Tools for Performing Pharmacokinetic-Pharmacodynamic Simulations

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Documentation for package ‘PKPDsim’ version 1.3.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

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_lagtime	Apply lagtime to a regimen
calculate_parameters	Calculate model-specific variables using a dummy call to sim_ode()
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).
check_obs_input	Checks obs input for valid combinations of cmt, var, scale
compile_sim_cpp	Compile ODE model to c++ function
covariates_table_to_list	Convert covariate table specified as data.frame
covariate_last_obs_only	Use only last observed covariate values
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