Creates xpose database from Certara.RsNLME output files

Imports results of an NLME run into xpose database Use to import NLME model output files into xpdb object that is compatible with existing model diagnostic function in Xpose package.

Usage

xposeNlme(
  dir = "",
  modelName = "",
  dmpFile = "dmp.txt",
  dmp.txt = NULL,
  dataFile = "data1.txt",
  logFile = "nlme7engine.log",
  ConvergenceData = NULL,
  progresstxt = "progress.txt"
)

Arguments

dir

Path to NLME Run directory. Current working directory is used if dir not given.

modelName

name of the model to be written in xpdb$summary$value with run label

dmpFile

NLME generated output file.

dmp.txt

NLME generated output from dmpFile (substitutes dmpFile if presented).

dataFile

Input file for NLME Run.

logFile

engine log file

ConvergenceData

optional data frame with Nlme convergence info.

progresstxt

optional NLME-generated file 'progress.txt' with convergence info. ConvergenceData has more priority if both are given.

Value

xpdb object

Details

Not all functionality from the xpose package is supported.

Examples

# \donttest{
# files in arguments supposed to be in the current working directory:
xp <- xposeNlme(
  dir = getwd(),
  modelName = "PMLModel",
  dmpFile = "dmp.txt",
  dataFile = "data1.txt",
  logFile = "nlme7engine.log",
  progresstxt = "progress.txt"
)
#> Error: File data1.txt not found in
#> C:/Repos/R-Xpose-NLME/docs/reference
#> Please check the path.

# using dmp.txt structure and Convergence Data loaded previously:
xp <- xposeNlme(
  dir = "~/Model1/",
  modelName = "Model1",
  dmp.txt = dmp.txt,
  dataFile = "Data.csv",
  logFile = "nlme7engine.log",
  ConvergenceData = ConvergenceData
)
#> Error: object 'dmp.txt' not found

# explore unique covariate plots specific to Certara.Xpose.NLME:
nlme.cov.splom(xp, covColNames = c("AGE", "WT"))
#> Error: object 'xp' not found
nlme.par.vs.cov(xp, covColNames = c("AGE", "WT"))
#> Error: object 'xp' not found

res_vs_cov(xp, covariate = "AGE", res = "IWRES")
#> Error: object 'xp' not found

# or use existing plotting functions from the xpose package
library(xpose)
#> Loading required package: ggplot2
#> 
#> Attaching package: 'xpose'
#> The following object is masked from 'package:stats':
#> 
#>     filter
dv_vs_pred(xp)
#> Error: object 'xp' not found
res_vs_idv(xp)
#> Error: object 'xp' not found
# }