Man pages for dlill/petab
PEtab support for R
| add_stepcolumn | Add step column and fitrank |
| as.data.table.reportYaml | Title |
| cf_applyPaginate | Get list of paginated plots |
| cf_as.parframe | Better as_parframe |
| cfcolors | Colors copied and adapted from dMod |
| cfcolorsFULL | Colors Copied from dMod |
| cfggplot | cfggplot |
| cfgrab | Grab a base plot into grid object |
| cf_outputFigure | Output figures |
| cfoutput_MdTable | Output table as markdown |
| cf_parf_getMeta | Title |
| cf_parf_getPars | Select parameter columns of parframe |
| cf_parf_getStepRepresentatives | Title |
| cf_parf_metaNames | Title |
| cf_parf_parNames | get Parameter names of a parframe |
| cf_parframe | Improved version of parframe |
| cf_parf_rbindlist | Rbind some parframes |
| cf_predict | predict.prdfn with options bowser and verbose |
| cf_profile_getOpenProfiles | Title |
| cf_profile_getOptimum | Title |
| cf_profile_getProfilesOptimumBelowFit | getProfiles with optimum below the fit$argument |
| cf_profile_getStartPar | Title |
| cf_profile_plotPathsAffected | Title |
| cf_profile_prepareAffectedPaths | Prepare parameters affected by a profile |
| check_clusterTimeStamp | Check for the time stamp |
| clusterStatusMessage | Title |
| dco_expandPatterns | Expand columns which have a specified pattern |
| dMod_files | Consistent dMod filenames |
| dmod_obs_2_petab_obs | dMod Observables to PEtab converter |
| dMod_readL1 | Title |
| dMod_readMstrust | Title |
| dMod_readProfiles | Title |
| dMod_saveL1 | Title |
| dMod_saveMstrust | Title |
| dMod_saveProfiles | Consistently save profiles |
| eqnlist_addDefaultCompartment | Title |
| fitModelPEtabSBML | Fit a model imported via importPEtabSBML |
| getCompartmentInfo | get compartmentInfo |
| getConditionsSBML | Import condition.grid from PEtab |
| getDataPEtabSBML | Import Data from PEtab |
| getEventInfo | Title |
| getFacets | Title |
| getInitialsSBML | Import initials from SBML. |
| getObservablesSBML | Import observables from PEtab. |
| getPaginateInfo | get the pagination info from a plot |
| getParametersSBML | Import Parameters from PEtab |
| getParInfo | Extract parInfo data.table from equationlist |
| getReactionInfo | Title |
| getReactionsSBML | Import reactions from SBML. |
| getSpeciesInfo | Extract speciesInfo data.table from equationlist |
| getTrafoType | Determine the type of trafo for each element of a vector |
| getUnitInfo | Assemble unitInfo |
| importPEtabSBML | Import an SBML model and corresponding PEtab objects |
| importPEtabSBML_indiv | Import an SBML model and corresponding PEtab objects |
| indiv2Classic | Title |
| indiv2Classic_compileTrafo | Compile classic trafo |
| indiv2classic_getFasterVersion | Get the faster version of classic and indiv |
| indiv2Classic_gridlist2cond.grid | Title |
| indiv2Classic_merge_grids | Title |
| indiv2Classic_trafo | Title |
| initPd | Title |
| inputFileChanged | Determine if intput file is newer than output file |
| inverse_scale | Title |
| knechtStatusMessage | Title |
| L1_augmentL1Info | Title |
| L1_getModelCandidates | Title |
| L1_getParameterFormulaInjection | Create L1 Trafo, depending on parameterScale |
| lin | Identity |
| pars2parframe | Turn a pars vector into a single-row parframe |
| pd_addObjPrior | Title |
| pd_cluster_L1 | Fit model on cluster |
| pd_cluster_L1_fitUnbiasedEachMstrust | Fit model on cluster |
| pd_cluster_L1_fitUnbiasedEachOnce | Fit model on cluster |
| pd_cluster_L1_mstrust | Fit model on cluster |
| pd_cluster_mstrust | Fit model on cluster |
| pd_cluster_profile | Run profiles on cluster |
| pd_debug_p0 | Mainly to have the code accessible |
| pd_files | Title |
| pd_fit | Run a fit only for observation parameters |
| pd_fitMstrust | Run a mstrust locally |
| pd_fitObsPars | Fit only obsPars |
| pd_guessPetabYaml | Title |
| pdIndiv_getBaseScales | Title |
| pdIndiv_getParameters_conditionGrid | Title |
| pdIndiv_initializeGridlist | Title |
