{ "_id": "6a106a1cacfb0bcc41ca9e2c", "Type": "Package", "Package": "campsismod", "Title": "Generic Implementation of a PK/PD Model", "Version": "1.3.2", "Authors@R": "person(\"Nicolas\", \"Luyckx\", , \"nicolas.luyckx@calvagone.com\", role = c(\"aut\", \"cre\"))", "Description": "A generic, easy-to-use and expandable implementation of a\npharmacokinetic (PK) / pharmacodynamic (PD) model based on the\nS4 class system. This package allows the user to read and write\npharmacometric models from and to files, including a JSON-based\ninterface to import Campsis models defined using a formal JSON\nschema distributed with the package. Models can be adapted\nfurther on the fly in the R environment using an intuitive API\nto add, modify or delete equations, ordinary differential\nequations (ODEs), model parameters or compartment properties\n(such as infusion duration or rate, bioavailability and initial\nvalues). The package also provides export facilities for use\nwith the simulation packages 'rxode2' and 'mrgsolve'. The\npackage itself is licensed under the GPL (>= 3); the JSON\nschema file shipped in inst/extdata is licensed separately\nunder the Creative Commons Attribution 4.0 International (CC BY\n4.0). This package is designed and intended to be used with\nthe package 'campsis', a PK/PD simulation platform built on top\nof 'rxode2' and 'mrgsolve'.", "License": "GPL (>= 3)", "URL": "https://github.com/Calvagone/campsismod,\nhttps://calvagone.github.io/,\nhttps://calvagone.github.io/campsismod.doc/", "BugReports": "https://github.com/Calvagone/campsismod/issues", "VignetteBuilder": "knitr", "Encoding": "UTF-8", "Language": "en-US", "LazyData": "true", "RoxygenNote": "7.3.3", "Collate": "'global.R' 'data.R' 'utilities.R' 'special_operators.R'\n'check.R' 'json_element.R' 'generic.R' 'generic_element_list.R'\n'generic_element_position.R' 'generic_list.R' 'pattern.R'\n'model_statement.R' 'model_statements.R'\n'model_unknown_statement.R' 'model_comment.R'\n'model_line_break.R' 'model_equation.R' 'model_ode.R'\n'model_if_statement.R' 'compartment.R' 'compartment_property.R'\n'compartment_properties.R' 'compartment_bioavailability.R'\n'compartment_lag_time.R' 'compartment_infusion_duration.R'\n'compartment_infusion_rate.R' 'compartment_initial_condition.R'\n'compartments.R' 'parameter.R' 'parameters.R' 'code_record.R'\n'code_records.R' 'model_parser.R' 'campsis_model.R'\n'omega_block.R' 'omega_blocks.R'\n'parameter_uncertainty_utils.R' 'replication_settings.R'\n'replicated_campsis_model.R' 'model_add_suffix.R'\n'rxode_model.R' 'rxode_conversion.R' 'mrgsolve_model.R'\n'mrgsolve_conversion.R' 'json_interface.R'", "Config/pak/sysreqs": "libicu-dev libssl-dev libnode-dev libx11-dev", "Repository": "https://calvagone.r-universe.dev", "Date/Publication": "2026-05-07 11:52:29 UTC", "RemoteUrl": "https://github.com/calvagone/campsismod", "RemoteRef": "HEAD", "RemoteSha": "c1a282e25a07fe4881387319f503a7eb70e268eb", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-07 14:41:03 UTC", "User": "root" }, "Author": "Nicolas Luyckx [aut, cre]", "Maintainer": "Nicolas Luyckx ", "MD5sum": "049f03804f81dadbf1c95e90294bb602", "_user": "calvagone", "_type": "src", "_file": "campsismod_1.3.2.tar.gz", "_fileid": "a600cef5ceb2425a72c0c9884e57ed69b5ce177219a51d23ae4632fdb47141b6", "_filesize": 957618, "_sha256": "a600cef5ceb2425a72c0c9884e57ed69b5ce177219a51d23ae4632fdb47141b6", "_created": "2026-05-07T14:41:03.000Z", "_published": "2026-06-06T05:55:12.353Z", "_distro": "noble", "_jobs": [ { "job": 77401489605, "time": 226, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "6858226763" }, { "job": 77401489705, "time": 227, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "6858230600" }, { "job": 77401489956, "time": 268, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "6858232724" }, { "job": 77401489136, "time": 245, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "6858217953" }, { "job": 77401488870, "time": 245, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "6858135747" }, { "job": 77401488626, "time": 126, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7163144184" }, { "job": 