Magritt operator for piping.

Description

Magritt operator for piping.

Usage

lhs %>% rhs

Colon-equals operator.

Description

Colon-equals operator.

Usage

`:=`(x, y)

Create auto replication settings.

Description

By default, all model parameters are sampled from a multivariate normal distribution, whose characteristics are specified by the variance-covariance matrix. OMEGAs and SIGMAs can be sampled from scaled inverse chi-squared or Wishart distributions by setting the wishart argument to TRUE. In that case, THETAs are still sampled from a multivariate normal distribution, while OMEGAS and SIGMAs are sampled from scaled inverse chi-squared (univariate OMEGA/SIGMA distribution) and Wishart (block of OMEGAs/SIGMAs) distribution, respectively. When wishart is set to TRUE, the degrees of freedom of the distribution must be specified, respectively, odf for the OMEGAs and sdf for the SIGMAs.

Usage

AutoReplicationSettings(
  wishart = FALSE,
  odf = NA,
  sdf = NA,
  checkMinMax = TRUE,
  checkPosDef = FALSE,
  quiet = NA
)

Arguments

Value

replication settings

Create a bioavailability for the specified compartment.

Description

Create a bioavailability for the specified compartment.

Usage

Bioavailability(compartment, rhs = "")

Arguments

Value

a bioavailability property

Create a new Campsis model.

Description

Create a new Campsis model.

Usage

CampsisModel()

Value

a Campsis model, empty

Create a list of code records.

Description

Create a list of code records.

Usage

CodeRecords()

Value

an empty list of code records

Create a new comment.

Description

Create a new comment.

Usage

Comment(x)

Arguments

Value

a comment

Create a compartment.

Description

Create a compartment.

Usage

Compartment(index, name = NA)

Arguments

Value

an empty list of compartments

Create a list of compartments

Description

Create a list of compartments

Usage

Compartments()

Value

an empty list of compartments

Create a new equation.

Description

Create a new equation.

Usage

Equation(lhs, rhs = "", comment = as.character(NA))

Arguments

Value

an equation

Create ERROR code record.

Description

Create ERROR code record.

Usage

ErrorRecord(code = character())

Arguments

Value

an ERROR code record

Create a new IF-statement.

Description

Create a new IF-statement.

Usage

IfStatement(condition, equation, comment = as.character(NA))

Arguments

Value

an IF-statement

Create an infusion duration.

Description

Create an infusion duration.

Usage

InfusionDuration(compartment, rhs = "")

Arguments

Value

an infusion duration property

Create an infusion rate.

Description

Create an infusion rate.

Usage

InfusionRate(compartment, rhs = "")

Arguments

Value

an infusion rate property

Create an initial condition.

Description

Create an initial condition.

Usage

InitialCondition(compartment, rhs = "")

Arguments

Value

an initial condition property

Create a lag time for the specified compartment.

Description

Create a lag time for the specified compartment.

Usage

LagTime(compartment, rhs = "")

Arguments

Value

a lag time property

Create a new line break.

Description

Create a new line break.

Usage

LineBreak()

Value

a line break

Create MAIN code record.

Description

Create MAIN code record.

Usage

MainRecord(code = character())

Arguments

Create manual replication settings.

Description

Create manual replication settings.

Usage

ManualReplicationSettings(data)

Arguments

Details

Use these settings to import custom replicated model parameters.

Value

replication settings

Create an empty list of model statements.

Description

Create an empty list of model statements.

Usage

ModelStatements()

Value

a model statements object

Create a new ordinary differential equation (ODE).

Description

Create a new ordinary differential equation (ODE).

Usage

Ode(lhs, rhs = "", comment = as.character(NA))

Arguments

Value

an ODE

Create ODE code record.

Description

Create ODE code record.

Usage

OdeRecord(code = character())

Arguments

Value

an ODE code record

Create an OMEGA parameter.

Description

Create an OMEGA parameter.

Usage

Omega(
  name = NA,
  index = NA,
  index2 = NA,
  value = NA,
  min = NA,
  max = NA,
  fix = FALSE,
  type = NULL,
  same = NA,
  label = NA,
  comment = NA
)

Arguments

Value

an OMEGA parameter

Create a block of OMEGA's.

Description

Create a block of OMEGA's.

Usage

OmegaBlock()

Create a list of OMEGA blocks.

Description

Create a list of OMEGA blocks.

Usage

OmegaBlocks()

Create a list of parameters.

Description

Create a list of parameters.

Usage

Parameters()

Value

an empty list of parameters

Create a pattern.

Description

Create a pattern.

Usage

Pattern(x)

Arguments

Value

a pattern

Element position in list.

Description

Element position in list.

Usage

Position(x, after = TRUE)

Arguments

Value

a position object

Create a SIGMA parameter.

Description

Create a SIGMA parameter.

Usage

Sigma(
  name = NA,
  index = NA,
  index2 = NA,
  value = NA,
  min = NA,
  max = NA,
  fix = FALSE,
  type = NULL,
  label = NA,
  comment = NA
)

Arguments

Value

a SIGMA parameter

Create a THETA parameter.

Description

Create a THETA parameter.

Usage

Theta(
  name = NA,
  index = NA,
  value = NA,
  min = NA,
  max = NA,
  fix = FALSE,
  label = NA,
  unit = NA,
  comment = NA
)

Arguments

Value

a THETA parameter

Create a new ordinary differential equation (ODE).

Description

Create a new ordinary differential equation (ODE).

Usage

UnknownStatement(line, comment = as.character(NA))

Arguments

Value

an unknown statement

Unknown destination engine exception.

Description

Unknown destination engine exception.

Usage

UnsupportedDestException()

Value

no return value

Create a variable pattern.

Description

Create a variable pattern.

