amp.dm (version 0.2.0)

read_data: read external data with logging of results

Description

This function reads external data with support for file types that are most commonly used in clinical and pre-clinical data, and provide manual functions for less common types

Usage

read_data(
  file,
  manfunc = NULL,
  comment = "",
  verbose = TRUE,
  ascii_check = "xls",
  ...
)

Value

data frame containing a representation of the data in the file

Arguments

file

character with the name of the file to read (see details for more information)

manfunc

character with the manual function to use to read data (can have the form "package::function")

comment

character with comment/information for the data that was read-in

verbose

logical indicating if information regarding the data that is read is printed in console

ascii_check

character of length one defining if the data that has been read in should be checked for valid ASCII characters (see details)

...

Additional arguments passed to the read data functions. This can be used to add arguments to for instance read.table or read_excel or for the function defined in manfunc

Author

Richard Hooijmaijers

Details

The function reads in data, and uses the file extension to select the applicable function for reading. Below is a list of extensions that are recognized and the corresponding function that is used to read the data:

• sas7bdat: haven::read_sas

• xpt: haven::read_xpt

• xls/xlsx: readxl::read_excel

• prn/par: read.table

• csv: read.csv

The prn and par file formats are basically space delimited files but with some specifics for modeling software (e.g. prn is NONMEM input file with header starting with '#' and par is NONMEM output file as defined in $TABLE). This function can be used to read any type of data by using the manfunc argument. Any function available in R can be used here and even user written functions (see example section). This argument has precedence over the recognition of extensions. This means for instance that a CSV file can also be read-in using a different function (e.g. using data.table::fread). This flexibility is build in to ensure all possible data can be read in using this single function. This is mainly important for documentation purposes, to ensure all used data can be logged and documented. The data can be checked for valid ASCII characters using the "ascii_check" argument. By default this is done for excel files with extension xls or xlsx (ascii_check="xls") other options are "none" to never perform a check or "all" to perform a check regardless of the way it is read in. The default is chosen as it is likely that excel files are created manually and could therefore include non ASCII characters, and because it puts additional overhead on function otherwise.

Examples

# For a known filetype you can use:
dat <- read_data(paste0(R.home(),"/doc/CRAN_mirrors.csv"))

# We can use the arguments from the underlying package that does the reading
xmpl <- system.file("example/Attr.Template.xlsx",package = "amp.dm")
dat  <- read_data(xmpl, range="A2:B3")

# In case we get a file format not directly supported by the function
# we can use the manfunc to use another function
sav <- system.file("examples", "iris.sav", package = "haven")
dat <- read_data(sav,manfunc = "haven::read_sav")

# It is also possible to write your own function that reads data
# (as long as it returns a data.frame or tibble), e.g.:
read_nd <- function(x) read.csv(x) |> dplyr::distinct(ID, .keep_all = TRUE)
xmpl    <- system.file("example/NM.theoph.V1.csv", package = "amp.dm")
dat     <- read_data(xmpl,manfunc = "read_nd")