77401488892, "time": 179, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "6858208646" }, { "job": 77401489667, "time": 166, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "6858203453" }, { "job": 77401489569, "time": 176, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "6858207812" } ], "_buildurl": "https://github.com/r-universe/calvagone/actions/runs/25502575822", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/calvagone/campsismod", "_commit": { "id": "c1a282e25a07fe4881387319f503a7eb70e268eb", "author": "luyckxn <43413317+luyckxn@users.noreply.github.com>", "committer": "GitHub ", "message": "Merge pull request #121 from Calvagone/develop\n\nDevelop", "time": 1778154749 }, "_maintainer": { "name": "Nicolas Luyckx", "email": "nicolas.luyckx@calvagone.com", "login": "luyckxn", "uuid": 43413317 }, 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"LineBreak", "loadFromJSON", "MainRecord", "ManualReplicationSettings", "mapJSONPropertiesToS4Slots", "mapS4SlotsToJSONProperties", "maxIndex", "minIndex", "ModelStatements", "move", "mrgsolveBlock", "mrgsolveCapture", "mrgsolveCompartment", "mrgsolveMain", "mrgsolveMatrix", "mrgsolveOde", "mrgsolveParam", "mrgsolveTable", "Ode", "OdeRecord", "Omega", "OmegaBlock", "OmegaBlocks", "Parameters", "Pattern", "Position", "processExtraArg", "read", "read.allparameters", "read.campsis", "read.model", "read.parameters", "read.pmxmod", "read.varcov", "removeNaColumn", "replace", "replaceAll", "replicate", "rxodeCode", "rxodeMatrix", "rxodeParams", "select", "setMinMax", "shiftOmegaIndexes", "Sigma", "sort", "standardise", "Theta", "toString", "trim", "UnknownStatement", "updateCompartments", "VariablePattern", "write" ], "_datasets": [ { "name": "model_suite", "title": "Campsis model suite.", "object": "model_suite", "class": [ "list" ], "fields": [], "table": false, "tojson": false } ], "_help": [ { "page": "add", "title": "Add element to list.", "topics": [ "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" ] }, { "page": "addRSE", "title": "Add relative standard error (RSE) to the specified parameter.", "topics": [ "addRSE", "addRSE,campsis_model,parameter,numeric-method", "addRSE,parameters,parameter,numeric-method" ] }, { "page": "addSuffix", "title": "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.", "topics": [ "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" ] }, { "page": "as.data.frame", "title": "As data frame method.", "topics": [ "as.data.frame", "as.data.frame,omega,character,logical-method", "as.data.frame,sigma,character,logical-method", "as.data.frame,theta,character,logical-method" ] }, { "page": "assertSingleCharacterString", "title": "Assert the given character vector is a single character string.", "topics": [ "assertSingleCharacterString" ] }, { "page": "auto_replication_settings-class", "title": "Auto replication settings class.", "topics": [ "auto_replication_settings-class" ] }, { "page": "autoDetectNONMEM", "title": "Auto-detect special variables from NONMEM as compartment properties. Bioavailabilities, infusion durations/rates and lag times will be automatically detected.", "topics": [ "autoDetectNONMEM", "autoDetectNONMEM,campsis_model-method" ] }, { "page": "AutoReplicationSettings", "title": "Create auto replication settings.", "topics": [ "AutoReplicationSettings" ] }, { "page": "Bioavailability", "title": "Create a bioavailability for the specified compartment.", "topics": [ "Bioavailability" ] }, { "page": "campsis_model-class", "title": "Campsis model class.", "topics": [ "campsis_model-class" ] }, { "page": "CampsisModel", "title": "Create a new Campsis model.", "topics": [ "CampsisModel" ] }, { "page": "code_record-class", "title": "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)", "topics": [ "code_record-class" ] }, { "page": "CodeRecords", "title": "Create a list of code records.", "topics": [ "CodeRecords" ] }, { "page": "Comment", "title": "Create a new comment.", "topics": [ "Comment" ] }, { "page": "comment-class", "title": "Comment class. A statement starting with #.", "topics": [ "comment-class" ] }, { "page": "Compartment", "title": "Create a compartment.", "topics": [ "Compartment" ] }, { "page": "compartment_bioavailability-class", "title": "Compartment bioavailability class.", "topics": [ "compartment_bioavailability-class" ] }, { "page": "compartment_infusion_duration-class", "title": "Compartment infusion duration class.", "topics": [ "compartment_infusion_duration-class" ] }, { "page": "compartment_infusion_rate-class", "title": "Compartment infusion rate class.", "topics": [ "compartment_infusion_rate-class" ] }, { "page": "compartment_initial_condition-class", "title": "Compartment initial condition class.", "topics": [ "compartment_initial_condition-class" ] }, { "page": "compartment_lag_time-class", "title": "Compartment lag time class.", "topics": [ "compartment_lag_time-class" ] }, { "page": "compartment_properties-class", "title": "Compartment properties class.", "topics": [ "compartment_properties-class" ] }, { "page": "compartment_property-class", "title": "Compartment property class.", "topics": [ "compartment_property-class" ] }, { "page": "compartment-class", "title": "Compartment class.", "topics": [ "compartment-class" ] }, { "page": "Compartments", "title": "Create a list of compartments", "topics": [ "Compartments" ] }, { "page": "compartments-class", "title": "Compartments class.", "topics": [ "compartments-class" ] }, { "page": "default", "title": "Get default element from list.", "topics": [ "default" ] }, { "page": "delete", "title": "Delete an element from this list.", "topics": [ "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" ] }, { "page": "disable", "title": "Disable.", "topics": [ "disable", "disable,campsis_model,character-method", "disable,parameters,character-method" ] }, { "page": "double_array_parameter-class", "title": "Double-array parameter class. This parameter has 2 indexes. It can thus be used to define correlations between parameters.", "topics": [ "double_array_parameter-class" ] }, { "page": "duration_record-class", "title": "(Infusion)-duration record class.", "topics": [ "duration_record-class" ] }, { "page": "Equation", "title": "Create a new equation.", "topics": [ "Equation" ] }, { "page": "equation-class", "title": "Equation class. Any statement in the form A = B.", "topics": [ "equation-class" ] }, { "page": "error_record-class", "title": "Error record class.", "topics": [ "error_record-class" ] }, { "page": "ErrorRecord", "title": "Create ERROR code record.", "topics": [ "ErrorRecord" ] }, { "page": "export", "title": "Export function.", "topics": [ "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" ] }, { "page": "export_type-class", "title": "Export type class.", "topics": [ "export_type-class" ] }, { "page": "exportToJSON", "title": "Export the given object to a JSON object, ready to be written to files.", "topics": [ "exportToJSON", "exportToJSON,campsis_model-method", "exportToJSON,omega-method", "exportToJSON,parameters-method", "exportToJSON,sigma-method", "exportToJSON,theta-method" ] }, { "page": "extractLhs", "title": "Extract left-hand-side expression.", "topics": [ "extractLhs" ] }, { "page": "extractRhs", "title": "Extract right-hand-side expression.", "topics": [ "extractRhs" ] }, { "page": "extractTextBetweenBrackets", "title": "Extract text between brackets.", "topics": [ "extractTextBetweenBrackets" ] }, { "page": "f_record-class", "title": "Bioavailability record class.", "topics": [ "f_record-class" ] }, { "page": "find", "title": "Find an element in list.", "topics": [ "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" ] }, { "page": "fixOmega", "title": "Fix omega matrix for SAME OMEGA parameters that have NA values due to imperfections in Pharmpy import.", "topics": [ "fixOmega", "fixOmega,parameters-method" ] }, { "page": "getByIndex", "title": "Get element by index.", "topics": [ "getByIndex", "getByIndex,compartment_properties,compartment_property-method", "getByIndex,parameters,parameter-method", "getByIndex,pmx_list,integer-method", "getByIndex,pmx_list,numeric-method" ] }, { "page": "getByName", "title": "Get an element from a