Usage

VariablePattern(x)

Arguments

Value

a variable pattern

Add element to list.

Description

Add element to list.

Usage

add(object, x, ...)

## S4 method for signature 'pmx_list,pmx_element'
add(object, x, pos = NULL)

## S4 method for signature 'pmx_list,pmx_list'
add(object, x)

## S4 method for signature 'pmx_list,list'
add(object, x)

## S4 method for signature 'compartments,compartment_property'
add(object, x)

## S4 method for signature 'compartments,compartments'
add(object, x)

## S4 method for signature 'parameters,single_array_parameter'
add(object, x)

## S4 method for signature 'parameters,double_array_parameter'
add(object, x)

## S4 method for signature 'parameters,parameters'
add(object, x)

## S4 method for signature 'code_record,model_statement'
add(object, x, pos = NULL)

## S4 method for signature 'code_record,code_record'
add(object, x)

## S4 method for signature 'code_records,code_records'
add(object, x)

## S4 method for signature 'code_records,model_statement'
add(object, x, pos = NULL)

## S4 method for signature 'campsis_model,compartment_property'
add(object, x)

## S4 method for signature 'campsis_model,parameter'
add(object, x)

## S4 method for signature 'campsis_model,code_record'
add(object, x)

## S4 method for signature 'campsis_model,model_statement'
add(object, x, pos = NULL)

## S4 method for signature 'campsis_model,campsis_model'
add(object, x)

## S4 method for signature 'campsis_model,list'
add(object, x)

## S4 method for signature 'omega_block,double_array_parameter'
add(object, x)

## S4 method for signature 'omega_blocks,omega_block'
add(object, x)

## S4 method for signature 'omega_blocks,parameters'
add(object, x)

Arguments

Value

modified list object

Add ODE compartment to compartments object.

Description

Add ODE compartment to compartments object.

Usage

addODECompartment(compartments, ode)

Arguments

Value

a compartments object

Add properties to compartments object.

Description

Add properties to compartments object.

Usage

addProperties(compartments, records, name, init)

Arguments

Value

updated compartments object

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

Description

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

Usage

addRSE(object, parameter, value, ...)

## S4 method for signature 'parameters,parameter,numeric'
addRSE(object, parameter, value, ...)

## S4 method for signature 'campsis_model,parameter,numeric'
addRSE(object, parameter, value, ...)

Arguments

Value

updated object

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.

Description

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.

Usage

addSuffix(object, suffix, separator = NULL, ...)

## S4 method for signature 'parameters,character,character'
addSuffix(object, suffix, separator = NULL, ...)

## S4 method for signature 'code_records,character,character'
addSuffix(object, suffix, separator = NULL, ...)

## S4 method for signature 'code_record,character,character'
addSuffix(object, suffix, separator = NULL, ...)

## S4 method for signature 'compartments,character,character'
addSuffix(object, suffix, separator = NULL, ...)

## S4 method for signature 'campsis_model,character,character'
addSuffix(object, suffix, separator = NULL, ...)

Arguments

Value

updated object of the same class as the provided object, unless 'model' was specified, in that case the model is returned

Check is vector has NA's only.

Description

Check is vector has NA's only.

Usage

allNa(x)

Arguments

Value

TRUE if all values are NA, FALSE otherwise

Append code records

Description

Append code records

Usage

appendCodeRecords(records1, records2)

Arguments

Value

the resulting set of code records

Append comment.

Description

Append comment.

Usage

appendComment(str, object, dest)

Arguments

Value

single character string followed by comment

Append compartments.

Description

Append compartments.

Usage

appendCompartments(compartments1, compartments2)

Arguments

Value

the resulting set of compartments

Append model (or simply add).

Description

Append model (or simply add).

Usage

appendModel(model1, model2)

Arguments

Value

the resulting Campsis model

Append parameters.

Description

Append parameters.

Usage

appendParameters(params1, params2)

Arguments

Value

the resulting set of parameters

As data frame method.

Description

As data frame method.

Usage

as.data.frame(x, row.names = NULL, optional = FALSE, ...)

## S4 method for signature 'theta,character,logical'
as.data.frame(x, row.names = NULL, optional = FALSE, ...)

## S4 method for signature 'omega,character,logical'
as.data.frame(x, row.names = NULL, optional = FALSE, ...)

## S4 method for signature 'sigma,character,logical'
as.data.frame(x, row.names = NULL, optional = FALSE, ...)

Arguments

Value

data frame

Assert the given character vector is a single character string.

Description

Assert the given character vector is a single character string.

Usage

assertSingleCharacterString(x)

Arguments

Value

no return value

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

Description

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

Usage

autoDetectNONMEM(object, ...)

## S4 method for signature 'campsis_model'
autoDetectNONMEM(object, ...)

Arguments

Value

updated object

Auto replication settings class.

Description

Auto replication settings class.

Slots

wishart

logical, sample OMEGAs and SIGMAs from scaled inverse chi-squared or Wishart distributions

odf

the degrees of freedom for the scaled inverse chi-squared/Wishart distribution with regards to the OMEGAs, integer vector

sdf

the degrees of freedom for the scaled inverse chi-squared/Wishart distribution with regards to the SIGMAs, integer vector

quiet

logical, suppress info messages

max_iterations

number of iterations maximum to sample the parameters

max_chunk_size

maximum number of rows to sample at once, default value will be the number of replicates, unless specified.

check_min_max

logical, check for min/max values when sampling the parameters

check_pos_def

logical, check for positive definiteness when sampling the OMEGA/SIGMA parameters

wishart_correction

logical, FALSE is default, see https://github.com/metrumresearchgroup/simpar/issues/11

Campsis model class.

Description

Campsis model class.

Slots

model

a list of code records

parameters

model parameters

compartments

model compartments

Check OMEGA/SIGMA matrix for positive definiteness.

