Generic Implementation of a PK/PD Model

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Documentation for package ‘campsismod’ version 1.1.1

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A B C D E F G H I L M O P R S T U V W

-- A --

add Add element to list.
add-method Add element to list.
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.
addSuffix-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.
as.data.frame As data frame method.
as.data.frame-method As data frame method.
assertSingleCharacterString Assert the given character vector is a single character string.
autoDetectNONMEM Auto-detect special variables from NONMEM as compartment properties. Bioavailabilities, infusion durations/rates and lag times will be automatically detected.
autoDetectNONMEM-method Auto-detect special variables from NONMEM as compartment properties. Bioavailabilities, infusion durations/rates and lag times will be automatically detected.

-- B --

Bioavailability Create a bioavailability for the specified compartment.

-- C --

CampsisModel Create a new CAMPSIS model.
campsis_model-class CAMPSIS model class.
CodeRecords Create a list of code records.
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 Create a new comment.
comment-class Comment class. A statement starting with #.
Compartment Create a compartment.
compartment-class Compartment class.
Compartments Create a list of compartments
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.

-- D --

default Get default element from list.
delete Delete an element from this list.
delete-method Delete an element from this list.
disable Disable.
disable-method Disable.
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.

-- E --

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-method 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.

-- F --

find Find an element in list.
find-method Find an element in list.
fixOmega Fix omega matrix for SAME OMEGA parameters that have NA values due to imperfections in Pharmpy import.
fixOmega-method Fix omega matrix for SAME OMEGA parameters that have NA values due to imperfections in Pharmpy import.
f_record-class Bioavailability record class.

-- G --

getByIndex Get element by index.
getByIndex-method Get element by index.
getByName Get an element from a list by name. Never return more than 1 element.
getByName-method Get an element from a list by name. Never return more than 1 element.
getCompartmentIndex Get the compartment index for the specified compartment name.
getCompartmentIndex-method Get the compartment index for the specified compartment name.
getName Get element name.
getName-method Get element name.
getNameInModel Get the name of the given parameter in the CAMPSIS model.
getNameInModel-method Get the name of the given parameter in the CAMPSIS model.
getNames Get element names from list.
getNames-method Get element names from list.
getNONMEMName Get NONMEM name.
getNONMEMName-method Get NONMEM name.
getPrefix Get prefix.
getPrefix-method Get prefix.
getRecordDelimiter Get record delimiter.
getRecordName Get record name.
getRecordName-method Get record name.
getUncertainty Get uncertainty on the parameters.
getUncertainty-method Get uncertainty on the parameters.
getVarCov Get variance-covariance matrix.
getVarCov-method Get variance-covariance matrix.

-- H --

hasComment Check if string contains CAMPSIS-style comments.

-- I --

IfStatement Create a new IF-statement.
if_statement-class If-statement class. Any statement in the form if (condition) A = B.
indexOf Get the index of an element in list.
indexOf-method 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.
isComment Check if string is a CAMPSIS comment (i.e. not an equation).
isDiag Is diagonal.
isDiag-method 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.
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.

-- L --

LagTime Create a lag time for the specified compartment.
lag_record-class Lag record class.
LineBreak Create a new line break.
line_break-class Line-break class. A linebreak in the model.

-- M --

MainRecord Create MAIN code record.
main_record-class Main record class.
maxIndex Max index.
maxIndex-method Max index.
minIndex Min index.
minIndex-method Min index.
ModelStatements Create an empty list of model statements.
model_statement-class Model statement class. Any statement in a code record.
model_statements-class Model statements class. A list of statements.
model_suite CAMPSIS model suite.
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.

-- O --

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.
omega-class Omega parameter class.

-- P --

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 already called and returned TRUE.
parseStatements Parse statements code and return CAMPSIS statements.
Pattern Create a pattern.
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.
Position Element position in list.
processExtraArg Process extra arguments.
properties_record-class Properties record class.

-- R --

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.varcov Read variance-covariance file.
replace Replace element by another in list.
replace-method Replace element by another in list.
replaceAll Replace all occurrences in object.
replaceAll-method Replace all occurrences in object.
rxodeCode Get code for RxODE.
rxodeMatrix Get the OMEGA/SIGMA matrix for RxODE.
rxodeParams Get the parameters vector for RxODE.
rxode_type-class RxODE export type class.

-- S --

select Get a subset of an object.
select-method Get a subset of an object.
Sigma Create a SIGMA parameter.
sigma-class Sigma parameter class.
single_array_parameter-class Single-array parameter class. This parameter has a single index value.
sort Sort the specified list.
sort-method Sort the specified list.
standardise Standardise.
standardise-method Standardise.
statements_record-class Statements record class.

-- T --

Theta Create a THETA parameter.
theta-class Theta parameter class.
toString ToString generic method.
toString-method ToString generic method.
trim Trim character vector. Remove all leading and trailing spaces.

-- U --

UnknownStatement Create a new ordinary differential equation (ODE).
unknown_statement-class Unknown statement class. Any statement not recognized by campsismod.
updateCompartments Update compartments list from the persisted records. Exported especially for package pmxtran. However, this method should not be called.

-- V --

VariablePattern Create a variable pattern.
variable_pattern-class Variable pattern class.

-- W --

write Write generic object to files.
write-method Write generic object to files.
writeParameters Write subset of parameters (theta, omega or sigma).
writeVarcov Write variance-covariance matrix.