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.

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

if (FALSE) {
# 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"
)

# 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
)

# explore unique covariate plots specific to Certara.Xpose.NLME:
nlme.cov.splom(xp, covColNames = c("AGE", "WT"))
nlme.par.vs.cov(xp, covColNames = c("AGE", "WT"))

res_vs_cov(xp, covariate = "AGE", res = "IWRES")

# or use existing plotting functions from the xpose package
library(xpose)
dv_vs_pred(xp)
res_vs_idv(xp)
}