Description

Check OMEGA/SIGMA matrix for positive definiteness.

Usage

checkMatrixIsPositiveDefinite(table, parameters)

Arguments

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)

Description

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)

Slots

comment

a comment, single character value

statements

model statements

Comment class. A statement starting with #.

Description

Comment class. A statement starting with #.

Compartment class.

Description

Compartment class.

Slots

name

compartment name (without prefix)

index

compartment index

Compartment bioavailability class.

Description

Compartment bioavailability class.

Compartment infusion duration class.

Description

Compartment infusion duration class.

Compartment infusion rate class.

Description

Compartment infusion rate class.

Compartment initial condition class.

Description

Compartment initial condition class.

Compartment lag time class.

Description

Compartment lag time class.

Compartment properties class.

Description

Compartment properties class.

Compartment property class.

Description

Compartment property class.

Slots

compartment

related compartment index

rhs

right-hand side formula

comment

comment if any, single character string

Compartments class.

Description

Compartments class.

Slots

properties

compartment properties of the compartments defined in this class

Check if an element exists in list.

Description

Check if an element exists in list.

Usage

contains(object, x)

## S4 method for signature 'pmx_list,pmx_element'
contains(object, x)

## S4 method for signature 'statements_record,model_statement'
contains(object, x)

## S4 method for signature 'campsis_model,pmx_element'
contains(object, x)

Arguments

Value

logical value, TRUE or FALSE

Convert CAMPSIS comment style to C/C++ code. Only the first # is translated to //.

Description

Convert CAMPSIS comment style to C/C++ code. Only the first # is translated to //.

Usage

convertAnyComment(x)

Arguments

Value

same line with comments translated to C/C++

Convert outvars argument to capture. Variables that are already in error block will be discarded.

Description

Convert outvars argument to capture. Variables that are already in error block will be discarded.

Usage

convertOutvarsToCapture(outvars, model)

Arguments

Value

all variables to capture

Get default element from list.

Description

Get default element from list.

Usage

default(object, ...)

Arguments

Value

the default element from list

Delete an element from this list.

Description

Delete an element from this list.

Usage

delete(object, x)

## S4 method for signature 'pmx_list,pmx_element'
delete(object, x)

## S4 method for signature 'pmx_list,integer'
delete(object, x)

## S4 method for signature 'compartments,compartment_property'
delete(object, x)

## S4 method for signature 'parameters,single_array_parameter'
delete(object, x)

## S4 method for signature 'parameters,double_array_parameter'
delete(object, x)

## S4 method for signature 'statements_record,model_statement'
delete(object, x)

## S4 method for signature 'statements_record,integer'
delete(object, x)

## S4 method for signature 'code_records,model_statement'
delete(object, x)

## S4 method for signature 'campsis_model,compartment_property'
delete(object, x)

## S4 method for signature 'campsis_model,parameter'
delete(object, x)

## S4 method for signature 'campsis_model,code_record'
delete(object, x)

## S4 method for signature 'campsis_model,model_statement'
delete(object, x)

Arguments

Value

the updated list

Disable.

Description

Disable.

Usage

disable(object, x, ...)

## S4 method for signature 'parameters,character'
disable(object, x, ...)

## S4 method for signature 'campsis_model,character'
disable(object, x, ...)

Arguments

Value

object with some disabled features

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

Description

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

(Infusion)-duration record class.

Description

(Infusion)-duration record class.

Equation class. Any statement in the form A = B.

Description

Equation class. Any statement in the form A = B.

Slots

lhs

left-hand side expression

rhs

right-hand side expression

Error record class.

Description

Error record class.

Export function.

Description

Export function.

Usage

export(object, dest, ...)

## S4 method for signature 'campsis_model,character'
export(object, dest, ...)

## S4 method for signature 'replicated_campsis_model,campsis_model'
export(object, dest = CampsisModel(), index, ...)

## S4 method for signature 'campsis_model,rxode_type'
export(object, dest, ...)

## S4 method for signature 'campsis_model,mrgsolve_type'
export(object, dest, outvars = NULL, extra_params = character(0))

Arguments

Value

specific object depending on given destination

Export type class.

Description

Export type class.

Extract left-hand-side expression.

Description

Extract left-hand-side expression.

Usage

extractLhs(x, split = "=")

Arguments

Value

left-hand-side expression, not trimmed

Extract right-hand-side expression.

Description

Extract right-hand-side expression.

Usage

extractRhs(x, split = "=")

Arguments

Value

right-hand side expression

Extract text between brackets.

Description

Extract text between brackets.

Usage

extractTextBetweenBrackets(x)

Arguments

Value

text between brackets (trimmed)

Bioavailability record class.

Description

Bioavailability record class.

Find an element in list.

Description

Find an element in list.

Usage

find(object, x)

## S4 method for signature 'pmx_list,pmx_element'
find(object, x)

## S4 method for signature 'compartments,compartment_property'
find(object, x)

## S4 method for signature 'statements_record,model_statement'
find(object, x)

## S4 method for signature 'code_records,model_statement'
find(object, x)

## S4 method for signature 'campsis_model,compartment'
find(object, x)

## S4 method for signature 'campsis_model,compartment_property'
find(object, x)

## S4 method for signature 'campsis_model,parameter'
find(object, x)

## S4 method for signature 'campsis_model,code_record'
find(object, x)

## S4 method for signature 'campsis_model,model_statement'
find(object, x)

Arguments

Value

the element from the list that has same name as x, or NULL if no element was found

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

Description

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

Usage

fixOmega(object)

## S4 method for signature 'parameters'
fixOmega(object)

Arguments

Value

the parameter that matches

Flag all parameter rows that have at least one parameter out of the specified range or that have a non positive definite OMEGA or SIGMA matrix.