| pdIndiv_rebuildPrdObj | Rebuild the high-level prediction and objective function |
| pdIndiv_updateControls | Quickly set "controls" amd update all high-level functions |
| pd_knecht_L1 | Fit model on knecht |
| pd_knecht_L1_fitUnbiasedEachMstrust | Fit model on knecht |
| pd_knecht_L1_fitUnbiasedEachOnce | Fit model on knecht |
| pd_knecht_L1_mstrust | Fit model on knecht |
| pd_knecht_mstrust | Fit model on knecht |
| pd_knecht_profile | Run profiles on knecht |
| pd_L1_createPetabFromUnbiasedFit | Title |
| pd_L1_getModelCandidates | Title |
| pd_L1_getObjBounds | Title |
| pd_L1_getUnbiasedParframeAllCandidates | Title |
| pd_L1_getUnbiasedValues | Title |
| pd_L1_plotDevianceVsLambda | Title |
| pd_L1_plotIsConvergedVsLambda | Title |
| pd_L1_plotModelCandidates | Title |
| pd_L1_plotMstrustScanWaterfalls | Title |
| pd_L1_plotParValueVsLambda | Plot L1 Parameter values vs lambda |
| pd_L1_plotValueVsLambda | Title |
| pd_L1_preparePlottingData | Prepare data for some L1 plots |
| pd_mstrust | Run mstrust |
| pd_objtimes | Wrapper around predtimes |
| pd_parf_collect | Collect parameters for simultaneous prediction or plotting |
| pd_parf_collectL1 | Title |
| pd_parf_collectMstrust | Title |
| pd_parf_collectPars | Title |
| pd_parf_collectProfile | Title |
| pd_pars_getFixedOnBoundary | Get parameters which are fixed on the boundary |
| pd_petabSelect_collectEstimatedParameters | Collect list of estimated parameters |
| pd_petabSelect_collectParameters | Collect Parameters from PD |
| pd_petabSelect_collectReportYamlCriteria | Collect AIC and BIC from pd |
| pd_petabSelect_reportYaml | Create the reportYaml from a PD |
| pd_plot_compareParameters | Plot multiple parameter vectors in parf as barplots next to... |
| pd_plotParsParallelLines | Plot resulting parameters from mstrust |
| pd_plotProfile | Title |
| pd_plotProfilePaths | Plot affected paths of profiles |
| pd_predictAndPlot2 | Title |
| pd_predtimes | Wrapper around predtimes |
| pd_profile | Title |
| pd_profile_getParsNotYetProfiled | Determine which pars were not yet profiled |
| pd_rdsfile | Get the rds file path in one simple command |
| pd_removeProfiles | Title |
| pd_tests | Some tests |
| pd_updateEstPars | Update parameters |
| pe_L1_addL1ParsToExperimentalCondition | Add parameter columns to experimentalCondition |
| pe_L1_createL1Problem | From a petab, create a petab which encodes an L1 problem |
| pe_L1_updateParameterFormulaInjection | Title |
| pepy_sample_parameter_startpoints | Sample parameter start points |
| pe_sample_parameter_startpoints | Title |
| petab | Collector function for petab files |
| petab_applyInverseObservableTransformation | Title |
| petab_applyObservableTransformation | Title |
| petab_columns | Get list of column names in petab |
| petab_combine | Combine two petabs |
| petab_combine_experimentalCondition | Title |
| petab_combine_measurementData | Title |
| petab_combine_observables | Title |
| petab_combine_parameters | Title |
| petab_createObjPrior | Create the prior function specified in parameters_df |
| petab_create_parameter_df | Original petab function didn't work |
| petab_dput | dput for petab variables |
| petab_duplicateControls | Duplicate control data points |
| petab_exampleList | List all available examples |
| petab_examplePath | Get paths of an example |
| petab_exampleRead | Read an example |
| petab_experimentalCondition | Constructor for Conditions |
| petab_files | List petab files |
| petab_files_default | Get default filenames |
| petab_files_fromYaml | Read list of filenames from a petabYaml |
| petab_fixErrorModel | Replace error parameters in measurementData by sensible... |
| petab_getMeasurementParsMapping | Parse the parameters columns in measurementData |
| petab_getParameterBoundaries | Title |
| petab_getParametersExperimentalCondition | Get parameter names from pe$experimentalCondition |
| petab_getParametersToEstimate | Title |
| petab_getParameterType | Get a mapping of parameter types |
| petab_getPars_estScale | Get parameters on outer scale |