list by name. Never return more than 1 element.", "topics": [ "getByName", "getByName,pmx_list,character-method" ] }, { "page": "getCampsismodOption", "title": "Get Campsismod option logic.", "topics": [ "getCampsismodOption" ] }, { "page": "getCompartmentIndex", "title": "Get the compartment index for the specified compartment name.", "topics": [ "getCompartmentIndex", "getCompartmentIndex,campsis_model,character-method", "getCompartmentIndex,compartments,character-method" ] }, { "page": "getName", "title": "Get element name.", "topics": [ "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,omega_block-method", "getName,rate_record-method", "getName,sigma-method", "getName,theta-method", "getName,unknown_statement-method" ] }, { "page": "getNameInModel", "title": "Get the name of the given parameter in the Campsis model.", "topics": [ "getNameInModel", "getNameInModel,omega-method", "getNameInModel,sigma-method", "getNameInModel,theta-method" ] }, { "page": "getNames", "title": "Get element names from list.", "topics": [ "getNames", "getNames,pmx_list-method" ] }, { "page": "getNONMEMName", "title": "Get NONMEM name.", "topics": [ "getNONMEMName", "getNONMEMName,omega-method", "getNONMEMName,sigma-method", "getNONMEMName,theta-method" ] }, { "page": "getOmegaBlock", "title": "Get the right block of OMEGA's.", "topics": [ "getOmegaBlock", "getOmegaBlock,omega_blocks,double_array_parameter-method" ] }, { "page": "getOmegaIndexes", "title": "Get the indexes of the omegas.", "topics": [ "getOmegaIndexes", "getOmegaIndexes,omega_block-method" ] }, { "page": "getPrefix", "title": "Get prefix.", "topics": [ "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" ] }, { "page": "getRecordDelimiter", "title": "Get record delimiter.", "topics": [ "getRecordDelimiter" ] }, { "page": "getRecordName", "title": "Get record name.", "topics": [ "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" ] }, { "page": "getUncertainty", "title": "Get uncertainty on the parameters.", "topics": [ "getUncertainty", "getUncertainty,campsis_model-method", "getUncertainty,parameter-method", "getUncertainty,parameters-method" ] }, { "page": "getVarCov", "title": "Get variance-covariance matrix.", "topics": [ "getVarCov", "getVarCov,campsis_model-method", "getVarCov,parameters-method" ] }, { "page": "hasComment", "title": "Check if string contains Campsis-style comments.", "topics": [ "hasComment" ] }, { "page": "hasExactMethod", "title": "Has exact method allows to check the existence of a S4 method in Campsis based on its signature.", "topics": [ "hasExactMethod" ] }, { "page": "hasOffDiagonalOmegas", "title": "Has off-diagonal omegas.", "topics": [ "hasOffDiagonalOmegas", "hasOffDiagonalOmegas,omega_block-method" ] }, { "page": "if_statement-class", "title": "If-statement class. Any statement in the form if (condition) A = B.", "topics": [ "if_statement-class" ] }, { "page": "IfStatement", "title": "Create a new IF-statement.", "topics": [ "IfStatement" ] }, { "page": "indexOf", "title": "Get the index of an element in list.", "topics": [ "indexOf", "indexOf,pmx_list,pmx_element-method" ] }, { "page": "InfusionDuration", "title": "Create an infusion duration.", "topics": [ "InfusionDuration" ] }, { "page": "InfusionRate", "title": "Create an infusion rate.", "topics": [ "InfusionRate" ] }, { "page": "init_record-class", "title": "Init record class.", "topics": [ "init_record-class" ] }, { "page": "InitialCondition", "title": "Create an initial condition.", "topics": [ "InitialCondition" ] }, { "page": "isComment", "title": "Check if string is a Campsis comment (i.e. not an equation).", "topics": [ "isComment" ] }, { "page": "isDiag", "title": "Is diagonal.", "topics": [ "isDiag", "isDiag,double_array_parameter-method" ] }, { "page": "isEmptyLine", "title": "Check if string is an empty line.", "topics": [ "isEmptyLine" ] }, { "page": "isEquation", "title": "Say if line in record is an equation not.", "topics": [ "isEquation" ] }, { "page": "isIfStatement", "title": "Say if line in record is an IF-statement.", "topics": [ "isIfStatement" ] }, { "page": "isMatrixPositiveDefinite", "title": "Is