pmx_nm: Creates pmx controller from NONMEM model outputs
In ggPMX: 'ggplot2' Based Tool to Facilitate Diagnostic Plots for NLME Models

pmx_nm

R Documentation

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.

Author(s)

The ggPMX NONMEM reader (pmx_nm) is strongly based on NONMEM reading functions of the xpose package (v.0.4.11) (Thanks to Benjamin Guiastrennec) To avoid conflicts with the xpose package, the necessary xpose-based functions have been renamed with a "pmx_" prefix. If the user wants to use individual functions e.g. "read_nm_tables" please use the xpose-package

Examples

## 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")

ggPMX documentation built on May 29, 2024, 1:40 a.m.