Package: campsismod 1.1.1
Nicolas Luyckx
campsismod: Generic Implementation of a PK/PD Model
A generic, easy-to-use and expandable implementation of a pharmacokinetic (PK) / pharmacodynamic (PD) model based on the S4 class system. This package allows the user to read/write a pharmacometric model from/to files and adapt it further on the fly in the R environment. For this purpose, this package provides an intuitive API to add, modify or delete equations, ordinary differential equations (ODE's), model parameters or compartment properties (like infusion duration or rate, bioavailability and initial values). Finally, this package also provides a useful export of the model for use with simulation packages 'rxode2' and 'mrgsolve'. This package is designed and intended to be used with package 'campsis', a PK/PD simulation platform built on top of 'rxode2' and 'mrgsolve'.
Authors:
campsismod_1.1.1.tar.gz
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campsismod_1.1.1.tgz(r-4.4-any)campsismod_1.1.1.tgz(r-4.3-any)
campsismod_1.1.1.tar.gz(r-4.5-noble)campsismod_1.1.1.tar.gz(r-4.4-noble)
campsismod_1.1.1.tgz(r-4.4-emscripten)campsismod_1.1.1.tgz(r-4.3-emscripten)
campsismod.pdf |campsismod.html✨
campsismod/json (API)
NEWS
| # Install 'campsismod' in R: |
| install.packages('campsismod', repos = c('https://calvagone.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/calvagone/campsismod/issues
Datasets:
- model_suite - CAMPSIS model suite.
Last updated 9 months agofrom:df0ac21274. Checks:OK: 7. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 12 2024 |
| R-4.5-win | OK | Nov 12 2024 |
| R-4.5-linux | OK | Nov 12 2024 |
| R-4.4-win | OK | Nov 12 2024 |
| R-4.4-mac | OK | Nov 12 2024 |
| R-4.3-win | OK | Nov 12 2024 |
| R-4.3-mac | OK | Nov 12 2024 |
Exports:%>%addaddSuffixallNaas.data.frameassertSingleCharacterStringautoDetectNONMEMBioavailabilityCampsisModelCodeRecordsCommentCompartmentCompartmentscontainsdefaultdeletedisableEquationErrorRecordexportextractLhsextractRhsextractTextBetweenBracketsfindfixOmegagetByIndexgetByNamegetCompartmentIndexgetNamegetNameInModelgetNamesgetNONMEMNamegetPrefixgetRecordDelimitergetRecordEquationNamesgetRecordNamegetUncertaintygetVarCovhasCommentIfStatementindexOfInfusionDurationInfusionRateInitialConditionisCommentisDiagisEmptyLineisEquationisIfStatementisODEisRecordDelimiterisStrictRecordDelimiterLagTimeLineBreakMainRecordmaxIndexminIndexModelStatementsmrgsolveBlockmrgsolveCapturemrgsolveCompartmentmrgsolveMainmrgsolveMatrixmrgsolveOdemrgsolveParammrgsolveTableOdeOdeRecordOmegaParametersPatternPositionprocessExtraArgreadread.allparametersread.campsisread.modelread.parametersread.pmxmodread.varcovremoveNaColumnreplacereplaceAllrxodeCoderxodeMatrixrxodeParamsselectSigmasortstandardiseThetatoStringtrimUnknownStatementupdateCompartmentsVariablePatternwrite
Dependencies:assertthatbitbit64clicliprcpp11crayondplyrfansigenericsgluehmslifecyclemagrittrpillarpkgconfigplyrprettyunitsprogresspurrrR6Rcppreadrrlangtibbletidyselecttzdbutf8vctrsvroomwithr
Adapt your model
Rendered fromv03_model_adaptation.Rmdusingknitr::rmarkdownon Nov 12 2024.Last update: 2021-10-04
Started: 2021-10-04
Adapt your parameters
Rendered fromv05_parameters.Rmdusingknitr::rmarkdownon Nov 12 2024.Last update: 2022-06-17
Started: 2021-10-04
Append a model to another
Rendered fromv06_append_pd_model.Rmdusingknitr::rmarkdownon Nov 12 2024.Last update: 2023-10-11
Started: 2021-10-04
Create a minimalist model
Rendered fromv01_model_creation.Rmdusingknitr::rmarkdownon Nov 12 2024.Last update: 2021-11-30
Started: 2021-10-04
Get started with CAMPSIS model
Rendered fromcampsismod.Rmdusingknitr::rmarkdownon Nov 12 2024.Last update: 2022-06-17
Started: 2021-10-04
Insight on the structural model
Rendered fromv02_structural_model.Rmdusingknitr::rmarkdownon Nov 12 2024.Last update: 2021-10-04
Started: 2021-10-04
Play with compartment properties
Rendered fromv04_compartment_properties.Rmdusingknitr::rmarkdownon Nov 12 2024.Last update: 2021-10-04
Started: 2021-10-04
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Add element to list. | add add,campsis_model,campsis_model-method add,campsis_model,code_record-method add,campsis_model,compartment_property-method add,campsis_model,model_statement-method add,campsis_model,parameter-method add,code_record,code_record-method add,code_record,model_statement-method add,code_records,code_records-method add,code_records,model_statement-method add,compartments,compartments-method add,compartments,compartment_property-method add,parameters,double_array_parameter-method add,parameters,parameters-method add,parameters,single_array_parameter-method add,pmx_list,list-method add,pmx_list,pmx_element-method add,pmx_list,pmx_list-method |