matrix positive definite. Same check as 'mvtnorm' does.", "topics": [ "isMatrixPositiveDefinite" ] }, { "page": "isODE", "title": "Say if line(s) in record is/are ODE or not.", "topics": [ "isODE" ] }, { "page": "isRecordDelimiter", "title": "Is record delimiter. A record delimiter is any line starting with [...].", "topics": [ "isRecordDelimiter" ] }, { "page": "isStrictRecordDelimiter", "title": "Is strict record delimiter. A strict record delimiter is any line starting with [...] and followed by nothing but spaces or a possible comment.", "topics": [ "isStrictRecordDelimiter" ] }, { "page": "json_element-class", "title": "JSON element class.", "topics": [ "json_element-class" ] }, { "page": "JSONElement", "title": "Instantiate a JSON element.", "topics": [ "JSONElement" ] }, { "page": "jsonToOffDiagParameter", "title": "Convert JSON correlation parameter (OMEGA or SIGMA) into a Campsis parameter.", "topics": [ "jsonToOffDiagParameter" ] }, { "page": "jsonToParameter", "title": "JSON to Campsis parameter.", "topics": [ "jsonToParameter" ] }, { "page": "lag_record-class", "title": "Lag record class.", "topics": [ "lag_record-class" ] }, { "page": "LagTime", "title": "Create a lag time for the specified compartment.", "topics": [ "LagTime" ] }, { "page": "line_break-class", "title": "Line-break class. A linebreak in the model.", "topics": [ "line_break-class" ] }, { "page": "LineBreak", "title": "Create a new line break.", "topics": [ "LineBreak" ] }, { "page": "loadFromJSON", "title": "Fill-in S4 object from the JSON content.", "topics": [ "loadFromJSON", "loadFromJSON,campsis_model,character-method", "loadFromJSON,campsis_model,json_element-method", "loadFromJSON,omega,json_element-method", "loadFromJSON,sigma,json_element-method", "loadFromJSON,theta,json_element-method" ] }, { "page": "main_record-class", "title": "Main record class.", "topics": [ "main_record-class" ] }, { "page": "MainRecord", "title": "Create MAIN code record.", "topics": [ "MainRecord" ] }, { "page": "manual_replication_settings-class", "title": "Manual replication settings class.", "topics": [ "manual_replication_settings-class" ] }, { "page": "ManualReplicationSettings", "title": "Create manual replication settings.", "topics": [ "ManualReplicationSettings" ] }, { "page": "mapJSONPropertiesToS4Slots", "title": "Map JSON properties to S4 slots.", "topics": [ "mapJSONPropertiesToS4Slots" ] }, { "page": "mapS4SlotsToJSONProperties", "title": "Map S4 slots to JSON properties.", "topics": [ "mapS4SlotsToJSONProperties" ] }, { "page": "maxIndex", "title": "Max index.", "topics": [ "maxIndex", "maxIndex,parameters-method" ] }, { "page": "minIndex", "title": "Min index.", "topics": [ "minIndex", "minIndex,parameters-method" ] }, { "page": "model_statement-class", "title": "Model statement class. Any statement in a code record.", "topics": [ "model_statement-class" ] }, { "page": "model_statements-class", "title": "Model statements class. A list of statements.", "topics": [ "model_statements-class" ] }, { "page": "model_suite", "title": "Campsis model suite.", "topics": [ "model_suite" ] }, { "page": "ModelStatements", "title": "Create an empty list of model statements.", "topics": [ "ModelStatements" ] }, { "page": "move", "title": "Move element 'x' from object to a certain place.", "topics": [ "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" ] }, { "page": "mrgsolve_type-class", "title": "Mrgsolve export type class.", "topics": [ "mrgsolve_type-class" ] }, { "page": "mrgsolveBlock", "title": "Convert code record for mrgsolve.", "topics": [ "mrgsolveBlock" ] }, { "page": "mrgsolveCapture", "title": "Get the CAPTURE block for mrgsolve.", "topics": [ "mrgsolveCapture" ] }, { "page": "mrgsolveCompartment", "title": "Get the compartment block for mrgsolve.", "topics": [ "mrgsolveCompartment" ] }, { "page": "mrgsolveMain", "title": "Get the MAIN block for mrgsolve.", "topics": [ "mrgsolveMain" ] }, { "page": "mrgsolveMatrix", "title": "Get the OMEGA/SIGMA matrix for mrgsolve.", "topics": [ "mrgsolveMatrix" ] }, { "page": "mrgsolveOde", "title": "Get