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Read a Pmetrics .csv Matrix Input File

Source: R/PMreadMatrix.R
PMreadMatrix.Rd

PMreadMatrix reads an NPAG .csv matrix input file into R.

Usage

PMreadMatrix(
  file,
  skip = 1,
  sep = getPMoptions("sep"),
  dec = getPMoptions("dec"),
  date_format = "%AD",
  time_format = "%AT",
  quiet = F,
  ...
)

Arguments

file

The name of the file to be loaded, including the full path if not in the current working directory (check with getwd).

skip

Skip n lines, with default set to 0.

sep

Delimiter between columns, which is a comma by default, but can be changed with setPMoptions.

dec

Decimal separator, which is a period by default, but can be changed with setPMoptions.

date_format

Format for any dates. Default is set as year month day, with flexible separator. See parse_date in the readr package for more information on formatting dates. #' @param time_format Format for any clock times. Default is set as hours:minutes. See parse_date in the readr package for more information on formatting times.

quiet

Default is false. If true, there will be no report to the console on the contents of file.

...

Other parameters to be passed to read.table

Value

PMreadMatrix returns a data.frame of class “PMmatrix” with one row per event and the following columns.

id

The id value for each event.

evid

The evid value for each event, with 0=observation, 1=dose, 4=dose reset, which resets the time to 0 and all compartment amounts to 0. Note that evid=2 and 3 are not currently implemented.

time

Relative time of the event in hours.

dur

Duration of the dose. If dose is instantaneous, e.g. an oral dose into an absorptive compartment, dur should be 0. Any values greater than 0 are interpreted to mean a constant infusion of that duration, equalling the dose.

dose

The dose. Be sure that the units are consistent with out.

addl

Optional number of additional doses to add at an interval specified in ii. The default if missing is 0. A value of -1 will cause steady state conditions to be approximated. Any value for addl other than 0 or missing requires input in ii.

ii

The interdose interval for addl doses or dosing at steady state.

input

The input number corresponding to dose.

out

The measured output, equivalent to “DV” in some other PK modeling software tools.

outeq

The number of the output equation specified in the model file which corresponds to the out value.

C0

Assay error polynomial coefficient, e.g. SD = C0 + C1obs + C2obs^2 + C3*obs^3

C1

See C0

C2

See C0

C3

See C0

...

Additional columns are interpreted to be covariates.

If the file is successfully read and quiet=F, the column headers of the scanned file will be reported to the console as a validation check.

Details

The structure of a valid .csv file is fairly rigid. See PMcheckMatrix for details. Note that PMreadMatrix converts the column headers in the matrixfile from upper to lowercase for convenient referencing in R.

See also

PMwriteMatrix, PMcheckMatrix, and plot.PMmatrix

Author

Michael Neely