| petab_getPars_linScale | Get parameters on nominal scale |
| petab_hash | Hash a petab |
| petab_joinDCO | Create one big table containing measurementData, observables... |
| petab_lint | Own little linter until petab.py lint is stable |
| petab_measurementData | Constructor for Measurements |
| petab_mergeParameters | Merge parameter values from one petab into another petab |
| petab_meta | Additional Information |
| petab_metaInformation_getPatterns | Get "patterns" from metaInformation |
| petab_model | PEtab structural model without sbml |
| petab_modelname_path | Consistent file names |
| petab_mutateDCO | Consistently mutate the dco |
| petab_observables | Constructor for Observables |
| petab_overview | Print some overview stuff |
| petab_overviewDCONames | Print available names in the DCO |
| petab_overviewObsPerCond | Generate overview table which observables are in which... |
| petab_parameterFormulaInjection | Create a parameterFormulaInjection |
| petab_parameters | Constructor for Parameters |
| petab_parameters_mergeParameters | Title |
| petab_plotData | Plot Petab data |
| petab_plotHelpers_aeslist | Title |
| petab_plotHelpers_meanMeasurementsValue | Title |
| petab_plotHelpers_parameterOrder | Title |
| petab_plotHelpers_variableOrder | Title |
| petab_python_installPackages | Reinstall the python setup |
| petab_python_setup | Setup the connection to python petab |
| petabSelect_collectReportYamlCriteria | Ensure consistent naming of Criteria |
| petabSelect_compareModels | Compare models |
| petab_select_examplePath | Get paths of an select example |
| petabSelect_LRT | Likelihood ratio test |
| petabSelect_readReportYaml | Read report yaml content |
| petabSelect_reportYaml | Collect all information for the reportYaml |
| petabSelect_searchYamls | List yaml files in subdirectories based on a pattern |
| petabSelect_writeReportYaml | Title |
| petab_setPars_estScale | Title |
| petab_setPars_linScale | Title |
| petab_transformPars_est2Lin | Title |
| petab_transformPars_lin2Est | Title |
| petab_unjoinDCO | Unjoin DataConditonObs |
| petabYaml | Gather all filenames in the list structure of a petab.yaml |
| plotParameterComparison | Compare two parameter vectors by plotting their difference as... |
| plotPEtabSBML | Plot observables and states of an SBML/PEtab model |
| readPd | Read a pd and load dlls |
| readPetab | Read PEtab files |
| reexports | Reexports |
| sanitizePowers | Sanitize pow(x,y) equations |
| sbml_addOneCompartment | Add compartment |
| sbml_addOneEvent | Title |
| sbml_addOneParameter | Title |
| sbml_addOneReaction | Title |
| sbml_addOneSpecies | Title |
| sbml_addOneUnit | Add unit |
| sbml_exportEquationList | Write sbml model to filename |
| sbmlImport_getCompartmentsFromSBML | Extract compartments from SBML |
| sbmlImport_getEventsFromTrueEvents | Get Events from "events" entries in SBML |
| sbmlImport_getFunctionInfo | Get function info |
| sbmlImport_getInitialsFromSBML | Import initials from SBML. |
| sbmlImport_getParametersFromSBML | Extract parameters from SBML |
| sbmlImport_getReactionDetails | Title |
| sbml_initialize | Initialize the sbml document |
| sbml_kineticLawAddParameters | Title |
| sbml_reactionAddKineticLaw | Title |
| sbml_reactionAddModifiers | Title |
| sbml_reactionAddProducts | Title |
| sbml_reactionAddReactants | Title |
| sbml_validateSBML | From libSBML example |
| scale_color_cf | scalecolorcf Copied from dMod |
| smblImport_replaceFunctions | Replace function calls by their mathematical expressions |
| stepMax | Plot resulting parameters from mstrust |
| subsetPredictionToData | Subset predictions to observables and conditions observed in... |
| testPEtabSBML | Test PEtabSBML import |
| theme_cf | Nice ggplot theme |
| updateParscalesToBaseTrafo | Rename parscales to the names needed in the base trafo |
| write_clusterTimeStamp | Write the time stamp when you logged into the cluster |
| writePd | Title |
| writePetab | Title |