Description

Flag all parameter rows that have at least one parameter out of the specified range or that have a non positive definite OMEGA or SIGMA matrix.

Usage

flagSampledParameterRows(table, minMax, settings, parameters)

Arguments

Get element by index.

Description

Get element by index.

Usage

getByIndex(object, x)

## S4 method for signature 'pmx_list,integer'
getByIndex(object, x)

## S4 method for signature 'pmx_list,numeric'
getByIndex(object, x)

## S4 method for signature 'compartment_properties,compartment_property'
getByIndex(object, x)

## S4 method for signature 'parameters,parameter'
getByIndex(object, x)

Arguments

Value

element from the list whose index matches with provided index

Get an element from a list by name. Never return more than 1 element.

Description

Get an element from a list by name. Never return more than 1 element.

Usage

getByName(object, name)

## S4 method for signature 'pmx_list,character'
getByName(object, name)

Arguments

Value

the element that was found or NULL if no element was found with the same name

Get the compartment index for the specified compartment name.

Description

Get the compartment index for the specified compartment name.

Usage

getCompartmentIndex(object, name)

## S4 method for signature 'compartments,character'
getCompartmentIndex(object, name)

## S4 method for signature 'campsis_model,character'
getCompartmentIndex(object, name)

Arguments

Value

the corresponding compartment index

Detect all compartments names from the code records. Only for model instantiation. Not exported.

Description

Detect all compartments names from the code records. Only for model instantiation. Not exported.

Usage

getCompartments(records)

Arguments

Value

a list of compartments

Return a matrix filled in with OMEGA/SIGMA names to be mapped with the values. Nonexistent parameters are filled in with the empty string.

Description

Return a matrix filled in with OMEGA/SIGMA names to be mapped with the values. Nonexistent parameters are filled in with the empty string.

Usage

getMappingMatrix(parameters, type)

Arguments

Value

a matrix with the names of the OMEGA/SIGMA parameters

Get NONMEM name.

Description

Get NONMEM name.

Usage

getNONMEMName(object)

## S4 method for signature 'theta'
getNONMEMName(object)

## S4 method for signature 'omega'
getNONMEMName(object)

## S4 method for signature 'sigma'
getNONMEMName(object)

Arguments

Value

the NONMEM name associated with this object

Get element name.

Description

Get element name.

Usage

getName(x)

## S4 method for signature 'unknown_statement'
getName(x)

## S4 method for signature 'comment'
getName(x)

## S4 method for signature 'line_break'
getName(x)

## S4 method for signature 'equation'
getName(x)

## S4 method for signature 'ode'
getName(x)

## S4 method for signature 'if_statement'
getName(x)

## S4 method for signature 'compartment'
getName(x)

## S4 method for signature 'compartment_bioavailability'
getName(x)

## S4 method for signature 'compartment_lag_time'
getName(x)

## S4 method for signature 'compartment_infusion_duration'
getName(x)

## S4 method for signature 'compartment_infusion_rate'
getName(x)

## S4 method for signature 'compartment_initial_condition'
getName(x)

## S4 method for signature 'theta'
getName(x)

## S4 method for signature 'omega'
getName(x)

## S4 method for signature 'sigma'
getName(x)

## S4 method for signature 'main_record'
getName(x)

## S4 method for signature 'ode_record'
getName(x)

## S4 method for signature 'f_record'
getName(x)

## S4 method for signature 'lag_record'
getName(x)

## S4 method for signature 'duration_record'
getName(x)

## S4 method for signature 'rate_record'
getName(x)

## S4 method for signature 'init_record'
getName(x)

## S4 method for signature 'error_record'
getName(x)

## S4 method for signature 'omega_block'
getName(x)

Arguments

Value

the name of this element

Get the name of the given parameter in the CAMPSIS model.

Description

Get the name of the given parameter in the CAMPSIS model.

Usage

getNameInModel(x)

## S4 method for signature 'theta'
getNameInModel(x)

## S4 method for signature 'omega'
getNameInModel(x)

## S4 method for signature 'sigma'
getNameInModel(x)

Arguments

Value

the name of this parameter

Get element names from list.

Description

Get element names from list.

Usage

getNames(object)

## S4 method for signature 'pmx_list'
getNames(object)

Arguments

Value

character vector with all the element names of this list

Get the right block of OMEGA's.

Description

Get the right block of OMEGA's.

Usage

getOmegaBlock(object, x)

## S4 method for signature 'omega_blocks,double_array_parameter'
getOmegaBlock(object, x)

Arguments

Value

the corresponding OMEGA block or NULL if not found

Get the indexes of the omegas.

Description

Get the indexes of the omegas.

Usage

getOmegaIndexes(object)

## S4 method for signature 'omega_block'
getOmegaIndexes(object)

Arguments

Value

a list of integers

Get prefix.

Description

Get prefix.

Usage

getPrefix(object, ...)

## S4 method for signature 'compartment_bioavailability'
getPrefix(object, ...)

## S4 method for signature 'compartment_lag_time'
getPrefix(object, ...)

## S4 method for signature 'compartment_infusion_duration'
getPrefix(object, ...)

## S4 method for signature 'compartment_infusion_rate'
getPrefix(object, ...)

## S4 method for signature 'compartment_initial_condition'
getPrefix(object, ...)

Arguments

Value

the prefix of this object

Get record delimiter.

Description

Get record delimiter.

Usage

getRecordDelimiter(line)

Arguments

Value

the record delimiter between brackets

Get record equation names

Description

Get record equation names

Usage

getRecordEquationNames(record)

Arguments

Value

a character vector with the equation names

Get record name.

Description

Get record name.