| Generic function to add a suffix to various objects like parameters, code records, compartment names or a model (all previous objects at the same time). This makes it an extremely powerful function to combine 2 models or more (using function 'add'), that have similar equation, parameter or compartment names. | addSuffix addSuffix,campsis_model,character,character-method addSuffix,code_record,character,character-method addSuffix,code_records,character,character-method addSuffix,compartments,character,character-method addSuffix,parameters,character,character-method |
| As data frame method. | as.data.frame as.data.frame,omega,character,logical-method as.data.frame,sigma,character,logical-method as.data.frame,theta,character,logical-method |
| Assert the given character vector is a single character string. | assertSingleCharacterString |
| Auto-detect special variables from NONMEM as compartment properties. Bioavailabilities, infusion durations/rates and lag times will be automatically detected. | autoDetectNONMEM autoDetectNONMEM,campsis_model-method |
| Create a bioavailability for the specified compartment. | Bioavailability |
| CAMPSIS model class. | campsis_model-class |
| Create a new CAMPSIS model. | CampsisModel |
| Code record class. See this code record as an abstract class. 2 implementations are possible: - properties record (lag, duration, rate & bioavailability properties) - statements record (main, ode & error records) | code_record-class |
| Create a list of code records. | CodeRecords |
| Create a new comment. | Comment |
| Comment class. A statement starting with #. | comment-class |
| Create a compartment. | Compartment |
| Compartment bioavailability class. | compartment_bioavailability-class |
| Compartment infusion duration class. | compartment_infusion_duration-class |
| Compartment infusion rate class. | compartment_infusion_rate-class |
| Compartment initial condition class. | compartment_initial_condition-class |
| Compartment lag time class. | compartment_lag_time-class |
| Compartment properties class. | compartment_properties-class |
| Compartment property class. | compartment_property-class |
| Compartment class. | compartment-class |
| Create a list of compartments | Compartments |
| Compartments class. | compartments-class |
| Get default element from list. | default |
| Delete an element from this list. | delete delete,campsis_model,code_record-method delete,campsis_model,compartment_property-method delete,campsis_model,model_statement-method delete,campsis_model,parameter-method delete,code_records,model_statement-method delete,compartments,compartment_property-method delete,parameters,double_array_parameter-method delete,parameters,single_array_parameter-method delete,pmx_list,integer-method delete,pmx_list,pmx_element-method delete,statements_record,integer-method delete,statements_record,model_statement-method |
| Disable. | disable disable,campsis_model,character-method disable,parameters,character-method |
| Double-array parameter class. This parameter has 2 indexes. It can thus be used to define correlations between parameters. | double_array_parameter-class |
| (Infusion)-duration record class. | duration_record-class |
| Create a new equation. | Equation |
| Equation class. Any statement in the form A = B. | equation-class |
| Error record class. | error_record-class |
| Create ERROR code record. | ErrorRecord |
| Export function. | export export,campsis_model,character-method export,campsis_model,mrgsolve_type-method export,campsis_model,rxode_type-method |
| Export type class. | export_type-class |
| Extract left-hand-side expression. | extractLhs |
| Extract right-hand-side expression. | extractRhs |
| Extract text between brackets. | extractTextBetweenBrackets |
| Bioavailability record class. | f_record-class |
| Find an element in list. | find find,campsis_model,code_record-method find,campsis_model,compartment-method find,campsis_model,compartment_property-method find,campsis_model,model_statement-method find,campsis_model,parameter-method find,code_records,model_statement-method find,compartments,compartment_property-method find,pmx_list,pmx_element-method find,statements_record,model_statement-method |
| Fix omega matrix for SAME OMEGA parameters that have NA values due to imperfections in Pharmpy import. | fixOmega fixOmega,parameters-method |
| Get element by index. | getByIndex getByIndex,compartment_properties,compartment_property-method getByIndex,parameters,parameter-method getByIndex,pmx_list,integer-method getByIndex,pmx_list,numeric-method |
