write.nonmem.csv: Read/Write NONMEM Data

In benjaminrich/PCSmisc: Useful functions for longitudinal data set construction and manipulation.

Read/Write NONMEM Data

Description

These convenience functions are simple wrappers to the standard read/write functions that make reading and writing NONMEM data files and tables easier and more consistent.

Usage

  write.nonmem.csv(x, file, digits = 6, colnames.toupper = TRUE)
  read.nonmem.csv(file, colnames.tolower = TRUE)
  read.nonmem.table(file, colnames.tolower = TRUE)

Arguments

x	A data.frame.
file	A character string naming a file.
digits	An integer specifying the number of decimal digits to keep for number variables.
colnames.toupper	Should column names be converted to uppercase before writing?
colnames.tolower	Should column names be converted to lowercase after reading?

Details

write.nonmem.csv calls write.csv after: (1) rounding all numeric columns according to digits; (2) converting all column names to uppercase (if colnames.toupper = TRUE, the default); and (3) pre-pending '#' to the name of the first column (so that NONMEM will ignore the line containing the variable names).

read.nonmem.csv is for reading NONMEM datasets. It call read.csv with na.strings = c(".", "", "NA") and then: (1) removing 'X.' from the name of the first column if present (by default, R converts the '#' prefix to 'X.'); and (2) converting all column named to lowercase (if colnames.tolower = TRUE, the default).

read.nonmem.table is for reading table files produced by NONMEM '$TABLE' statements. These tables typically look something like:

TABLE NO.  1
 ID          DV          MDV         ETA1        ETA2        ETA3        ETA4        IPRED       CWRES       DV          PRED        RES         WRES
  1.0001E+04  0.0000E+00  1.0000E+00 -1.3065E-01 -5.8225E-01  0.0000E+00  0.0000E+00  0.0000E+00  0.0000E+00  0.0000E+00  0.0000E+00  0.0000E+00  0.0000E+00
  1.0001E+04  0.0000E+00  1.0000E+00 -1.3065E-01 -5.8225E-01  0.0000E+00  0.0000E+00  0.0000E+00  0.0000E+00  0.0000E+00  0.0000E+00  0.0000E+00  0.0000E+00
  1.0001E+04  2.5200E+03  0.0000E+00 -1.3065E-01 -5.8225E-01  0.0000E+00  0.0000E+00  1.6347E+03  2.5442E+00  2.5200E+03  5.4237E+02  1.9776E+03  3.5474E+00
  1.0001E+04  0.0000E+00  1.0000E+00 -1.3065E-01 -5.8225E-01  0.0000E+00  0.0000E+00  4.1236E+02  0.0000E+00  0.0000E+00  5.3607E+02  0.0000E+00  0.0000E+00
  ...

read.nonmem.table calls read.table with skip = 1, header = TRUE and na.strings = c(".", "") before converting all column named to lowercase (if colnames.tolower = TRUE, the default) and changing 'ID' to a factor (with asID.

Value

write.nonmem.csv is called for its side-effects (returns an invisible 'NULL').

read.nonmem.csv and read.nonmem.table both return a data.frame.

Author(s)

Benjamin Rich <[e-mail]>

See Also

• write.csv

• read.csv read.table

• tolower toupper

• asID

benjaminrich/PCSmisc documentation built on Feb. 11, 2024, 9:25 p.m.