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Execute an IT2B run.

Source: R/ITrun.R
ITrun.Rd

[Superseded]

Runs a parametric IT2B search for parameter values. This is largely superseded by the $run method for PM_fit objects.

Usage

ITrun(
  model = "model.txt",
  data = "data.csv",
  run,
  include,
  exclude,
  ode = -4,
  tol = 0.001,
  salt,
  cycles = 100,
  xdev = 5,
  icen = "median",
  auto = T,
  intern = F,
  quiet = F,
  overwrite = F,
  nocheck = F,
  report = T
)

Arguments

model

Name of a suitable model file template in the working directory or an existing (previous) run number corresponding to a folder in the current working directory that used the same model file as will be used in the current run. If this is supplied, then the model file will be copied into the current working directory for convenience. If not supplied, the default is "model.txt". This file will be converted to a fortran model file. If it is detected to already be a fortran file, then the analysis will proceed without any further file conversion.

data

Name of a suitable data file (see PM_data) or an existing (previous) run number corresponding to a folder in the current working directory that used the same data file as will be used in the current run. If this is supplied, then previously made '.ZMQ' files will be copied into the current working directory, bypassing the need to re-convert the .csv file and speeding up the run..

run

Specify the run number of the output folder. Default if missing is the next available number.

include

Vector of subject id values in the data file to include in the analysis. The default (missing) is all.

exclude

A vector of subject IDs to exclude in the plot, e.g. c(4,6:14,16:20)

ode

Ordinary Differential Equation solver log tolerance or stiffness. Default is -4, i.e. 0.0001. Higher values will result in faster runs, but parameter estimates may not be as accurate.

tol

Tolerance for convergence, with default of 0.001.

salt

Vector of salt fractions for each ndrug, default is 1 for each drug. This is not the same as bioavailability.

cycles

Number of cycles to run. Default is 100.

xdev

Multiple of standard deviations for parameters to be sent to NPAG as a range. Default is 5.

icen

Summary of parameter distributions to be used to calculate predictions in HTML report. Default is "median", but could be "mean". #Predictions based on both summaries will be available in objects loaded by PM_load.

auto

If auto is FALSE you can answer all questions about the run environment manually. This might be helpful for beginners. Default is TRUE.

intern

MacOSX only: Run IT2B in the R console without a batch script. Default is false. This will be ignored on Windows systems. On the latter, the behavior of cmd.exe (DOS window) with R is poor - it does not update until the end of execution, so you cannot see any output that indicates that IT2B is running. If intern=TRUE the HTML summary page will not be automatically loaded at the end of the run, but all post-run processing will occur normally, and you can find the HTML summary page in the /outputs folder: IT2Breport.html.

quiet

Boolean operator controlling whether a model summary report is given. Default is TRUE.

overwrite

Overwrite existing run result folders. Default is FALSE.

nocheck

Suppress the automatic checking of the data file with PM_data. Default is FALSE.

report

Generate a report at the end of a run. Default is TRUE.

Value

A successful IT2B run will result in creation of a new folder in the working directory. This folder will be named numerically and sequentially with respect to previous runs. Within this folder will be four subfolders: etc, inputs, outputs, and wrkcopy, described below.

  • etc Control files for IT2B generally not needed by the user after a completed run.

  • inputs This folder will contain the .csv data file and the model file.

  • outputs This folder will contain the output from the IT2B run. These files will be prefixed by DENF, ILOG, OUTF, OUFF, LAST, FROM and RFILE, with appended numbers, usually 0001. DEN is the density file which contains the joint posterior density which can be passed to IT2B. OUTF and OUFF are full and truncated textfiles containing all output of IT2B. OUFF is missing density file. LAST contains last cycle Bayesian posterior parameters and predictions for each subject. FROM contains estimated parameter ranges which can be passed to IT2B. RFILE contains IT2B output formatted for easy import into R, and is the file read by the ITparse command. Finally, there will also be an itlog.txt file containing additional run information.

  • wrkcopy The working copy format which is used by IT2B. Invisibly to the user, the .csv input file is converted to these text files, one file per subject.

Details

If all function arguments are default, the simplest execution of this command is ITrun(). This will result in generation of a batch file. On Unix (Mac) systems will be launched automatically in a terminal window. On Windows systems, the user must execute the batch file from the current working directory, which will launch IT2B in a command prompt (DOS-like) window. In either case, IT2B will run independently of R so that R can be used for other purposes if desired.

See also

ITparse, NPrun

Author

Michael Neely