Package index • campsismod

Campsis model

CampsisModel(): Create a new Campsis model.

autoDetectNONMEM(): Auto-detect special variables from NONMEM as compartment properties. Bioavailabilities, infusion durations/rates and lag times will be automatically detected.

read.campsis(): Read a CAMPSIS model.

read.model(): Read model file.

addSuffix(): 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.

Code records

CodeRecords(): Create a list of code records.

MainRecord(): Create MAIN code record.

OdeRecord(): Create ODE code record.

ErrorRecord(): Create ERROR code record.

getRecordName(): Get record name.

Statement type

ModelStatements(): Create an empty list of model statements.

Comment(): Create a new comment.

Equation(): Create a new equation.

IfStatement(): Create a new IF-statement.

LineBreak(): Create a new line break.

Ode(): Create a new ordinary differential equation (ODE).

UnknownStatement(): Create a new ordinary differential equation (ODE).

Parameters

Parameters(): Create a list of parameters.

Theta(): Create a THETA parameter.

Omega(): Create an OMEGA parameter.

Sigma(): Create a SIGMA parameter.

addRSE(): Add relative standard error (RSE) to the specified parameter.

as.data.frame(): As data frame method.

getNameInModel(): Get the name of the given parameter in the CAMPSIS model.

getNONMEMName(): Get NONMEM name.

getUncertainty(): Get uncertainty on the parameters.

getVarCov(): Get variance-covariance matrix.

isDiag(): Is diagonal.

maxIndex(): Max index.

minIndex(): Min index.

read.allparameters(): Read all parameters files at once.

read.parameters(): Read parameters file.

read.varcov(): Read variance-covariance file.

setMinMax(): Set the minimum and maximum value on a model parameter.

writeParameters(): Write subset of parameters (theta, omega or sigma).

writeVarcov(): Write variance-covariance matrix.

Compartments

Compartment(): Create a compartment.

Compartments(): Create a list of compartments

getCompartmentIndex(): Get the compartment index for the specified compartment name.

Compartment properties

Bioavailability(): Create a bioavailability for the specified compartment.

InfusionDuration(): Create an infusion duration.

InfusionRate(): Create an infusion rate.

InitialCondition(): Create an initial condition.

LagTime(): Create a lag time for the specified compartment.

getPrefix(): Get prefix.

Model parameters replication

AutoReplicationSettings(): Create auto replication settings.

ManualReplicationSettings(): Create manual replication settings.

replicate(): Replicate generic object.

Generic list

add(): Add element to list.

delete(): Delete an element from this list.

find(): Find an element in list.

indexOf(): Get the index of an element in list.

getByIndex(): Get element by index.

getByName(): Get an element from a list by name. Never return more than 1 element.

getNames(): Get element names from list.

move(): Move element 'x' from object to a certain place.

replace(): Replace element by another in list.

sort(): Sort the specified list.

default(): Get default element from list.

Position(): Element position in list.

Generic list element

getName(): Get element name.

Generic methods

export(): Export function.

disable(): Disable.

fixOmega(): Fix omega matrix for SAME OMEGA parameters that have NA values due to imperfections in Pharmpy import.

read(): Generic read method to read data from a file or a folder.

select(): Get a subset of an object.

standardise(): Standardise.

toString(): ToString generic method.

write(): Write generic object to files.

Mrgsolve export

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.

RxODE export

rxodeCode(): Get code for rxode2

rxodeMatrix(): Get the OMEGA/SIGMA matrix for rxode2.

rxodeParams(): Get the parameters vector for rxode2.

Exported classes

auto_replication_settings-class: Auto replication settings class.

campsis_model-class: Campsis model class.

code_record-class: 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)

comment-class: Comment class. A statement starting with #.

compartment-class: Compartment class.

compartments-class: Compartments class.

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.

double_array_parameter-class: Double-array parameter class. This parameter has 2 indexes. It can thus be used to define correlations between parameters.

duration_record-class: (Infusion)-duration record class.

equation-class: Equation class. Any statement in the form A = B.

error_record-class: Error record class.

export_type-class: Export type class.

f_record-class: Bioavailability record class.

if_statement-class: If-statement class. Any statement in the form if (condition) A = B.

init_record-class: Init record class.

lag_record-class: Lag record class.

line_break-class: Line-break class. A linebreak in the model.

main_record-class: Main record class.

manual_replication_settings-class: Manual replication settings class.

model_statement-class: Model statement class. Any statement in a code record.

model_statements-class: Model statements class. A list of statements.

mrgsolve_type-class: Mrgsolve export type class.

pattern-class: Pattern class.

pmx_element-class: PMX element class.

pmx_position-class: PMX position class.

pmx_position_by_element-class: PMX position by element class.

pmx_position_by_index-class: PMX position by index class.

ode-class: ODE class. Any statement in the form d/dt(A_CMT) = B.

ode_record-class: ODE record class.

omega-class: Omega parameter class.

parameter-class: Parameter class. Any parameter in a pharmacometric model.

parameters-class: Parameters class.

properties_record-class: Properties record class.

rate_record-class: (Infusion)-rate record class.

replicated_campsis_model-class: Replicated Campsis model class.

replication_settings-class: Replication settings interface.

rxode_type-class: RxODE/rxode2 export type class.

sigma-class: Sigma parameter class.

single_array_parameter-class: Single-array parameter class. This parameter has a single index value.

statements_record-class: Statements record class.

theta-class: Theta parameter class.

unknown_statement-class: Unknown statement class. Any statement not recognized by campsismod.

variable_pattern-class: Variable pattern class.

Parsing utilities

extractLhs(): Extract left-hand-side expression.

extractRhs(): Extract right-hand-side expression.

extractTextBetweenBrackets(): Extract text between brackets.

getRecordDelimiter(): Get record delimiter.

hasComment(): Check if string contains CAMPSIS-style comments.

isComment(): Check if string is a CAMPSIS comment (i.e. not an equation).

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.

isODE(): Say if line(s) in record is/are ODE or not.

isRecordDelimiter(): Is record delimiter. A record delimiter is any line starting with [...].

isStrictRecordDelimiter(): Is strict record delimiter. A strict record delimiter is any line starting with [...] and followed by nothing but spaces or a possible comment.

parseIfStatement(): Parse IF-statement. Assumption: isIfStatement method already called and returned TRUE.

parseStatements(): Parse statements code and return CAMPSIS statements.

trim(): Trim character vector. Remove all leading and trailing spaces.

Replace occurrences

replaceAll(): Replace all occurrences in object.

Pattern(): Create a pattern.

VariablePattern(): Create a variable pattern.

Model library

model_suite: CAMPSIS model suite.

Advanced use

updateCompartments(): Update compartments list from the persisted records. Exported especially for package campsistrans. However, this method should not be called.

isMatrixPositiveDefinite(): Is matrix positive definite. Same check as mvtnorm does.

getOmegaBlock(): Get the right block of OMEGA's.

getOmegaIndexes(): Get the indexes of the omegas.

hasOffDiagonalOmegas(): Has off-diagonal omegas.

OmegaBlock(): Create a block of OMEGA's.

OmegaBlocks(): Create a list of OMEGA blocks.

shiftOmegaIndexes(): Shift OMEGA indexes.

Other exported methods

assertSingleCharacterString(): Assert the given character vector is a single character string.

processExtraArg(): Process extra arguments.