Execute an NPAG run.

This is largely superseded by the $run method for PM_fit objects.

NPrun will execute an NPAG run.

Usage

NPrun(
  model = "model.txt",
  data = "data.csv",
  run,
  include,
  exclude,
  ode = -4,
  tol = 0.01,
  salt,
  cycles = 100,
  indpts,
  icen = "median",
  aucint,
  idelta = 12,
  prior,
  auto = TRUE,
  intern = FALSE,
  quiet = FALSE,
  overwrite = FALSE,
  nocheck = FALSE,
  parallel = NA,
  report = TRUE,
  artifacts = TRUE
)

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 analysis, 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 of NPAG. Smaller numbers make it harder to converge. Default value is 0.01.
salt: Vector of salt fractions for each drug in the data file, default is 1 for each drug. This is not the same as bioavailability.
cycles: Number of cycles to run. Default is 100.
indpts: Index of starting grid point number. Default is missing, which allows NPAG to choose depending on the number of random parameters: 1 or 2 = index of 1; 3 = 3; 4 = 4, 5 = 6, 6 or more is 10+number of multiples for each parameter greater than 5, e.g. 6 = 101; 7 = 102, up to 108 for 13 or more parameters.
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.
aucint: Maintained for backwards compatibility and not used currently. Interval for AUC calculations. Default is 24 hours if the number of intervals is not greater than 48; otherwise it defaults to the interval which allows for <= 48 intervals.
idelta: Interval in 1/60 time unit, typically minutes, for predictions at times other than observations. Default is 12.
prior: Name of a suitable NPAG output object from a prior run loaded with PM_load, i.e. the NPdata object. A prior may be specified if the user wishes to start from a non-uniform prior distribution for the NPAG run. The default value is -99, which translates in NPAG to a uniform prior distribution. An alternative is to include a DEN0001 file from the prior NPAG run in the working directory of the new run, and specify this as the value for prior, e.g. prior = 'DEN0001'.
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 NPAG in the R console without a batch script. Default is false. This will be ignored if on Windows systems. On the latter, the behavior of cmd.exe (aka the DOS window) with R is poor - it does not update until the end of execution, so you cannot see any output that indicates that NPAG 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: NPAGreport.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.
parallel: Run NPAG in parallel. Default is NA, which will be set to TRUE for models that use differential equations, and FALSE for algebraic/explicit models. The majority of the benefit for parallelization comes in the first cycle, with a speed-up of approximately 80\ will speed up the first cycle by 0.8 * 8 = 6.4-fold. Subsequent cycles approach about 50\ machine. Overall speed up for a run will therefore depend on the number of cycles run and the number of cores.
report: Generate a report at the end of a run. Default is TRUE.
artifacts: Default is TRUE. Set to FALSE to suppress creating the etc folder. This folder will contain all the compilation artifacts created during the compilation and run steps.

Value

A successful NPAG 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 NPAG 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 NPAG run. These files will be prefixed by DEN, ILOG, OUT, OUTT, PRTB and RFILE, with appended numbers, usually 0001. DEN is the density file which can be used to specifiy a non-uniform prior parameter value distribution for a subsequent NPAG run of the same model via the prior argument above. ILOG is a summary of cycle objective function values, gamma/lambda, and gridpoints. OUT and OUTT are full and truncated textfiles containing all output of NPAG. OUTT is missing density file. PRTB contains Bayesian posterior individual predictions for each subject and output at timepoints specified in the NPAG instructions (e.g. every 2, 4, 8, 12 minutes) as well as predictions at each observation time. RFILE contains NPAG output formatted for easy import into R, and is the file read by the NPparse command. Finally, there will also be an nplog.txt file containing additional run information.
wrkcopy The working copy format which is used by NPAG. 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 NPrun(). 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 NPAG in a command prompt (DOS-like) window. In either case, NPAG will run independently of R so that R can be used for other purposes if desired.

Author

Michael Neely

Usage

Arguments

Value

Details

See also

Author