Man pages for campsismod
Generic Implementation of a PK/PD Model

add	Add element to list.
add_ode_compartment	Add ODE compartment to compartments object.
add_properties	Add properties to compartments object.
add_rse	Add relative standard error (RSE) to the specified parameter.
add_suffix	Generic function to add a suffix to various objects like...
addSuffix	Generic function to add a suffix to various objects like...
all_na	Check is vector has NA's only.
append_code_records	Append code records
append_comment	Append comment.
appendCompartments	Append compartments.
appendModel	Append model (or simply add).
append_parameters	Append parameters.
as.data.frame	As data frame method.
assert_single_character_string	Assert the given character vector is a single character...
auto_detect_nonmem	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.
check_matrix_is_positive_definite	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.
convert_any_comment	Convert Campsis comment style to C/C++ code. Only the first #...
convert_outvars_to_capture	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_to_json	Export the given object to a JSON object, ready to be written...
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.
find	Find an element in list.
fix_omega	Fix omega matrix for SAME OMEGA parameters that have NA...
fixOmega	Fix omega matrix for SAME OMEGA parameters that have NA...
flag_sampled_parameter_rows	Flag all parameter rows that have at least one parameter out...
f_record-class	Bioavailability record class.
get_by_index	Get element by index.
getByIndex	Get element by index.
get_by_name	Get an element from a list by name. Never return more than 1...
getByName	#' Get an element from a list by name.
get_campsismod_option	Get Campsismod option logic.
get_campsismod_options	Get the Campsismod options (R options).
get_compartment_index	Get the compartment index for the specified compartment name.
getCompartmentIndex	Get the compartment index for the specified compartment name.
get_compartments	Detect all compartments names from the code records. Only for...
get_mapping_matrix	Return a matrix filled in with OMEGA/SIGMA names to be mapped...
get_name	Get element name.
getName	Get element names from list.
get_name_in_model	Get the name of the given parameter in the Campsis model.
getNameInModel	Get the name of the given parameter in the Campsis model.
get_names	Get element names from list.
getNames	Get element names from list.
get_nonmem_name	Get NONMEM name.
get_omega_block	Get the right block of OMEGA's.
get_omega_indexes	Get the indexes of the omegas.
get_prefix	Get prefix.
get_record_delimiter	Get record delimiter.
get_record_equation_names	Get record equation names
get_record_name	Get record name.
get_uncertainty	Get uncertainty on the parameters.
getUncertainty	Get uncertainty on the parameters.
get_var_cov	Get variance-covariance matrix.
grapes-greater-than-grapes	Magritt operator for piping.
has_comment	Check if string contains Campsis-style comments.
has_exact_method	Has exact method allows to check the existence of a S4 method...
has_off_diagonal_omegas	Has off-diagonal omegas.
IfStatement	Create a new IF-statement.
if_statement-class	If-statement class. Any statement in the form if (condition)...
if_statement_pattern_str	Return the IF-statement pattern (string form).
index_of	Get the index of an element in list.
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.
is_block_fixed	Say if the block is fixed (i.e. all parameters are fixed).
is_comment	Check if string is a Campsis comment (i.e. not an equation).
is_diag	Is diagonal.
isDiag	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...
is_rxode	Check if the destination engine is RxODE or rxode2. Note that...
is_strict_record_delimiter	Is strict record delimiter. A strict record delimiter is any...
JSONElement	Instantiate a JSON element.
json_element-class	JSON element class.
json_to_campsis_model	JSON to Campsis dataset.
json_to_off_diag_parameter	Convert JSON correlation parameter (OMEGA or SIGMA) into a...
json_to_parameter	JSON to Campsis parameter.
jsonToParameter	JSON to Campsis parameter.
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.
load_from_json	Fill-in S4 object from the JSON content.
loadFromJSON	Fill-in S4 object from the JSON content.
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.
mapJSONPropertiesToS4Slots	Map JSON properties to S4 slots.
map_s4_slots_to_json_properties	Map S4 slots to JSON properties.
mapS4SlotsToJSONProperties	Map S4 slots to JSON properties.
match_double_array_parameter	Match double array parameter from list based on the name...
match_single_array_parameter	Match single array parameter from list based on the name...
max_index	Max index.
maxIndex	Max index.
methods_global_functions	A empty method only used to declare some of the global...
min_index	Min index.
minIndex	Min index.
min_max_default	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.
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.
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.
open_json	Open JSON file.
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...
parse_statements	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.
process_extra_arg	Process extra arguments.
processExtraArg	Process extra arguments.
process_json_double_array_parameter	Process JSON double array parameter.
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.
remove_na_column	Remove given column(s) if it has only NA's.
remove_trailing_line_breaks	Remove all trailing line breaks.
replace	Replace element by another in list.
replace_all	Replace all occurrences in object.
replaceAll	Replace all occurrences in object.
replicate	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.
rxodeMatrix	Get the OMEGA/SIGMA matrix for rxode2.
rxode_params	Get the parameters vector for rxode2.
rxode_type-class	RxODE/rxode2 export type class.
sample_from_inverse_chi_squared_core	Sample from scaled inverse chi-squared distribution (core...
sample_from_inverse_chi_squared_or_wishart	Sample parameters from inverse scaled chi-squared or wishart...
sample_from_inverse_wishart_core	Sample from scaled inverse Wishart distribution (core...
sample_from_multivariate_normal_distribution	Sample from a multivariate normal distribution.
sample_from_multivariate_normal_distribution_core	Sample from multivariate normal distribution (core method).
sample_generic	Generic function for parameter sampling according to the...
select	Get a subset of an object.
set_min_max	Set the minimum and maximum value on a model parameter.
shift_omega_indexes	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.
to_string	to_string generic method.
toString	to_string 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.
update_compartments	Update compartments list from the persisted records. Exported...
updateCompartments	Update compartments list from the persisted records. Exported...
update_omegas	Update OMEGAs that are same. Same OMEGAs are written as...
update_parameters	Update model parameters based on the parameters issued from...
VariablePattern	Create a variable pattern.
variable_pattern-class	Variable pattern class.
variable_pattern_no_start_str	Return the variable pattern (string form), without the first...
variable_pattern_str	Return the variable pattern (string form).
write	Write generic object to files.
write_parameters	Write subset of parameters (theta, omega or sigma).
write_record_delimiter	Write record delimiter line.
write_varcov	Write variance-covariance matrix.