| Get an element from a list by name. Never return more than 1 element. | getByName getByName,pmx_list,character-method |
| Get the compartment index for the specified compartment name. | getCompartmentIndex getCompartmentIndex,campsis_model,character-method getCompartmentIndex,compartments,character-method |
| Get element name. | getName getName,comment-method getName,compartment-method getName,compartment_bioavailability-method getName,compartment_infusion_duration-method getName,compartment_infusion_rate-method getName,compartment_initial_condition-method getName,compartment_lag_time-method getName,duration_record-method getName,equation-method getName,error_record-method getName,f_record-method getName,if_statement-method getName,init_record-method getName,lag_record-method getName,line_break-method getName,main_record-method getName,ode-method getName,ode_record-method getName,omega-method getName,rate_record-method getName,sigma-method getName,theta-method getName,unknown_statement-method |
| Get the name of the given parameter in the CAMPSIS model. | getNameInModel getNameInModel,omega-method getNameInModel,sigma-method getNameInModel,theta-method |
| Get element names from list. | getNames getNames,pmx_list-method |
| Get NONMEM name. | getNONMEMName getNONMEMName,omega-method getNONMEMName,sigma-method getNONMEMName,theta-method |
| Get prefix. | getPrefix getPrefix,compartment_bioavailability-method getPrefix,compartment_infusion_duration-method getPrefix,compartment_infusion_rate-method getPrefix,compartment_initial_condition-method getPrefix,compartment_lag_time-method |
| Get record delimiter. | getRecordDelimiter |
| Get record name. | getRecordName getRecordName,compartment_bioavailability-method getRecordName,compartment_infusion_duration-method getRecordName,compartment_infusion_rate-method getRecordName,compartment_initial_condition-method getRecordName,compartment_lag_time-method |
| Get uncertainty on the parameters. | getUncertainty getUncertainty,campsis_model-method getUncertainty,parameter-method getUncertainty,parameters-method |
| Get variance-covariance matrix. | getVarCov getVarCov,campsis_model-method getVarCov,parameters-method |
| Check if string contains CAMPSIS-style comments. | hasComment |
| If-statement class. Any statement in the form if (condition) A = B. | if_statement-class |
| Create a new IF-statement. | IfStatement |
| Get the index of an element in list. | indexOf indexOf,pmx_list,pmx_element-method |
| Create an infusion duration. | InfusionDuration |
| Create an infusion rate. | InfusionRate |
| Init record class. | init_record-class |
| Create an initial condition. | InitialCondition |
| Check if string is a CAMPSIS comment (i.e. not an equation). | isComment |
| Is diagonal. | isDiag isDiag,double_array_parameter-method |
| Check if string is an empty line. | isEmptyLine |
| Say if line in record is an equation not. | isEquation |
| Say if line in record is an IF-statement. | isIfStatement |
| Say if line(s) in record is/are ODE or not. | isODE |
| Is record delimiter. A record delimiter is any line starting with [...]. | isRecordDelimiter |
| Is strict record delimiter. A strict record delimiter is any line starting with [...] and followed by nothing but spaces or a possible comment. | isStrictRecordDelimiter |
| Lag record class. | lag_record-class |
| Create a lag time for the specified compartment. | LagTime |
| Line-break class. A linebreak in the model. | line_break-class |
| Create a new line break. | LineBreak |
| Main record class. | main_record-class |
| Create MAIN code record. | MainRecord |
| Max index. | maxIndex maxIndex,parameters-method |
| Min index. | minIndex minIndex,parameters-method |
| Model statement class. Any statement in a code record. | model_statement-class |
| Model statements class. A list of statements. | model_statements-class |
| CAMPSIS model suite. | model_suite |
| Create an empty list of model statements. | ModelStatements |
| Mrgsolve export type class. | mrgsolve_type-class |
| Convert code record for mrgsolve. | mrgsolveBlock |
| Get the CAPTURE block for mrgsolve. | mrgsolveCapture |
| Get the compartment block for mrgsolve. | mrgsolveCompartment |
| Get the MAIN block for mrgsolve. | mrgsolveMain |
| Get the OMEGA/SIGMA matrix for mrgsolve. | mrgsolveMatrix |
| Get the ODE block for mrgsolve. | mrgsolveOde |
| Get the parameters block for mrgsolve. | mrgsolveParam |
| Get the TABLE block for mrgsolve. | mrgsolveTable |
| Create a new ordinary differential equation (ODE). | Ode |
