Man pages for campsismod
Generic Implementation of a PK/PD Model
| add | Add element to list. |
| addODECompartment | Add ODE compartment to compartments object. |
| addProperties | Add properties to compartments object. |
| addRSE | Add relative standard error (RSE) to the specified parameter. |
| addSuffix | Generic function to add a suffix to various objects like... |
| allNa | Check is vector has NA's only. |
| appendCodeRecords | Append code records |
| appendComment | Append comment. |
| appendCompartments | Append compartments. |
| appendModel | Append model (or simply add). |
| appendParameters | Append parameters. |
| as.data.frame | As data frame method. |
| assertSingleCharacterString | Assert the given character vector is a single character... |
| autoDetectNONMEM | Auto-detect special variables from NONMEM as compartment... |
| AutoReplicationSettings | Create auto replication settings. |
| auto_replication_settings-class | Auto replication settings class. |
| Bioavailability | Create a bioavailability for the specified compartment. |
| CampsisModel | Create a new Campsis model. |
| campsis_model-class | Campsis model class. |
| checkMatrixIsPositiveDefinite | Check OMEGA/SIGMA matrix for positive definiteness. |
| code_record-class | Code record class. See this code record as an abstract class.... |
| CodeRecords | Create a list of code records. |
| colon-equals | Colon-equals operator. |
| Comment | Create a new comment. |
| comment-class | Comment class. A statement starting with #. |
| Compartment | Create a compartment. |
| compartment_bioavailability-class | Compartment bioavailability class. |
| compartment-class | Compartment 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. |
| Compartments | Create a list of compartments |
| compartments-class | Compartments class. |
| contains | Check if an element exists in list. |
| convertAnyComment | Convert CAMPSIS comment style to C/C++ code. Only the first #... |
| convertOutvarsToCapture | Convert outvars argument to capture. Variables that are... |
| default | Get default element from list. |
| delete | Delete an element from this list. |
| disable | Disable. |
| double_array_parameter-class | Double-array parameter class. This parameter has 2 indexes.... |
| duration_record-class | (Infusion)-duration record class. |
| Equation | Create a new equation. |
| equation-class | Equation class. Any statement in the form A = B. |
| ErrorRecord | Create ERROR code record. |
| error_record-class | Error record class. |
| export | Export function. |
| export_type-class | Export type class. |
| extractLhs | Extract left-hand-side expression. |
| extractRhs | Extract right-hand-side expression. |
| extractTextBetweenBrackets | Extract text between brackets. |
| find | Find an element in list. |
| fixOmega | Fix omega matrix for SAME OMEGA parameters that have NA... |
| flagSampledParameterRows | Flag all parameter rows that have at least one parameter out... |
| f_record-class | Bioavailability record class. |
| getByIndex | Get element by index. |
| getByName | Get an element from a list by name. Never return more than 1... |
| getCompartmentIndex | Get the compartment index for the specified compartment name. |
| getCompartments | Detect all compartments names from the code records. Only for... |
| getMappingMatrix | Return a matrix filled in with OMEGA/SIGMA names to be mapped... |
| getName | Get element name. |
| getNameInModel | Get the name of the given parameter in the CAMPSIS model. |
| getNames | Get element names from list. |
| getNONMEMName | Get NONMEM name. |
| getOmegaBlock | Get the right block of OMEGA's. |
| getOmegaIndexes | Get the indexes of the omegas. |
| getPrefix | Get prefix. |
| getRecordDelimiter | Get record delimiter. |
| getRecordEquationNames | Get record equation names |
| getRecordName | Get record name. |
| getUncertainty | Get uncertainty on the parameters. |
| getVarCov | Get variance-covariance matrix. |
| grapes-greater-than-grapes | Magritt operator for piping. |
| hasComment | Check if string contains CAMPSIS-style comments. |
| hasOffDiagonalOmegas | Has off-diagonal omegas. |
| IfStatement | Create a new IF-statement. |
| if_statement-class | If-statement class. Any statement in the form if (condition)... |
| ifStatementPatternStr | Return the IF-statement pattern (string form). |
| indexOf | Get the index of an element in list. |
| InfusionDuration | Create an infusion duration. |
| InfusionRate | Create an infusion rate. |
| InitialCondition | Create an initial condition. |
| init_record-class | Init record class. |
| isBlockFixed | Say if the block is fixed (i.e. all parameters are fixed). |
| isComment | Check if string is a CAMPSIS comment (i.e. not an equation). |
| isDiag | Is diagonal. |
| isEmptyLine | Check if string is an empty line. |
| isEquation | Say if line in record is an equation not. |
| isIfStatement | Say if line in record is an IF-statement. |
| isMatrixPositiveDefinite | Is matrix positive definite. Same check as 'mvtnorm' does. |
| isODE | Say if line(s) in record is/are ODE or not. |
| isRecordDelimiter | Is record delimiter. A record delimiter is any line starting... |
| isRxODE | Check if the destination engine is RxODE or rxode2. Note that... |
| isStrictRecordDelimiter | Is strict record delimiter. A strict record delimiter is any... |
| lag_record-class | Lag record class. |
| LagTime | Create a lag time for the specified compartment. |
| length | Return the length of this list. |
| LineBreak | Create a new line break. |
| line_break-class | Line-break class. A linebreak in the model. |
| MainRecord | Create MAIN code record. |
| main_record-class | Main record class. |