Usage

getRecordName(object)

## S4 method for signature 'compartment_bioavailability'
getRecordName(object)

## S4 method for signature 'compartment_lag_time'
getRecordName(object)

## S4 method for signature 'compartment_infusion_duration'
getRecordName(object)

## S4 method for signature 'compartment_infusion_rate'
getRecordName(object)

## S4 method for signature 'compartment_initial_condition'
getRecordName(object)

Arguments

Value

the name of the record

Get uncertainty on the parameters.

Description

Get uncertainty on the parameters.

Usage

getUncertainty(object, ...)

## S4 method for signature 'parameter'
getUncertainty(object, varcov, ...)

## S4 method for signature 'parameters'
getUncertainty(object, ...)

## S4 method for signature 'campsis_model'
getUncertainty(object, ...)

Arguments

Value

data frame with standard error (se) and relative standard error (rse

Get variance-covariance matrix.

Description

Get variance-covariance matrix.

Usage

getVarCov(object)

## S4 method for signature 'parameters'
getVarCov(object)

## S4 method for signature 'campsis_model'
getVarCov(object)

Arguments

Value

a variance-covariance matrix (data frame) or NULL if no matrix present

Check if string contains CAMPSIS-style comments.

Description

Check if string contains CAMPSIS-style comments.

Usage

hasComment(x)

Arguments

Value

logical value

Has off-diagonal omegas.

Description

Has off-diagonal omegas.

Usage

hasOffDiagonalOmegas(object)

## S4 method for signature 'omega_block'
hasOffDiagonalOmegas(object)

Arguments

Value

TRUE or FALSE

Return the IF-statement pattern (string form).

Description

Return the IF-statement pattern (string form).

Usage

ifStatementPatternStr()

Value

pattern (regular expression)

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

Description

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

Slots

condition

IF statement condition

equation

any equation or ODE

Get the index of an element in list.

Description

Get the index of an element in list.

Usage

indexOf(object, x)

## S4 method for signature 'pmx_list,pmx_element'
indexOf(object, x)

Arguments

Value

index of this element

Init record class.

Description

Init record class.

Say if the block is fixed (i.e. all parameters are fixed).

Description

Say if the block is fixed (i.e. all parameters are fixed).

Usage

isBlockFixed(block)

Arguments

Value

logical value

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

Description

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

Usage

isComment(x)

Arguments

Value

logical value

Is diagonal.

Description

Is diagonal.

Usage

isDiag(object)

## S4 method for signature 'double_array_parameter'
isDiag(object)

Arguments

Value

logical value

Check if string is an empty line.

Description

Check if string is an empty line.

Usage

isEmptyLine(x)

Arguments

Value

logical value

Say if line in record is an equation not.

Description

Say if line in record is an equation not.

Usage

isEquation(x)

Arguments

Value

logical value

Say if line in record is an IF-statement.

Description

Say if line in record is an IF-statement.

Usage

isIfStatement(x)

Arguments

Value

logical value

Is matrix positive definite. Same check as mvtnorm does.

Description

Is matrix positive definite. Same check as mvtnorm does.

Usage

isMatrixPositiveDefinite(matrix, tol = 1e-06)

Arguments

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

Description

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

Usage

isODE(x)

Arguments

Value

logical vector

Is record delimiter. A record delimiter is any line starting with [...].

Description

Is record delimiter. A record delimiter is any line starting with [...].

Usage

isRecordDelimiter(line)

Arguments

Value

a logical value

Check if the destination engine is RxODE or rxode2. Note that rxode2 is the successor of RxODE.

Description

Check if the destination engine is RxODE or rxode2. Note that rxode2 is the successor of RxODE.

Usage

isRxODE(dest)

Arguments

Value

TRUE if RxODE or rxode2, FALSE otherwise

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

Description

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

Usage

isStrictRecordDelimiter(line)

Arguments

Value

a logical value

Lag record class.

Description

Lag record class.

Return the length of this list.

Description

Return the length of this list.

Return the number of OMEGA's on the diagonal.

Usage

## S4 method for signature 'pmx_list'
length(x)

## S4 method for signature 'statements_record'
length(x)

## S4 method for signature 'omega_block'
length(x)

Arguments

Value

the length of this list, integer value

a number

Line-break class. A linebreak in the model.

Description

Line-break class. A linebreak in the model.

Main record class.

Description

Main record class.

Manual replication settings class.

Description

Manual replication settings class.

Slots

replicated_parameters

data frame, 1 row per replicate

Match double array parameter from list based on the name instead of the index. If a match is found, its indexes are automatically copied.

Description

Match double array parameter from list based on the name instead of the index. If a match is found, its indexes are automatically copied.

Usage

matchDoubleArrayParameter(object, x)

Arguments

Value

the same parameter is no match was found or the same parameter with updated indexes if a match was found

Match single array parameter from list based on the name instead of the index. If a match is found, its index is automatically copied.

Description

Match single array parameter from list based on the name instead of the index. If a match is found, its index is automatically copied.

Usage

matchSingleArrayParameter(object, x)

Arguments

Value

the same parameter is no match was found or the same parameter with updated index if a match was found

Max index.

Description

Max index.

Usage

maxIndex(object)

## S4 method for signature 'parameters'
maxIndex(object)

Arguments

Value

max index

A empty method only used to declare some of the global function definitions contained in the package 'methods', which are used intensively.

Description

A empty method only used to declare some of the global function definitions contained in the package 'methods', which are used intensively.

Usage

methodsGlobalFunctions()

Value

no return value

Min index.

Description

Min index.

Usage

minIndex(object)

## S4 method for signature 'parameters'
minIndex(object)

Arguments

Value

min index

Min/max default values for the given parameter.

Description

Min/max default values for the given parameter.

Usage

minMaxDefault(parameter)

Arguments

Value

a tibble with the min and max values

Model statement class. Any statement in a code record.

Description

Model statement class. Any statement in a code record.

