Function reference • PKPDsim

All functions

add_quotes(): Put vector values in quotes

add_ruv(): Add residual variability to the dependent variable

add_ruv_to_quantile(): Calculate the increase in a specific quantile for a distribution on y when residual variability is added

adherence_binomial(): Binomial adherence

adherence_markov(): Markov adherence model

advan(): ADVAN-style functions to calculate linear PK systems

advan_create_data(): Create ADVAN-style dataset

advan_parse_output(): Internal function to parse the raw output from ADVAN-style functions

advan_process_infusion_doses(): Add column RATEALL to ADVAN-style dataset to handle infusions

apply_duration_scale(): Apply infusion duration scale to a regimen

apply_lagtime(): Apply lagtime to a regimen

calc_auc_analytic(): Convenience function to calculate the AUC based on PK model parameters at any given moment, for linear iv models.

calc_dydP(): Calculate derivative

calc_ss_analytic(): Returns the state of a linear PK system at steady state (trough) using analytics equations (so for linear PK systems only).

calculate_parameters(): Calculate model-specific variables using a dummy call to sim_ode()

check_obs_input(): Checks obs input for valid combinations of cmt, var, scale

compile_sim_cpp(): Compile ODE model to c++ function

covariate_last_obs_only(): Use only last observed covariate values

covariates_table_to_list(): Convert covariate table specified as data.frame

cv_to_omega(): Create lower-diagonal omega matrix from CV for parameter estimates

detect_ode_syntax(): Auto-detect the syntax for the ODE code

f_cov(): covariate function builder

get_fixed_parameters(): Get fixed parameters

get_ode_model_size(): Get the number of states in the ODE from the code code C++ code for model

get_parameters_from_code(): Get model parameters from code

get_var_y(): Get expected variance/sd/ci of dependent variable based on PKPDsim model, parameters, and regimen

ifelse0(): ifelse function but then based on whether value is NULL or not

is_positive_definite(): Is matrix positive definite

join_cov_and_par(): Combines covariates and parameters into a single list, useful for reparametrization of the model.

join_regimen(): Join two dosing regimens

lower_triangle_mat_size(): Size of the lower triangle of the matrix

merge_regimen(): Merge two regimens together.

model_from_api(): Load model definition from API, and compile to R library

model_library(): Model library

mvrnorm2(): More powerful multivariate normal sampling function

na_locf(): Fill in NAs with the previous non-missing value

new_adherence(): Probabilistically model adherence

new_covariate(): New covariate

new_covariate_model(): covariate model function

new_ode_model(): Create new ODE model

new_regimen(): Dose regimen for sim_ode

nlmixr_parse_parameters(): Function to parse parameters for a model into a structure used by nlmixr

nm_to_regimen(): Create a regimen from NONMEM data

pkdata: PK dataset

pkpdsim_to_nlmixr(): Convert a model generated with PKPDsim to an object for nlmixr

pop_regimen(): Remove n doses (from tail) of PKPDsim regimen

print_list(): Return a list in R syntax

read_model_json(): Read model definition from JSON

regimen_to_nm(): Convert PKPDsim regimen to NONMEM table (doses only)

reparametrize(): Reparametrize model parameters using a reparametrization defined within the model.

search_replace_in_file(): Find string and replace in file

shift_regimen(): Remove n doses (from start) of PKPDsim regimen

sim(): Simulate ODE or analytical equation

sim_core(): Only core function of the simulation function, always just returns observations. Mostly useful for estimations / optimal design. Has no checks (for speed)!

sim_ode(): Deprecated function, renamed to sim()

sim_ode_shiny(): Simulate ODE and create a Shiny app

table_to_list(): Convert a table to a list

test_model(): Test a model

test_pointer(): Test if model still in memory

translate_ode(): Translate a model from/to various PKPD simulators

triangle_to_full(): Convert triangle omega matrix to full omega matrix