Generic Implementation of a PK/PD Model

Documentation for package ‘campsismod’ version 1.4.0

Help Pages

-- A --

add	Add element to list.
add-method	Add element to list.
add_rse	Add relative standard error (RSE) to the specified parameter.
add_rse-method	Add relative standard error (RSE) to the specified parameter.
add_suffix	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.
add_suffix-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.
assert_single_character_string	Assert the given character vector is a single character string.
AutoReplicationSettings	Create auto replication settings.
auto_detect_nonmem	Auto-detect special variables from NONMEM as compartment properties. Bioavailabilities, infusion durations/rates and lag times will be automatically detected.
auto_detect_nonmem-method	Auto-detect special variables from NONMEM as compartment properties. Bioavailabilities, infusion durations/rates and lag times will be automatically detected.
auto_replication_settings-class	Auto replication settings class.

-- 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_to_json	Export the given object to a JSON object, ready to be written to files.
export_to_json-method	Export the given object to a JSON object, ready to be written to files.
export_type-class	Export type class.
extract_lhs	Extract left-hand-side expression.
extract_rhs	Extract right-hand-side expression.
extract_text_between_brackets	Extract text between brackets.

-- F --

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

get_by_index	Get element by index.
get_by_index-method	Get element by index.
get_by_name	Get an element from a list by name. Never return more than 1 element.
get_by_name-method	Get an element from a list by name. Never return more than 1 element.
get_campsismod_option	Get Campsismod option logic.
get_compartment_index	Get the compartment index for the specified compartment name.
get_compartment_index-method	Get the compartment index for the specified compartment name.
get_name	Get element name.
get_name-method	Get element name.
get_names	Get element names from list.
get_names-method	Get element names from list.
get_name_in_model	Get the name of the given parameter in the Campsis model.
get_name_in_model-method	Get the name of the given parameter in the Campsis model.
get_nonmem_name	Get NONMEM name.
get_nonmem_name-method	Get NONMEM name.
get_omega_block	Get the right block of OMEGA's.
get_omega_block-method	Get the right block of OMEGA's.
get_omega_indexes	Get the indexes of the omegas.
get_omega_indexes-method	Get the indexes of the omegas.
get_prefix	Get prefix.
get_prefix-method	Get prefix.
get_record_delimiter	Get record delimiter.
get_record_name	Get record name.
get_record_name-method	Get record name.
get_uncertainty	Get uncertainty on the parameters.
get_uncertainty-method	Get uncertainty on the parameters.
get_var_cov	Get variance-covariance matrix.
get_var_cov-method	Get variance-covariance matrix.

-- H --

has_comment	Check if string contains Campsis-style comments.
has_exact_method	Has exact method allows to check the existence of a S4 method in Campsis based on its signature.
has_off_diagonal_omegas	Has off-diagonal omegas.
has_off_diagonal_omegas-method	Has off-diagonal omegas.

-- I --

IfStatement	Create a new IF-statement.
if_statement-class	If-statement class. Any statement in the form if (condition) A = B.
index_of	Get the index of an element in list.
index_of-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.
is_comment	Check if string is a Campsis comment (i.e. not an equation).
is_diag	Is diagonal.
is_diag-method	Is diagonal.
is_empty_line	Check if string is an empty line.
is_equation	Say if line in record is an equation not.
is_if_statement	Say if line in record is an IF-statement.
is_matrix_positive_definite	Is matrix positive definite. Same check as 'mvtnorm' does.
is_ode	Say if line(s) in record is/are ODE or not.
is_record_delimiter	Is record delimiter. A record delimiter is any line starting with [...].
is_strict_record_delimiter	Is strict record delimiter. A strict record delimiter is any line starting with [...] and followed by nothing but spaces or a possible comment.

-- J --

JSONElement	Instantiate a JSON element.
json_element-class	JSON element class.
json_to_parameter	JSON to Campsis parameter.

-- 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.
load_from_json	Fill-in S4 object from the JSON content.
load_from_json-method	Fill-in S4 object from the JSON content.

-- M --

MainRecord	Create MAIN code record.
main_record-class	Main record class.
ManualReplicationSettings	Create manual replication settings.
manual_replication_settings-class	Manual replication settings class.
map_json_properties_to_s4_slots	Map JSON properties to S4 slots.
map_s4_slots_to_json_properties	Map S4 slots to JSON properties.
max_index	Max index.
max_index-method	Max index.
min_index	Min index.
min_index-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.
move	Move element 'x' from object to a certain place.
move-method	Move element 'x' from object to a certain place.
mrgsolve_block	Convert code record for mrgsolve.
mrgsolve_capture	Get the CAPTURE block for mrgsolve.
mrgsolve_compartment	Get the compartment block for mrgsolve.
mrgsolve_main	Get the MAIN block for mrgsolve.
mrgsolve_matrix	Get the OMEGA/SIGMA matrix for mrgsolve.
mrgsolve_ode	Get the ODE block for mrgsolve.
mrgsolve_param	Get the parameters block for mrgsolve.
mrgsolve_table	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.
OmegaBlock	Create a block of OMEGA's.
OmegaBlocks	Create a list of OMEGA blocks.

-- P --

parameter-class	Parameter class. Any parameter in a pharmacometric model.
Parameters	Create a list of parameters.
parameters-class	Parameters class.
parse_if_statement	Parse IF-statement. Assumption: 'is_if_statement' method already called and returned TRUE.
parse_statements	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.
process_extra_arg	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.
replace_all	Replace all occurrences in object.
replace_all-method	Replace all occurrences in object.
replicate	Replicate generic object.
replicate-method	Replicate generic object.
replicated_campsis_model-class	Replicated Campsis model class.
replication_settings-class	Replication settings interface.
rxode_code	Get code for rxode2
rxode_matrix	Get the OMEGA/SIGMA matrix for rxode2.
rxode_params	Get the parameters vector for rxode2.
rxode_type-class	RxODE/rxode2 export type class.

-- S --

select	Get a subset of an object.
select-method	Get a subset of an object.
set_min_max	Set the minimum and maximum value on a model parameter.
set_min_max-method	Set the minimum and maximum value on a model parameter.
shift_omega_indexes	Shift OMEGA indexes.
shift_omega_indexes-method	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 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.
to_string	to_string generic method.
to_string-method	to_string 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.
update_compartments	Update compartments list from the persisted records. Exported especially for package 'campsistrans'. 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.
write_parameters	Write subset of parameters (theta, omega or sigma).
write_varcov	Write variance-covariance matrix.