Package index • campsismod

Campsis model

CampsisModel(): Create a new Campsis model.
auto_detect_nonmem(): 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.
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.

Code records

CodeRecords(): Create a list of code records.
MainRecord(): Create MAIN code record.
OdeRecord(): Create ODE code record.
ErrorRecord(): Create ERROR code record.
get_record_name(): 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.
add_rse(): Add relative standard error (RSE) to the specified parameter.
as.data.frame(): As data frame method.
get_name_in_model(): Get the name of the given parameter in the Campsis model.
get_nonmem_name(): Get NONMEM name.
get_uncertainty(): Get uncertainty on the parameters.
get_var_cov(): Get variance-covariance matrix.
is_diag(): Is diagonal.
max_index(): Max index.
min_index(): Min index.
read.allparameters(): Read all parameters files at once.
read.parameters(): Read parameters file.
read.varcov(): Read variance-covariance file.
set_min_max(): Set the minimum and maximum value on a model parameter.
write_parameters(): Write subset of parameters (theta, omega or sigma).
write_varcov(): Write variance-covariance matrix.

Compartments

Compartment(): Create a compartment.
Compartments(): Create a list of compartments
get_compartment_index(): 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.
get_prefix(): 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.
index_of(): Get the index of an element in list.
get_by_index(): Get element by index.
get_by_name(): Get an element from a list by name. Never return more than 1 element.
get_names(): 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

get_name(): Get element name.

Generic methods

export(): Export function.
disable(): Disable.
export_to_json(): Export the given object to a JSON object, ready to be written to files.
fix_omega(): Fix omega matrix for SAME OMEGA parameters that have NA values due to imperfections in Pharmpy import.
load_from_json(): Fill-in S4 object from the JSON content.
read(): Generic read method to read data from a file or a folder.
select(): Get a subset of an object.
standardise(): Standardise.
to_string(): to_string generic method.
write(): Write generic object to files.

Mrgsolve export

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.

rxode2 export

rxode_code(): Get code for rxode2
rxode_matrix(): Get the OMEGA/SIGMA matrix for rxode2.
rxode_params(): 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.
json_element-class: JSON element 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

extract_lhs(): Extract left-hand-side expression.
extract_rhs(): Extract right-hand-side expression.
extract_text_between_brackets(): Extract text between brackets.
get_record_delimiter(): Get record delimiter.
has_comment(): Check if string contains Campsis-style comments.
is_comment(): Check if string is a Campsis comment (i.e. not an equation).
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_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.
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.
trim(): Trim character vector. Remove all leading and trailing spaces.

Replace occurrences

replace_all(): Replace all occurrences in object.
Pattern(): Create a pattern.
VariablePattern(): Create a variable pattern.

Model library

model_suite: Campsis model suite.

Advanced use

JSONElement(): Instantiate a JSON element.
OmegaBlock(): Create a block of OMEGA's.
OmegaBlocks(): Create a list of OMEGA blocks.
assert_single_character_string(): Assert the given character vector is a single character string.
is_matrix_positive_definite(): Is matrix positive definite. Same check as mvtnorm does.
get_campsismod_option(): Get Campsismod option logic.
get_omega_block(): Get the right block of OMEGA's.
get_omega_indexes(): Get the indexes of the omegas.
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.
json_to_parameter(): JSON to Campsis parameter.
process_extra_arg(): Process extra arguments.
map_json_properties_to_s4_slots(): Map JSON properties to S4 slots.
map_s4_slots_to_json_properties(): Map S4 slots to JSON properties.
update_compartments(): Update compartments list from the persisted records. Exported especially for package campsistrans. However, this method should not be called.
shift_omega_indexes(): Shift OMEGA indexes.