| ManualReplicationSettings | Create manual replication settings. |
| manual_replication_settings-class | Manual replication settings class. |
| matchDoubleArrayParameter | Match double array parameter from list based on the name... |
| matchSingleArrayParameter | Match single array parameter from list based on the name... |
| maxIndex | Max index. |
| methodsGlobalFunctions | A empty method only used to declare some of the global... |
| minIndex | Min index. |
| minMaxDefault | Min/max default values for the given parameter. |
| model_statement-class | Model statement class. Any statement in a code record. |
| ModelStatements | Create an empty list of model statements. |
| model_statements-class | Model statements class. A list of statements. |
| model_suite | CAMPSIS model suite. |
| move | Move element 'x' from object to a certain place. |
| mrgsolveBlock | Convert code record for mrgsolve. |
| mrgsolveCapture | Get the CAPTURE block for mrgsolve. |
| mrgsolveCompartment | Get the compartment block for mrgsolve. |
| mrgsolveMain | Get the MAIN block for mrgsolve. |
| mrgsolveMatrix | Get the OMEGA/SIGMA matrix for mrgsolve. |
| mrgsolveOde | Get the ODE block for mrgsolve. |
| mrgsolveParam | Get the parameters block for mrgsolve. |
| mrgsolveTable | Get the TABLE block for mrgsolve. |
| mrgsolve_type-class | Mrgsolve export type class. |
| Ode | Create a new ordinary differential equation (ODE). |
| ode-class | ODE class. Any statement in the form d/dt(A_CMT) = B. |
| OdeRecord | Create ODE code record. |
| ode_record-class | ODE record class. |
| Omega | Create an OMEGA parameter. |
| OmegaBlock | Create a block of OMEGA's. |
| OmegaBlocks | Create a list of OMEGA blocks. |
| omega-class | Omega parameter class. |
| parameter-class | Parameter class. Any parameter in a pharmacometric model. |
| Parameters | Create a list of parameters. |
| parameters-class | Parameters class. |
| parseIfStatement | Parse IF-statement. Assumption: 'isIfStatement' method... |
| parseStatements | Parse statements code and return CAMPSIS statements. |
| Pattern | Create a pattern. |
| pattern-class | Pattern class. |
| pmx_element-class | PMX element class. |
| pmx_list-class | PMX list 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. |
| Position | Element position in list. |
| processDoubleArrayArguments | Process double array arguments. |
| processExtraArg | Process extra arguments. |
| properties_record-class | Properties record class. |
| rate_record-class | (Infusion)-rate record class. |
| read | Generic read method to read data from a file or a folder. |
| read.allparameters | Read all parameters files at once. |
| read.campsis | Read a CAMPSIS model. |
| read.model | Read model file. |
| read.parameters | Read parameters file. |
| read.pmxmod | Read a Campsis model (deprecated). |
| read.varcov | Read variance-covariance file. |
| removeNaColumn | Remove given column(s) if it has only NA's. |
| removeTrailingLineBreaks | Remove all trailing line breaks. |
| replace | Replace element by another in list. |
| replaceAll | Replace all occurrences in object. |
| replicate | Replicate generic object. |
| replicated_campsis_model-class | Replicated Campsis model class. |
| replication_settings-class | Replication settings interface. |
| rxodeCode | Get code for rxode2 |
| rxodeMatrix | Get the OMEGA/SIGMA matrix for rxode2. |
| rxodeParams | Get the parameters vector for rxode2. |
| rxode_type-class | RxODE/rxode2 export type class. |
| sampleFromInverseChiSquaredCore | Sample from scaled inverse chi-squared distribution (core... |
| sampleFromInverseChiSquaredOrWishart | Sample parameters from inverse scaled chi-squared or wishart... |
| sampleFromInverseWishartCore | Sample from scaled inverse Wishart distribution (core... |
| sampleFromMultivariateNormalDistribution | Sample from a multivariate normal distribution. |
| sampleFromMultivariateNormalDistributionCore | Sample from multivariate normal distribution (core method). |
| sampleGeneric | Generic function for parameter sampling according to the... |
| select | Get a subset of an object. |
| setMinMax | Set the minimum and maximum value on a model parameter. |
| shiftOmegaIndexes | Shift OMEGA indexes. |
| Sigma | Create a SIGMA parameter. |
| sigma-class | Sigma parameter class. |
| single_array_parameter-class | Single-array parameter class. This parameter has a single... |
| sort | Sort the specified list. |
| standardise | Standardise. |
| statements_record-class | Statements record class. |
| Theta | Create a THETA parameter. |
| theta-class | Theta parameter class. |
| toString | ToString generic method. |
| trim | Trim character vector. Remove all leading and trailing... |
| UnknownStatement | Create a new ordinary differential equation (ODE). |
| unknown_statement-class | Unknown statement class. Any statement not recognized by... |
| UnsupportedDestException | Unknown destination engine exception. |
| updateCompartments | Update compartments list from the persisted records. Exported... |
| updateOMEGAs | Update OMEGAs that are same. Same OMEGAs are written as... |
| updateParameters | Update model parameters based on the parameters issued from... |
| VariablePattern | Create a variable pattern. |
| variable_pattern-class | Variable pattern class. |
| variablePatternNoStartStr | Return the variable pattern (string form), without the first... |
| variablePatternStr | Return the variable pattern (string form). |
| write | Write generic object to files. |
| writeParameters | Write subset of parameters (theta, omega or sigma). |
| writeRecordDelimiter | Write record delimiter line. |
| writeVarcov | Write variance-covariance matrix. |
