pmx: Create a pmx object

In ggPMX: 'ggplot2' Based Tool to Facilitate Diagnostic Plots for NLME Models

Create a pmx object

Description

Create a pmx object from a data source

Usage

pmx(
  config,
  sys = "mlx",
  directory,
  input,
  dv,
  dvid,
  cats = NULL,
  conts = NULL,
  occ = NULL,
  strats = NULL,
  settings = NULL,
  endpoint = NULL,
  sim = NULL,
  bloq = NULL,
  id = NULL,
  time = NULL,
  sim_blq = NULL
)

pmx_mlx(
  config,
  directory,
  input,
  dv,
  dvid,
  cats,
  conts,
  occ,
  strats,
  settings,
  endpoint,
  sim,
  bloq,
  id,
  time,
  sim_blq
)

pmx_mlxtran(
  file_name,
  config = "standing",
  call = FALSE,
  endpoint,
  version = -1,
  ...
)

Arguments

config	Can be either : The complete path for the configuration file, the name of configuration within the built-in list of configurations, or a configuration object.
sys	the system name can "mlx" (for Monolix 2016) or "mlx18" (for Monolix 2018/19 and later)
directory	character modelling output directory.
input	character complete path to the modelling input file
dv	character the name of measurable variable used in the input modelling file
dvid	[Optional] character observation type parameter. This is mandatory in case of multiple endpoint (PKPD).
cats	[Optional]character vector of categorical covariates
conts	[Optional]character vector of continuous covariates
occ	[Optional]character occasional covariate variable name
strats	[Optional]character extra stratification variables
settings	[Optional]pmxSettingsClass pmx_settings shared between all plots
endpoint	pmxEndpointClass or integer or charcater default to NULL of the endpoint code. pmx_endpoint
sim	pmxSimClass default to NULL. pmx_sim used for VPC, e.g.: sim = pmx_sim(file=vpc_file, irun="rep",idv="TIME")
bloq	pmxBLOQClass default to NULL. pmx_bloq specify bloq, within controller: e.g. bloq=pmx_bloq(cens = "BLOQ_name", limit = "LIMIT_name")
id	[Optional] character the name of Indvidual variable used in the input modelling file
time	[Optional] character Time variable.
sim_blq	logical if TRUE uses sim_blq values for plotting. Only for Monolix 2018 and later.
file_name	character mlxtran file path.
call	logical if TRUE the result is the parameters parsed
version	integer Non-negative integer. Non-obligatory option, if you don't use a wildcard in the file_name. Otherwise you MUST provide version and wildcard will be substituted with "version", which represents the mlxtran model version.
...	extra arguments passed to pmx_mlx.

Details

pmx_mlx is a wrapper to mlx for the MONOLIX system ( sys="mlx")

pmx_mlxtran parses mlxtran file and guess pmx_mlx arguments. In case of multi endpoint the first endpoint is selected. You can though set the endpoint through the same argument. When you set call=TRUE,no controller is created but only the parameters parsed by mlxtran. This can be very helpful, in case you would like to customize parameters (adding settings vi pmx_settings, chnag eth edefault endpoint.)

Value

pmxClass controller object.

Examples

## Example to create the controller using theophylline data
theophylline <- file.path(system.file(package = "ggPMX"), "testdata",
                          "theophylline")
WORK_DIR <- file.path(theophylline, "Monolix")
input_file <- file.path(theophylline, "data_pk.csv")

## using only mandatory variables
ctr <- pmx(
  sys="mlx",
  config = "standing",
  directory = WORK_DIR,
  input = input_file,
  dv = "Y",
  dvid ="DVID"
)
## Using covariates
ctr <- pmx(
  sys="mlx",
  config = "standing",
  directory = WORK_DIR,
  input = input_file,
  dv = "Y",
  dvid ="DVID",
  cats=c("SEX"),
  conts=c("WT0","AGE0"),
  strats="STUD"
)
## using settings parameter
ctr <- pmx(
  sys="mlx",
  config = "standing",
  directory = WORK_DIR,
  input = input_file,
  dv = "Y",
  dvid ="DVID",
  settings=list(is.draft=FALSE)
)

## using mlxtran file
mlxtran_file <- 
  file.path(system.file(package = "ggPMX"), 
    "testdata","1_popPK_model","project.mlxtran")
pmx_mlxtran(mlxtran_file)

## mlxtran , call =TRUE to get the pmx_mlx argument parsed by  pmx_mlxtran
params <- pmx_mlxtran(mlxtran_file,call=TRUE)

str(params)
# $ directory: chr results_pathile 
# $ input    : chr observation file path
# $ dv       : chr "DV"
# $ cats     : chr [1:4] "SEX" "RACE" "DISE" "ILOW"
# $ conts    : chr [1:4] "AGE0" "WT0" "HT0" "TRT"
# $ occ      : chr "ISS"
# $ dvid     : chr "YTYPE"
# $ endpoint :List of 5
# ..$ code     : chr "1"
# ..$ label    : chr ""
# ..$ unit     : chr ""
# ..$ file.code: chr "1"
# ..$ trans    : NULL
# ..- attr(*, "class")= chr "pmxEndpointClass"
# $ config   : chr "standing"

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