5000
- Fix bug for shifted uncertainty in frem with bipp
- 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
- 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
- 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)
- 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.
- Fix broken parallelization for tools (workflows)
- Fix bug causing parsing of some NM-TRAN datasets to set a column index
- Fix issues with retrieving results after model runs
- 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
- 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
- Move plot_iofv_vs_iofv to modeling
- Add modeling.get_observations
- Add modeling.plot_individual_predictions
- 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)
- 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
- 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
- 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
- Use dask threaded for Windows, allow configuration of dispatcher type
- Filter out individuals without observations in .phi-file
- Correct residual calculation in simeval
- Correct how laplace estimation method is written
- 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
- 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
- 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
- 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
- 10-100 times Speedup of modeling.evaluate_expression
- Documentation fix for pharmr release
- Handle implicit ELSE clauses for NM-TRAN IF
- Fix bug #177
- Bugfixes
- Add function modeling.evaluate_expression
- Some documentation for modelfit_results
- Reworked interface to RandomVariables and Parameters
- Bugfixes
- Support COM(n) in NONMEM abbreviated code
- Fix stdin handling issue when running NONMEM from R
- 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)
- Fix regression for calling NONMEM
- New function modeling.set_peripheral_compartments
- New tool Model Search
- New model attribute estimation_steps to read and change $ESTIMATION
- Bugfixes (#99, #118)
- Add create_result to create results from PsN
- Add documentation for covariate effects
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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 $TABLE numbers
- Many bugfixes and improvements to NONMEM code record parser
- Add calculation of symbolic and numeric eta and eps gradients, population and individulal prediction and wres for PRED models
- Add option to use comments in NONMEM parameter records as names for parameters
- Reading of ODE systems from NONMEM non-$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
- 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
- New CLI command 'data append'
- Parameter names is now the index in Parameters.summary()
- FREM postprocessing
- Standardized results.yaml and results.csv
First release
Initial library development/testing directory structure.