ggPMX (version 1.2.8)

pmx_nm: Creates pmx controller from NONMEM model outputs

Description

Creates pmx controller from NONMEM model outputs

Usage

pmx_nm(
  file = NULL,
  directory = ".",
  runno = NULL,
  ext = ".lst",
  table_suffix = "",
  sim_suffix = "sim",
  simfile = NULL,
  prefix = "run",
  table_names = c("sdtab", "mutab", "patab", "catab", "cotab", "mytab", "extra",
    "xptab", "cwtab"),
  dvid = "DVID",
  pred = "PRED",
  time = "TIME",
  dv = "DV",
  conts,
  cats,
  npde,
  iwres,
  ipred,
  endpoint,
  strats = "",
  settings = pmx_settings(),
  vpc = TRUE,
  bloq = NULL,
  obs = FALSE,
  quiet = FALSE
)

Arguments

file

A character vector of path to the files or a nm_table_list object created with pmx_list_nm_tables.

directory

directory of the model files.

runno

run number which is used for generating the model file name, or used for alternative import of NONMEM-output tables.

ext

Extension to be used to generate model file name. Should be one of'.lst' (default), '.out', '.res', '.mod' or '.ctl' for NONMEM.

table_suffix

suffix of the output tables, standard is "" (no suffix).

sim_suffix

suffix of the simulation output tables, standard is "sim" (e.g. stdab1sim).

simfile

Useful if the simulation is peformed post-hoc and an additional simulation model file is generated e.g. "simulation.lst"; similar to "file" see above.

prefix

Prefix to be used to generate model file name. Used in combination with runno and ext.

table_names

contains the names of the NONMEM-output tables e.g. "sdtab", "patab", "cotab", "catab".

dvid

[Optional] character observation type parameter, mandatory in case of multiple endpoint (PKPD). Standard = "DVID"

pred

[Optional] character specifing variable name of the population prediction (standard ggPMX nomenclautre = "PRED")

time

[Optional] character specifing variable name of time (standard ggPMX nomenclautre = "TIME")

dv

character the name of measurable variable used in the input modelling file (standard ggPMX nomenclautre = "DV")

conts

[Optional] character vector of continuous covariates (automatically detected if "cotab" is provided)

cats

[Optional] character vector of categorical covariates (automatically detected if "catab" is provided)

npde

[Optional] character specifing variable name of the normalized population predictor (standard ggPMX nomenclautre = "NPDE")

iwres

[Optional] character specifing variable name of the individual weighted residuals (standard ggPMX nomenclautre = "IWRES")

ipred

[Optional] character specifing variable name of the individual population prediction (standard ggPMX nomenclautre = "IPRED")

endpoint

[Optional] pmxEndpointClass or integer or charcater default to NULL of the endpoint code. pmx_endpoint

strats

[Optional] character extra stratification variables

settings

pmxSettingsClass pmx_settings shared between all plots

vpc

logical a boolean indiacting if vpc should be calculated, simulation tables are required for VPC generation (by default TRUE)

bloq

pmxBLOQClass default to NULL. pmx_bloq specify bloq, within controller: e.g. bloq=pmx_bloq(cens = "BLOQ_name", limit = "LIMIT_name")

obs

logical if set to TRUE will filter dataset according to "MDV", default is FALSE

quiet

Logical, if FALSE messages are printed to the console.

Value

pmxClass controller object.

Examples

# NOT RUN {
## using only runnumber 
# ctr <- pmx_nm(
#  directory=model_dir,
#  runno = "001" 
#)

## using a model file (e.g. run001.lst)
#ctr <- pmx_nm(
#  directory=model_dir,
#  file = "run001.lst" 
#)

## if simulation was performed post-hoc, an additional simulation file can be loaded for VPC
#ctr <- pmx_nm(
#  directory=model_dir,
#  file = "run001.lst", 
#  simfile = "simulation.ctl"
#)

## loading with individual table(s)-names
#ctr <- pmx_nm(directory = model_dir,
#              runno = 3, 
#              table_names = "xptab")
# }