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Parameter data from csv

Source: R/readParsWide.R
readParsWide.Rd

Reads output table from simpar and returns a long format data.table. This is the same format as returned by NMreadExt() which can be used by NMsim.

Usage

readParsWide(
  data,
  col.model = NULL,
  strings.par.type = c(THETA = "^T.*", OMEGA = "^O.*", SIGMA = "^S."),
  as.fun
)

Arguments

data

A data.frame or a path to a delimited file to be read using `data.table::fread`.

col.model

Name of the model counter, default is "model". If the provided name is not found in data, it will be created as a row counter. Why needed? Each row in data represents a set of parameters, i.e. a model. In the long format result, each model will have multiple rows. Hence, a model identifier is needed to distinguish between models in results.

strings.par.type

Defines how column names get associated with THETA, OMEGA, and SIGMA. Default is to look for "T", "O", or "S" as starting letter. If customizing, make sure each no column name will be matched by more than one criterion.

as.fun

The default is to return data as a data.frame. Pass a function (say tibble::as_tibble) in as.fun to convert to something else. If data.tables are wanted, use as.fun="data.table". The default can be configured using NMdataConf.

Value

a long-format data.frame of model parameters

Details

The wide data format read by `readParsWide` is not a Nonmem format. It is used to bridge output from other tools such as simpar, and potentially PSN.

This function reads a data that is "wide" in parameters - it has a column for each parameter, and one row per parameter set or "model". It returns a data set that is "long" in model and parameters. The long format contains

  • id.model.par The unique model-parameter identifier. The row-identifier.

  • model Model identifier.

  • par.type ("THETA", "OMEGA", "SIGMA")

  • i and j indexes for the parameters (j is NA for par.type=="THETA").

  • value The parameter value

  • parameter Nonmem-style parameter names. THETA1, OMEGA(1,1) etc. Notice the inconsistent naming of THETA vs others.

  • name.wide The column name in the wide data where this value was taken

The columns or "measure variables" from which to read values are specified as three regular expressions, called THETA, OMEGA, and SIGMA. The default three regular expressions will associate a column name starting with "T" with THETAs, while "O" or "S" followed by anything means "OMEGA" or "SIGMA".

readParsWide extracts i and j indexes from sequences of digits in the column names. TH.1 would be TETA1, SG1.1 is SIGMA(1,1).

Examples

if (FALSE) { # \dontrun{
tab.ext <- readParsCsv("simpartab.csv")
## or
tab.simpar <- fread("simpartab.csv")
tab.ext <- readParsCsv(tab.simpar)
NMsim(...,method.sim=NMsim_VarCov,tab.ext=tab.ext)
} # }