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Run a simulation based on supplied parameters estimates, and combine into proper format for VPC

create_vpc_data.Rd

This rewrite of create_vpc_data() removes the Pharmpy/pharmr dependency from every step that runs before run_nlme(). The only Pharmpy touch is reading model$code as a string when a Pharmpy model is supplied. All subsequent manipulation of the NONMEM code (parameter updates, record removal/insertion, $EST -> $SIM conversion) and the input dataset (sanitisation of string-typed columns) is done in pure R, so the Python/R <-> reticulate serialisation cannot reject a value that NONMEM itself would accept. run_nlme() is still used to actually invoke nmfe, and post-processing of obs/sim is identical to the original.

Usage

create_vpc_data(
  fit = NULL,
  model = NULL,
  data = NULL,
  parameters = NULL,
  keep_columns = c(),
  n = 100,
  verbose = FALSE,
  id = NULL,
  use_pharmpy = TRUE,
  fix_input_heuristic = TRUE,
  seed = NULL,
  id_format = "sF11.0"
)

Arguments

fit

fit object from pharmr::run_modelfit(). Optional; alternative to model + parameters.

model

Either a Pharmpy model object (its $code is read), a character vector of NONMEM model code, or a path to a .mod file.

data

Path to the NONMEM-ready CSV. Optional; if missing, the function reads $DATA from the model code. For nlmixr2 models a data.frame is accepted too, and the default is the dataset the model was fitted against.

parameters

Named list of parameter inits, e.g. list(THETA_1 = 0.23, OMEGA_1_1 = 0.097, SIGMA_1_1 = 1). Optional.

keep_columns

character vector of column names in the original dataset to keep in the output.

n

number of simulation iterations.

verbose

verbose output?

id

run id used as folder name. Defaults to a random name. NONMEM models only; ignored (with a warning) for nlmixr2 models, which run through rxode2::rxSolve() and create no run folder.

use_pharmpy

retained for backward compatibility; controls whether PRED/TAD are transferred from obs to sim during post-processing. NONMEM models only; ignored (with a warning) for nlmixr2 models.

fix_input_heuristic

If TRUE (default), detect the common pharmr::set_dataset() side-effect that rewrites $INPUT to the CSV headers, and rebind TIME -> TAFD and (for log-transform-both-sides models) DV -> LNDV. Set to FALSE to leave $INPUT untouched. The LTBS detection only scans the $ERROR record (not the whole model) so a LOG() call in a covariate transform doesn't trigger a false swap. NONMEM models only; ignored (with a warning) for nlmixr2 models.

seed

integer seed passed to the simulation step. Default NULL draws a random seed per call (so repeated create_vpc_data() calls in one session aren't pinned to identical draws); supply a value for bit-reproducible runs.

id_format

NONMEM $TABLE IDFORMAT for the simulation table, which sets the output format of the ID column only. Defaults to sF11.0, so integer subject IDs of up to 10 digits are written in full instead of being truncated by NONMEM's default (~6 significant digits). All other columns keep NONMEM's default format. NULL uses the NONMEM default for ID too. NONMEM models only; ignored (with a warning) for nlmixr2 models.

Value

list with obs and sim data frames.

nlmixr2 models

Pharmpy models in nlmixr format are routed to an rxode2-based path (rxode2::rxSolve()) instead of NONMEM. fit, model, data, parameters, keep_columns, n, seed and verbose all apply there; the remaining arguments are NONMEM-specific and warn if set. sim$PRED is a genuine population prediction (a second solve with the between-subject random effects zeroed), except on rxode2 versions without zeroRe(), where it falls back to IPRED.