Prerequisite | Define the concentration | Define an error model | Simulate the observed concentration | A couple of useful functions in action
Package: campsismod 1.4.2
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 and write pharmacometric models from and to files, including a JSON-based interface to import Campsis models defined using a formal JSON schema distributed with the package. Models can be adapted further on the fly in the R environment using an intuitive API to add, modify or delete equations, ordinary differential equations (ODEs), model parameters or compartment properties (such as infusion duration or rate, bioavailability and initial values). The package also provides export facilities for use with the simulation packages 'rxode2' and 'mrgsolve'. The package itself is licensed under the GPL (>= 3); the JSON schema file shipped in inst/extdata is licensed separately under the Creative Commons Attribution 4.0 International (CC BY 4.0). This package is designed and intended to be used with the package 'campsis', a PK/PD simulation platform built on top of 'rxode2' and 'mrgsolve'.
Authors:
campsismod_1.4.2.tar.gz
campsismod_1.4.2.zip(r-4.7-any)campsismod_1.4.2.zip(r-4.6-any)campsismod_1.4.2.zip(r-4.5-any)
campsismod_1.4.2.tgz(r-4.6-any)campsismod_1.4.2.tgz(r-4.5-any)
campsismod_1.4.2.tar.gz(r-4.7-any)campsismod_1.4.2.tar.gz(r-4.6-any)
campsismod_1.4.2.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
campsismod/json (API)
| # Install 'campsismod' in R: |
| install.packages('campsismod', repos = c('https://campsisverse.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/calvagone/campsismod/issues
Datasets:
- model_suite - Campsis model suite.
Last updated from:9868639344. Checks:9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel | OK | 212 | ||
| source / vignettes | OK | 251 | ||
| linux-release | OK | 240 | ||
| macos-release | OK | 149 | ||
| macos-oldrel | OK | 151 | ||
| windows-devel | OK | 187 | ||
| windows-release | OK | 184 | ||
| windows-oldrel | OK | 113 | ||
| wasm-release | OK | 125 |
Exports::=%>%addadd_rseadd_suffixaddSuffixall_naas.data.frameassert_single_character_stringauto_detect_nonmemAutoReplicationSettingsBioavailabilityCampsisModelCodeRecordsCommentCompartmentCompartmentscontainsdefaultdeletedisableEquationErrorRecordexportexport_to_jsonextract_lhsextract_rhsextract_text_between_bracketsfindfix_omegafixOmegaget_by_indexget_by_nameget_campsismod_optionget_campsismod_optionsget_compartment_indexget_nameget_name_in_modelget_namesget_nonmem_nameget_omega_blockget_omega_indexesget_prefixget_record_delimiterget_record_equation_namesget_record_nameget_uncertaintyget_var_covgetByIndexgetByNamegetCompartmentIndexgetNamegetNameInModelgetNamesgetUncertaintyhas_commenthas_exact_methodhas_off_diagonal_omegasIfStatementindex_ofindexOfInfusionDurationInfusionRateInitialConditionis_commentis_diagis_empty_lineis_equationis_if_statementis_matrix_positive_definiteis_odeis_record_delimiteris_rxodeis_strict_record_delimiterisDiagjson_to_parameterJSONElementjsonToParameterLagTimeLineBreakload_from_jsonloadFromJSONMainRecordManualReplicationSettingsmap_json_properties_to_s4_slotsmap_s4_slots_to_json_propertiesmapJSONPropertiesToS4SlotsmapS4SlotsToJSONPropertiesmax_indexmaxIndexmin_indexminIndexModelStatementsmovemrgsolve_blockmrgsolve_capturemrgsolve_compartmentmrgsolve_mainmrgsolve_matrixmrgsolve_odemrgsolve_parammrgsolve_tableOdeOdeRecordOmegaOmegaBlockOmegaBlocksParametersPatternPositionprocess_extra_argprocessExtraArgreadread.allparametersread.campsisread.modelread.parametersread.pmxmodread.varcovremove_na_columnreplacereplace_allreplaceAllreplicaterxode_coderxode_matrixrxode_paramsrxodeMatrixselectset_min_maxshift_omega_indexesSigmasortstandardiseThetato_stringtoStringtrimUnknownStatementupdate_compartmentsupdateCompartmentsVariablePatternwrite
Dependencies:assertthatbitbit64clicliprcpp11crayoncurldplyrfarvergenericsggplot2gluegtablehmsisobandjsonlitejsonvalidatelabelingLaplacesDemonlifecyclemagrittrMASSpillarpkgconfigprettyunitsprogresspurrrR6RColorBrewerRcppreadrrlangS7scalesstringistringrtibbletidyrtidyselecttzdbutf8V8vctrsviridisLitevroomwithr
Adapt your model
Last update: 2026-09-29
Started: 2021-10-04
Adapt your parameters
Prerequisite | Retrieve your parameters | Access parameter values | Replace parameters | Delete parameters
Last update: 2026-09-29
Started: 2021-10-04
Append a model to another
Prerequisite | Load your base PK model | Load an effect-compartment model | Append PD model to PK model | Simulate our PK/PD model
Last update: 2026-09-29
Started: 2021-10-04
Create a minimalist model
Prerequisite | Create a minimalist model in the Notepad++ editor | Create the same model programmatically
Last update: 2026-09-29
Started: 2021-10-04
Get started with Campsis model
Load example from model library | Write Campsis model | Read Campsis model | Export Campsis model to rxode2 | Export Campsis model to mrgsolve
Last update: 2026-09-29
Started: 2021-10-04
Insight on the structural model
Prerequisite | Equation | Ordinary differential equation (ODE) | Line break | Comment | If-statement | Additional remarks
Last update: 2026-09-29
Started: 2021-10-04
Play with compartment properties
Prerequisite | Create new compartment properties | Simulate our model | A couple of useful functions in action
Last update: 2026-09-29