the ODE block for mrgsolve.", "topics": [ "mrgsolveOde" ] }, { "page": "mrgsolveParam", "title": "Get the parameters block for mrgsolve.", "topics": [ "mrgsolveParam" ] }, { "page": "mrgsolveTable", "title": "Get the TABLE block for mrgsolve.", "topics": [ "mrgsolveTable" ] }, { "page": "Ode", "title": "Create a new ordinary differential equation (ODE).", "topics": [ "Ode" ] }, { "page": "ode_record-class", "title": "ODE record class.", "topics": [ "ode_record-class" ] }, { "page": "ode-class", "title": "ODE class. Any statement in the form d/dt(A_CMT) = B.", "topics": [ "ode-class" ] }, { "page": "OdeRecord", "title": "Create ODE code record.", "topics": [ "OdeRecord" ] }, { "page": "Omega", "title": "Create an OMEGA parameter.", "topics": [ "Omega" ] }, { "page": "omega-class", "title": "Omega parameter class.", "topics": [ "omega-class" ] }, { "page": "OmegaBlock", "title": "Create a block of OMEGA's.", "topics": [ "OmegaBlock" ] }, { "page": "OmegaBlocks", "title": "Create a list of OMEGA blocks.", "topics": [ "OmegaBlocks" ] }, { "page": "parameter-class", "title": "Parameter class. Any parameter in a pharmacometric model.", "topics": [ "parameter-class" ] }, { "page": "Parameters", "title": "Create a list of parameters.", "topics": [ "Parameters" ] }, { "page": "parameters-class", "title": "Parameters class.", "topics": [ "parameters-class" ] }, { "page": "parseIfStatement", "title": "Parse IF-statement. Assumption: 'isIfStatement' method already called and returned TRUE.", "topics": [ "parseIfStatement" ] }, { "page": "parseStatements", "title": "Parse statements code and return Campsis statements.", "topics": [ "parseStatements" ] }, { "page": "Pattern", "title": "Create a pattern.", "topics": [ "Pattern" ] }, { "page": "pattern-class", "title": "Pattern class.", "topics": [ "pattern-class" ] }, { "page": "pmx_element-class", "title": "PMX element class.", "topics": [ "pmx_element-class" ] }, { "page": "pmx_position_by_element-class", "title": "PMX position by element class.", "topics": [ "pmx_position_by_element-class" ] }, { "page": "pmx_position_by_index-class", "title": "PMX position by index class.", "topics": [ "pmx_position_by_index-class" ] }, { "page": "pmx_position-class", "title": "PMX position class.", "topics": [ "pmx_position-class" ] }, { "page": "Position", "title": "Element position in list.", "topics": [ "Position" ] }, { "page": "processExtraArg", "title": "Process extra arguments.", "topics": [ "processExtraArg" ] }, { "page": "processJSONDoubleArrayParameter", "title": "Process JSON double array parameter.", "topics": [ "processJSONDoubleArrayParameter" ] }, { "page": "properties_record-class", "title": "Properties record class.", "topics": [ "properties_record-class" ] }, { "page": "rate_record-class", "title": "(Infusion)-rate record class.", "topics": [ "rate_record-class" ] }, { "page": "read", "title": "Generic read method to read data from a file or a folder.", "topics": [ "read" ] }, { "page": "read.allparameters", "title": "Read all parameters files at once.", "topics": [ "read.allparameters" ] }, { "page": "read.campsis", "title": "Read a Campsis model.", "topics": [ "read.campsis" ] }, { "page": "read.model", "title": "Read model file.", "topics": [ "read.model" ] }, { "page": "read.parameters", "title": "Read parameters file.", "topics": [ "read.parameters" ] }, { "page": "read.varcov", "title": "Read variance-covariance file.", "topics": [ "read.varcov" ] }, { "page": "replace", "title": "Replace element by another in list.", "topics": [ "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" ] }, { "page": "replaceAll", "title": "Replace all occurrences in object.", "topics": [ "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", "replaceAll,unknown_statement,pattern,character-method" ] }, { "page": "replicate", "title": "Replicate generic object.", "topics": [ "replicate", "replicate,campsis_model,integer,auto_replication_settings-method", "replicate,campsis_model,integer,manual_replication_settings-method" ] }, { "page": "replicated_campsis_model-class", "title": "Replicated Campsis model