Slots

comment

a comment associated to this model statement

Model statements class. A list of statements.

Description

Model statements class. A list of statements.

CAMPSIS model suite.

Description

A library of models of all kinds, ready to be simulated in Campsis. These model templates are sorted into the following categories: pharmacokinetic (PK), pharmacodynamic (PD), target-mediated drug disposition (TMDD), NONMEM, literature and other (custom models).

Usage

model_suite

Format

A list with all the models:

pk

extensive list of pharmacokinetic (PK) model templates

pd

list of pharmacodynamic (PD) model templates, to be plugged into any pharmacokinetic (PK) model

tmdd

extensive list of target-mediated drug disposition (TMDD) model templates

nonmem

list of model templates translated from standard NONMEM control streams

literature

a couple of models coming from the literature

other

a couple of custom models

Source

https://calvagone.github.io/campsis.doc/

https://www.iconplc.com/solutions/technologies/nonmem/

Move element 'x' from object to a certain place.

Description

Move element 'x' from object to a certain place.

Usage

move(object, x, to, ...)

## S4 method for signature 'code_records,model_statement,pmx_position'
move(object, x, to, ...)

## S4 method for signature 'code_records,list,pmx_position'
move(object, x, to, ...)

## S4 method for signature 'code_records,model_statements,pmx_position'
move(object, x, to, ...)

## S4 method for signature 'code_records,code_record,pmx_position'
move(object, x, to, ...)

## S4 method for signature 'campsis_model,ANY,pmx_position'
move(object, x, to, ...)

Arguments

Value

updated object

Convert code record for mrgsolve.

Description

Convert code record for mrgsolve.

Usage

mrgsolveBlock(record, init = NULL, capture = FALSE)

Arguments

Value

translated record for mrgsolve

Get the CAPTURE block for mrgsolve.

Description

Get the CAPTURE block for mrgsolve.

Usage

mrgsolveCapture(outvars, model)

Arguments

Value

CAPTURE block or character(0) if no variable in outvars

Get the compartment block for mrgsolve.

Description

Get the compartment block for mrgsolve.

Usage

mrgsolveCompartment(model)

Arguments

Value

character vector, each value is a line

Get the MAIN block for mrgsolve.

Description

Get the MAIN block for mrgsolve.

Usage

mrgsolveMain(model)

Arguments

Value

MAIN block

Get the OMEGA/SIGMA matrix for mrgsolve.

Description

Get the OMEGA/SIGMA matrix for mrgsolve.

Usage

mrgsolveMatrix(model, type = "omega")

Arguments

Value

named matrix or character(0) if matrix is empty

Get the ODE block for mrgsolve.

Description

Get the ODE block for mrgsolve.

Usage

mrgsolveOde(model)

Arguments

Value

ODE block

Get the parameters block for mrgsolve.

Description

Get the parameters block for mrgsolve.

Usage

mrgsolveParam(model, extra_params = character(0))

Arguments

Value

character vector, 1 parameter per line. First one is header [PARAM].

Get the TABLE block for mrgsolve.

Description

Get the TABLE block for mrgsolve.

Usage

mrgsolveTable(model)

Arguments

Value

TABLE block if at least one line in error record, character(0) otherwise

Mrgsolve export type class.

Description

Mrgsolve export type class.

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

Description

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

ODE record class.

Description

ODE record class.

Omega parameter class.

Description

Omega parameter class.

Slots

same

logical value, tell if this omega is the same as the previous one

Parameter class. Any parameter in a pharmacometric model.

Description

Parameter class. Any parameter in a pharmacometric model.

Slots

name

parameter name, optional (although recommended)

index

parameter index, integer

value

parameter value (e.g. the estimated value from a modelling tool)

min

minimum value for this parameter when parameter uncertainty is enabled

max

maximum value for this parameter when parameter uncertainty is enabled

fix

logical value, say if parameter was fixed in the modelling phase

label

parameter label, any string

comment

any comment on this parameter, any string

Parameters class.

Description

Parameters class.

Slots

varcov

associated variance-covariance matrix

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

Description

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

Usage

parseIfStatement(line, comment = as.character(NA))

Arguments

Value

an IF statement object

Parse statements code and return CAMPSIS statements.

Description

Parse statements code and return CAMPSIS statements.

Usage

parseStatements(code)

Arguments

Value

a list of CAMPSIS statements

Pattern class.

Description

Pattern class.

PMX element class.

Description

PMX element class.

PMX list class.

Description

PMX list class.

Slots

list

effective list which will contain the elements

type

type of the elements this list may contain

PMX position class.

Description

PMX position class.

PMX position by element class.

Description

PMX position by element class.

PMX position by index class.

Description

PMX position by index class.

Process double array arguments.

Description

Process double array arguments.

Usage

processDoubleArrayArguments(index, index2, type)

Arguments

Value

variance type

Process extra arguments.

Description

Process extra arguments.

Usage

processExtraArg(args, name, default = NULL, mandatory = FALSE)

Arguments

Value

requested argument value

Properties record class.

Description

Properties record class.

(Infusion)-rate record class.

Description

(Infusion)-rate record class.

Generic read method to read data from a file or a folder.

Description

Generic read method to read data from a file or a folder.

Usage

read(file, ...)

Arguments

Value

the object representation of the data contained in the file

Read all parameters files at once.

Description

Read all parameters files at once.

Usage

read.allparameters(folder)

Arguments

Value

parameters object

Read a CAMPSIS model.

Description

Read a CAMPSIS model.

Usage

read.campsis(file)

Arguments

Value

a CAMPSIS model

Read model file.

Description

Read model file.

Usage

read.model(file = NULL, text = NULL)

Arguments

Value

records object

Read parameters file.

Description

Read parameters file.