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,list-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,omega_block,double_array_parameter-method add,omega_blocks,omega_block-method add,omega_blocks,parameters-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 |
| Add relative standard error (RSE) to the specified parameter. | add_rse add_rse,campsis_model,parameter,numeric-method add_rse,parameters,parameter,numeric-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. | add_suffix add_suffix,campsis_model,character,character-method add_suffix,code_record,character,character-method add_suffix,code_records,character,character-method add_suffix,compartments,character,character-method add_suffix,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. | assert_single_character_string |
| Auto-detect special variables from NONMEM as compartment properties. Bioavailabilities, infusion durations/rates and lag times will be automatically detected. | auto_detect_nonmem auto_detect_nonmem,campsis_model-method |
| Auto replication settings class. | auto_replication_settings-class |
| Create auto replication settings. | AutoReplicationSettings |
| 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,replicated_campsis_model,campsis_model-method |
| Export the given object to a JSON object, ready to be written to files. | export_to_json export_to_json,campsis_model-method export_to_json,omega-method export_to_json,parameters-method export_to_json,sigma-method export_to_json,theta-method |
| Export type class. | export_type-class |
| Extract left-hand-side expression. | extract_lhs |
| Extract right-hand-side expression. | extract_rhs |
| Extract text between brackets. | extract_text_between_brackets |
| 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. | fix_omega fix_omega,parameters-method |
| Get element by index. | get_by_index get_by_index,compartment_properties,compartment_property-method get_by_index,parameters,parameter-method get_by_index,pmx_list,integer-method get_by_index,pmx_list,numeric-method |
| Get an element from a list by name. Never return more than 1 element. | get_by_name get_by_name,pmx_list,character-method |
| Get Campsismod option logic. | get_campsismod_option |
| Get the compartment index for the specified compartment name. | get_compartment_index get_compartment_index,campsis_model,character-method get_compartment_index,compartments,character-method |
| Get element name. | get_name get_name,ANY-method get_name,comment-method get_name,compartment-method get_name,compartment_bioavailability-method get_name,compartment_infusion_duration-method get_name,compartment_infusion_rate-method get_name,compartment_initial_condition-method get_name,compartment_lag_time-method get_name,duration_record-method get_name,equation-method get_name,error_record-method get_name,f_record-method get_name,if_statement-method get_name,init_record-method get_name,lag_record-method get_name,line_break-method get_name,main_record-method get_name,ode-method get_name,ode_record-method get_name,omega-method get_name,omega_block-method get_name,rate_record-method get_name,sigma-method get_name,theta-method get_name,unknown_statement-method |
| Get the name of the given parameter in the Campsis model. | get_name_in_model get_name_in_model,omega-method get_name_in_model,sigma-method get_name_in_model,theta-method |
| Get element names from list. | get_names get_names,pmx_list-method |
| Get NONMEM name. | get_nonmem_name get_nonmem_name,omega-method get_nonmem_name,sigma-method get_nonmem_name,theta-method |
| Get the right block of OMEGA's. | get_omega_block get_omega_block,omega_blocks,double_array_parameter-method |
| Get the indexes of the omegas. | get_omega_indexes get_omega_indexes,omega_block-method |
| Get prefix. | get_prefix get_prefix,compartment_bioavailability-method get_prefix,compartment_infusion_duration-method get_prefix,compartment_infusion_rate-method get_prefix,compartment_initial_condition-method get_prefix,compartment_lag_time-method |
| Get record delimiter. | get_record_delimiter |
| Get record name. | get_record_name get_record_name,compartment_bioavailability-method get_record_name,compartment_infusion_duration-method get_record_name,compartment_infusion_rate-method get_record_name,compartment_initial_condition-method get_record_name,compartment_lag_time-method |
| Get uncertainty on the parameters. | get_uncertainty get_uncertainty,campsis_model-method get_uncertainty,parameter-method get_uncertainty,parameters-method |
| Get variance-covariance matrix. | get_var_cov get_var_cov,campsis_model-method get_var_cov,parameters-method |
| Check if string contains Campsis-style comments. | has_comment |
| Has exact method allows to check the existence of a S4 method in Campsis based on its signature. | has_exact_method |
| Has off-diagonal omegas. | has_off_diagonal_omegas has_off_diagonal_omegas,omega_block-method |
| 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. | index_of index_of,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). | is_comment |
| Is diagonal. | is_diag is_diag,double_array_parameter-method |
| Check if string is an empty line. | is_empty_line |
| Say if line in record is an equation not. | is_equation |
| Say if line in record is an IF-statement. | is_if_statement |
| Is matrix positive definite | is_matrix_positive_definite |