class.", "topics": [ "replicated_campsis_model-class" ] }, { "page": "replication_settings-class", "title": "Replication settings interface.", "topics": [ "replication_settings-class" ] }, { "page": "rxode_type-class", "title": "RxODE/rxode2 export type class.", "topics": [ "rxode_type-class" ] }, { "page": "rxodeCode", "title": "Get code for rxode2", "topics": [ "rxodeCode" ] }, { "page": "rxodeMatrix", "title": "Get the OMEGA/SIGMA matrix for rxode2.", "topics": [ "rxodeMatrix" ] }, { "page": "rxodeParams", "title": "Get the parameters vector for rxode2.", "topics": [ "rxodeParams" ] }, { "page": "select", "title": "Get a subset of an object.", "topics": [ "select", "select,compartment_properties-method", "select,data.frame-method", "select,parameters-method" ] }, { "page": "setMinMax", "title": "Set the minimum and maximum value on a model parameter.", "topics": [ "setMinMax", "setMinMax,campsis_model,character,numeric,numeric-method", "setMinMax,campsis_model,parameter,numeric,numeric-method", "setMinMax,parameters,character,numeric,numeric-method", "setMinMax,parameters,parameter,numeric,numeric-method" ] }, { "page": "shiftOmegaIndexes", "title": "Shift OMEGA indexes.", "topics": [ "shiftOmegaIndexes", "shiftOmegaIndexes,omega_block-method" ] }, { "page": "Sigma", "title": "Create a SIGMA parameter.", "topics": [ "Sigma" ] }, { "page": "sigma-class", "title": "Sigma parameter class.", "topics": [ "sigma-class" ] }, { "page": "single_array_parameter-class", "title": "Single-array parameter class. This parameter has a single index value.", "topics": [ "single_array_parameter-class" ] }, { "page": "sort", "title": "Sort the specified list.", "topics": [ "sort", "sort,campsis_model-method", "sort,code_records-method", "sort,compartments-method", "sort,compartment_properties-method", "sort,omega_blocks-method", "sort,parameters-method" ] }, { "page": "standardise", "title": "Standardise.", "topics": [ "standardise", "standardise,campsis_model-method", "standardise,double_array_parameter-method", "standardise,parameters-method", "standardise,theta-method" ] }, { "page": "statements_record-class", "title": "Statements record class.", "topics": [ "statements_record-class" ] }, { "page": "Theta", "title": "Create a THETA parameter.", "topics": [ "Theta" ] }, { "page": "theta-class", "title": "Theta parameter class.", "topics": [ "theta-class" ] }, { "page": "toString", "title": "ToString generic method.", "topics": [ "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" ] }, { "page": "trim", "title": "Trim character vector. Remove all leading and trailing spaces.", "topics": [ "trim" ] }, { "page": "unknown_statement-class", "title": "Unknown statement class. Any statement not recognized by campsismod.", "topics": [ "unknown_statement-class" ] }, { "page": "UnknownStatement", "title": "Create a new ordinary differential equation (ODE).", "topics": [ "UnknownStatement" ] }, { "page": "updateCompartments", "title": "Update compartments list from the persisted records. Exported especially for package 'campsistrans'. However, this method should not be called.", "topics": [ "updateCompartments" ] }, { "page": "variable_pattern-class", "title": "Variable pattern class.", "topics": [ "variable_pattern-class" ] }, { "page": "VariablePattern", "title": "Create a variable pattern.", "topics": [ "VariablePattern" ] }, { "page": "write", "title": "Write generic object to files.", "topics": [ "write", "write,campsis_model,character-method", "write,code_records,character-method", "write,json_element,character-method", "write,parameters,character-method" ] }, { "page": "writeParameters", "title": "Write subset of parameters (theta, omega or sigma).", "topics": [ "writeParameters" ] }, { "page": "writeVarcov", "title": "Write variance-covariance matrix.", "topics": [ "writeVarcov" ] } ], "_pkglogo": "https://github.com/calvagone/campsismod/raw/HEAD/man/figures/logo.png", "_readme": "https://github.com/calvagone/campsismod/raw/HEAD/README.md", "_rundeps": [ "assertthat", "bit", "bit64", "cli", "clipr", "cpp11", 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