Usage

read.parameters(file, type)

Arguments

Value

parameters sub list

Read a Campsis model (deprecated).

Description

Read a Campsis model (deprecated).

Usage

read.pmxmod(file)

Arguments

Value

a Campsis model

Read variance-covariance file.

Description

Read variance-covariance file.

Usage

read.varcov(file)

Arguments

Value

variance-covariance matrix

Remove given column(s) if it has only NA's.

Description

Remove given column(s) if it has only NA's.

Usage

removeNaColumn(x, column)

Arguments

Value

updated data frame

Remove all trailing line breaks.

Description

Remove all trailing line breaks.

Usage

removeTrailingLineBreaks(x)

Arguments

Value

a character vector

Replace element by another in list.

Description

Replace element by another in list.

Usage

replace(object, x)

## S4 method for signature 'pmx_list,pmx_element'
replace(object, x)

## S4 method for signature 'pmx_list,pmx_list'
replace(object, x)

## S4 method for signature 'pmx_list,list'
replace(object, x)

## S4 method for signature 'compartments,compartment_property'
replace(object, x)

## S4 method for signature 'parameters,single_array_parameter'
replace(object, x)

## S4 method for signature 'parameters,double_array_parameter'
replace(object, x)

## S4 method for signature 'statements_record,model_statement'
replace(object, x)

## S4 method for signature 'code_records,model_statement'
replace(object, x)

## S4 method for signature 'campsis_model,compartment'
replace(object, x)

## S4 method for signature 'campsis_model,compartment_property'
replace(object, x)

## S4 method for signature 'campsis_model,parameter'
replace(object, x)

## S4 method for signature 'campsis_model,code_record'
replace(object, x)

## S4 method for signature 'campsis_model,model_statement'
replace(object, x)

Arguments

Value

list object or an error if the element does not exist in the list

Replace all occurrences in object.

Description

Replace all occurrences in object.

Usage

replaceAll(object, pattern, replacement, ...)

## S4 method for signature 'character,variable_pattern,character'
replaceAll(object, pattern, replacement, ...)

## S4 method for signature 'character,pattern,character'
replaceAll(object, pattern, replacement, ...)

## S4 method for signature 'model_statement,pattern,character'
replaceAll(object, pattern, replacement, ...)

## S4 method for signature 'equation,pattern,character'
replaceAll(object, pattern, replacement, ...)

## S4 method for signature 'if_statement,pattern,character'
replaceAll(object, pattern, replacement, ...)

## S4 method for signature 'compartment_property,pattern,character'
replaceAll(object, pattern, replacement, ...)

## S4 method for signature 'code_record,pattern,character'
replaceAll(object, pattern, replacement, ...)

## S4 method for signature 'code_records,pattern,character'
replaceAll(object, pattern, replacement, ...)

## S4 method for signature 'campsis_model,pattern,character'
replaceAll(object, pattern, replacement, ...)

## S4 method for signature 'campsis_model,character,character'
replaceAll(object, pattern, replacement, ...)

Arguments

Value

the same object with all occurrences replaced

Replicate generic object.

Description

Replicate generic object.

Usage

replicate(object, n, settings = NULL, ...)

## S4 method for signature 'campsis_model,integer,auto_replication_settings'
replicate(object, n, settings)

## S4 method for signature 'campsis_model,integer,manual_replication_settings'
replicate(object, n, settings)

Arguments

Value

object replicated n times

Replicated Campsis model class.

Description

Replicated Campsis model class.

Replication settings interface.

Description

Replication settings interface.

Get code for rxode2

Description

Get code for rxode2

Usage

rxodeCode(model)

Arguments

Value

corresponding model code for rxode2

Get the OMEGA/SIGMA matrix for rxode2.

Description

Get the OMEGA/SIGMA matrix for rxode2.

Usage

rxodeMatrix(model, type = "omega")

Arguments

Value

omega/sigma named matrix

Get the parameters vector for rxode2.

Description

Get the parameters vector for rxode2.

Usage

rxodeParams(model)

Arguments

Value

named vector with THETA values

RxODE/rxode2 export type class.

Description

RxODE/rxode2 export type class.

Sample from scaled inverse chi-squared distribution (core method).

Description

Sample from scaled inverse chi-squared distribution (core method).

Usage

sampleFromInverseChiSquaredCore(n, df, scale, variable)

Arguments

Value

a data frame with the unique sampled parameter

Sample parameters from inverse scaled chi-squared or wishart distribution(s).

Description

Sample parameters from inverse scaled chi-squared or wishart distribution(s).

Usage

sampleFromInverseChiSquaredOrWishart(parameters, n, settings)

Arguments

Value

a data frame with the sampled parameters

Sample from scaled inverse Wishart distribution (core method).

Description

Sample from scaled inverse Wishart distribution (core method).

Usage

sampleFromInverseWishartCore(n, df, mat, allColnames, wishartCorrection)

Arguments

Value

a data frame with the sampled parameters

Sample from a multivariate normal distribution.

Description

Sample from a multivariate normal distribution.

Usage

sampleFromMultivariateNormalDistribution(parameters, n, settings)

Arguments

Value

a data frame with the sampled parameters

Sample from multivariate normal distribution (core method).

Description

Sample from multivariate normal distribution (core method).

Usage

sampleFromMultivariateNormalDistributionCore(n, mean, varcov)

Arguments

Value

a data frame with the sampled parameters

Generic function for parameter sampling according to the minimum and maximum values. This function will sample parameters a first time and check if some parameters are out of range. Based on the success rate, it will sample more parameters to reach the desired number of rows.

Description

Generic function for parameter sampling according to the minimum and maximum values. This function will sample parameters a first time and check if some parameters are out of range. Based on the success rate, it will sample more parameters to reach the desired number of rows.