| Say if line(s) in record is/are ODE or not. | is_ode |
| Is record delimiter. A record delimiter is any line starting with [...]. | is_record_delimiter |
| Is strict record delimiter. A strict record delimiter is any line starting with [...] and followed by nothing but spaces or a possible comment. | is_strict_record_delimiter |
| JSON element class. | json_element-class |
| JSON to Campsis parameter. | json_to_parameter |
| Instantiate a JSON element. | JSONElement |
| 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 |
| Fill-in S4 object from the JSON content. | load_from_json load_from_json,campsis_model,character-method load_from_json,campsis_model,json_element-method load_from_json,omega,json_element-method load_from_json,sigma,json_element-method load_from_json,theta,json_element-method |
| Main record class. | main_record-class |
| Create MAIN code record. | MainRecord |
| Manual replication settings class. | manual_replication_settings-class |
| Create manual replication settings. | ManualReplicationSettings |
| Map JSON properties to S4 slots. | map_json_properties_to_s4_slots |
| Map S4 slots to JSON properties. | map_s4_slots_to_json_properties |
| Max index. | max_index max_index,parameters-method |
| Min index. | min_index min_index,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 |
| Move element 'x' from object to a certain place. | move move,campsis_model,ANY,pmx_position-method move,code_records,code_record,pmx_position-method move,code_records,list,pmx_position-method move,code_records,model_statement,pmx_position-method move,code_records,model_statements,pmx_position-method |
| Convert code record for mrgsolve. | mrgsolve_block |
| Get the CAPTURE block for mrgsolve. | mrgsolve_capture |
| Get the compartment block for mrgsolve. | mrgsolve_compartment |
| Get the MAIN block for mrgsolve. | mrgsolve_main |
| Get the OMEGA/SIGMA matrix for mrgsolve. | mrgsolve_matrix |
| Get the ODE block for mrgsolve. | mrgsolve_ode |
| Get the parameters block for mrgsolve. | mrgsolve_param |
| Get the TABLE block for mrgsolve. | mrgsolve_table |
| Mrgsolve export type class. | mrgsolve_type-class |
| 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 |
| Create a block of OMEGA's. | OmegaBlock |
| Create a list of OMEGA blocks. | OmegaBlocks |
| Parameter class. Any parameter in a pharmacometric model. | parameter-class |
| Create a list of parameters. | Parameters |
| Parameters class. | parameters-class |
| Parse IF-statement. Assumption: 'is_if_statement' method already called and returned TRUE. | parse_if_statement |
| Parse statements code and return Campsis statements. | parse_statements |
| 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. | process_extra_arg |
| 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. | replace_all replace_all,campsis_model,character,character-method replace_all,campsis_model,pattern,character-method replace_all,character,pattern,character-method replace_all,character,variable_pattern,character-method replace_all,code_record,pattern,character-method replace_all,code_records,pattern,character-method replace_all,compartment_property,pattern,character-method replace_all,equation,pattern,character-method replace_all,if_statement,pattern,character-method replace_all,model_statement,pattern,character-method replace_all,unknown_statement,pattern,character-method |
| Replicate generic object. | replicate replicate,campsis_model,integer,auto_replication_settings-method replicate,campsis_model,integer,manual_replication_settings-method |
| Replicated Campsis model class. | replicated_campsis_model-class |
| Replication settings interface. | replication_settings-class |
| Get code for rxode2 | rxode_code |
| Get the OMEGA/SIGMA matrix for rxode2. | rxode_matrix |
| Get the parameters vector for rxode2. | rxode_params |
| RxODE/rxode2 export type class. | rxode_type-class |
| Get a subset of an object. | select select,compartment_properties-method select,data.frame-method select,parameters-method |
| Set the minimum and maximum value on a model parameter. | set_min_max set_min_max,campsis_model,character,numeric,numeric-method set_min_max,campsis_model,parameter,numeric,numeric-method set_min_max,parameters,character,numeric,numeric-method set_min_max,parameters,parameter,numeric,numeric-method |
| Shift OMEGA indexes. | shift_omega_indexes shift_omega_indexes,omega_block-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,omega_blocks-method sort,parameters-method |
| Standardise. | standardise standardise,campsis_model-method 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 |
| to_string generic method. | to_string to_string,comment-method to_string,compartment-method to_string,compartment_initial_condition-method to_string,compartment_property-method to_string,equation-method to_string,if_statement-method to_string,line_break-method to_string,mrgsolve_model-method to_string,ode-method to_string,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 'campsistrans'. However, this method should not be called. | update_compartments |
| 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,json_element,character-method write,parameters,character-method |
| Write subset of parameters (theta, omega or sigma). | write_parameters |
| Write variance-covariance matrix. | write_varcov |