| ODE record class. | ode_record-class |
| ODE class. Any statement in the form d/dt(A_CMT) = B. | ode-class |
| Create ODE code record. | OdeRecord |
| Create an OMEGA parameter. | Omega |
| Omega parameter class. | omega-class |
| Parameter class. Any parameter in a pharmacometric model. | parameter-class |
| Create a list of parameters. | Parameters |
| Parameters class. | parameters-class |
| Parse IF-statement. Assumption: isIfStatement method already called and returned TRUE. | parseIfStatement |
| Parse statements code and return CAMPSIS statements. | parseStatements |
| Create a pattern. | Pattern |
| Pattern class. | pattern-class |
| PMX element class. | pmx_element-class |
| PMX position by element class. | pmx_position_by_element-class |
| PMX position by index class. | pmx_position_by_index-class |
| PMX position class. | pmx_position-class |
| Element position in list. | Position |
| Process extra arguments. | processExtraArg |
| Properties record class. | properties_record-class |
| (Infusion)-rate record class. | rate_record-class |
| Generic read method to read data from a file or a folder. | read |
| Read all parameters files at once. | read.allparameters |
| Read a CAMPSIS model. | read.campsis |
| Read model file. | read.model |
| Read parameters file. | read.parameters |
| Read variance-covariance file. | read.varcov |
| Replace element by another in list. | replace replace,campsis_model,code_record-method replace,campsis_model,compartment-method replace,campsis_model,compartment_property-method replace,campsis_model,model_statement-method replace,campsis_model,parameter-method replace,code_records,model_statement-method replace,compartments,compartment_property-method replace,parameters,double_array_parameter-method replace,parameters,single_array_parameter-method replace,pmx_list,list-method replace,pmx_list,pmx_element-method replace,pmx_list,pmx_list-method replace,statements_record,model_statement-method |
| Replace all occurrences in object. | replaceAll replaceAll,campsis_model,character,character-method replaceAll,campsis_model,pattern,character-method replaceAll,character,pattern,character-method replaceAll,character,variable_pattern,character-method replaceAll,code_record,pattern,character-method replaceAll,code_records,pattern,character-method replaceAll,compartment_property,pattern,character-method replaceAll,equation,pattern,character-method replaceAll,if_statement,pattern,character-method replaceAll,model_statement,pattern,character-method |
| RxODE export type class. | rxode_type-class |
| Get code for RxODE. | rxodeCode |
| Get the OMEGA/SIGMA matrix for RxODE. | rxodeMatrix |
| Get the parameters vector for RxODE. | rxodeParams |
| Get a subset of an object. | select select,compartment_properties-method select,data.frame-method select,parameters-method |
| Create a SIGMA parameter. | Sigma |
| Sigma parameter class. | sigma-class |
| Single-array parameter class. This parameter has a single index value. | single_array_parameter-class |
| Sort the specified list. | sort sort,campsis_model-method sort,code_records-method sort,compartments-method sort,compartment_properties-method sort,parameters-method |
| Standardise. | standardise standardise,double_array_parameter-method standardise,parameters-method standardise,theta-method |
| Statements record class. | statements_record-class |
| Create a THETA parameter. | Theta |
| Theta parameter class. | theta-class |
| ToString generic method. | toString toString,comment-method toString,compartment-method toString,compartment_initial_condition-method toString,compartment_property-method toString,equation-method toString,if_statement-method toString,line_break-method toString,mrgsolve_model-method toString,ode-method toString,unknown_statement-method |
| Trim character vector. Remove all leading and trailing spaces. | trim |
| Unknown statement class. Any statement not recognized by campsismod. | unknown_statement-class |
| Create a new ordinary differential equation (ODE). | UnknownStatement |
| Update compartments list from the persisted records. Exported especially for package pmxtran. However, this method should not be called. | updateCompartments |
| Variable pattern class. | variable_pattern-class |
| Create a variable pattern. | VariablePattern |
| Write generic object to files. | write write,campsis_model,character-method write,code_records,character-method write,parameters,character-method |
| Write subset of parameters (theta, omega or sigma). | writeParameters |
| Write variance-covariance matrix. | writeVarcov |