Usage

sampleGeneric(fun, args, n, minMax, msg, settings, parameters = NULL)

Arguments

Value

tibble with the sampled parameters (1 parameter per column + REPLICATE column)

Get a subset of an object.

Description

Get a subset of an object.

Usage

select(object, ...)

## S4 method for signature 'data.frame'
select(object, ...)

## S4 method for signature 'compartment_properties'
select(object, ...)

## S4 method for signature 'parameters'
select(object, ...)

Arguments

Value

subset of an object

Set the minimum and maximum value on a model parameter.

Description

Set the minimum and maximum value on a model parameter.

Usage

setMinMax(object, parameter, min, max, ...)

## S4 method for signature 'parameters,parameter,numeric,numeric'
setMinMax(object, parameter, min, max, ...)

## S4 method for signature 'parameters,character,numeric,numeric'
setMinMax(object, parameter, min, max, ...)

## S4 method for signature 'campsis_model,parameter,numeric,numeric'
setMinMax(object, parameter, min, max, ...)

## S4 method for signature 'campsis_model,character,numeric,numeric'
setMinMax(object, parameter, min, max, ...)

Arguments

Value

updated object

Shift OMEGA indexes.

Description

Shift OMEGA indexes.

Usage

shiftOmegaIndexes(object)

## S4 method for signature 'omega_block'
shiftOmegaIndexes(object)

Arguments

Value

same block but shifted

Sigma parameter class.

Description

Sigma parameter class.

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

Description

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

Sort the specified list.

Description

Sort the specified list.

Usage

sort(x, decreasing = FALSE, ...)

## S4 method for signature 'compartment_properties'
sort(x, decreasing = FALSE, ...)

## S4 method for signature 'compartments'
sort(x, decreasing = FALSE, ...)

## S4 method for signature 'parameters'
sort(x, decreasing = FALSE, ...)

## S4 method for signature 'code_records'
sort(x, decreasing = FALSE, ...)

## S4 method for signature 'campsis_model'
sort(x, decreasing = FALSE, ...)

## S4 method for signature 'omega_blocks'
sort(x, decreasing = FALSE, ...)

Arguments

Value

same list but ordered

Standardise.

Description

Standardise.

Usage

standardise(object, ...)

## S4 method for signature 'theta'
standardise(object, ...)

## S4 method for signature 'double_array_parameter'
standardise(object, parameters = NULL, ...)

## S4 method for signature 'parameters'
standardise(object, ...)

## S4 method for signature 'campsis_model'
standardise(object, ...)

Arguments

Value

standardised object

Statements record class.

Description

Statements record class.

Theta parameter class.

Description

Theta parameter class.

Slots

unit

parameter unit

ToString generic method.

Description

ToString generic method.

Usage

toString(object, ...)

## S4 method for signature 'unknown_statement'
toString(object, ...)

## S4 method for signature 'comment'
toString(object, ...)

## S4 method for signature 'line_break'
toString(object, ...)

## S4 method for signature 'equation'
toString(object, ...)

## S4 method for signature 'ode'
toString(object, ...)

## S4 method for signature 'if_statement'
toString(object, ...)

## S4 method for signature 'compartment'
toString(object, ...)

## S4 method for signature 'compartment_property'
toString(object, ...)

## S4 method for signature 'compartment_initial_condition'
toString(object, ...)

## S4 method for signature 'mrgsolve_model'
toString(object, ...)

Arguments

Value

character value/vector

Trim character vector. Remove all leading and trailing spaces.

Description

Trim character vector. Remove all leading and trailing spaces.

Usage

trim(x)

Arguments

Value

character vector without leading and trailing spaces

Unknown statement class. Any statement not recognized by campsismod.

Description

Unknown statement class. Any statement not recognized by campsismod.

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

Description

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

Usage

updateCompartments(model)

Arguments

Value

an updated Campsis model, with an updated compartments list

Update OMEGAs that are same. Same OMEGAs are written as follows: OMEGA1 same is FALSE (first one, estimated) OMEGA2 same is TRUE OMEGA3 same is TRUE, etc. OMEGA2 and OMEGA3 will take the same value as OMEGA1.

Description

Update OMEGAs that are same. Same OMEGAs are written as follows: OMEGA1 same is FALSE (first one, estimated) OMEGA2 same is TRUE OMEGA3 same is TRUE, etc. OMEGA2 and OMEGA3 will take the same value as OMEGA1.

Usage

updateOMEGAs(model)

Arguments

Value

updated Campsis model

Update model parameters based on the parameters issued from the model replication.

Description

Update model parameters based on the parameters issued from the model replication.

Usage

updateParameters(model, row)

Arguments

Value

updated Campsis model

Return the variable pattern (string form), without the first character.

Description

Return the variable pattern (string form), without the first character.

Usage

variablePatternNoStartStr()

Value

pattern (regular expression)

Return the variable pattern (string form).

Description

Return the variable pattern (string form).

Usage

variablePatternStr()

Value

pattern (regular expression)

Variable pattern class.

Description

Variable pattern class.

Write generic object to files.

Description

Write generic object to files.

Usage

write(object, file, ...)

## S4 method for signature 'parameters,character'
write(object, file, ...)

## S4 method for signature 'code_records,character'
write(object, file, ...)

## S4 method for signature 'campsis_model,character'
write(object, file, ...)

Arguments

Value

logical value, TRUE for success, FALSE for failure

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

Description

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

Usage

writeParameters(object, file, ...)

Arguments

Value

TRUE if success

Write record delimiter line.

Description

Write record delimiter line.

Usage

writeRecordDelimiter(object)

Arguments

Value

a record delimiter line

Write variance-covariance matrix.

Description

Write variance-covariance matrix.

Usage

writeVarcov(object, file)

Arguments

Value

TRUE if success