read_wides {gcplyr}

Read wides

Description

A function that imports widemeasures in files into the R environment

Usage

read_wides(
  files,
  filetype = NULL,
  startrow = NULL,
  endrow = NULL,
  startcol = NULL,
  endcol = NULL,
  header = TRUE,
  sheet = NULL,
  run_names = NULL,
  run_names_header = "file",
  run_names_dot = FALSE,
  run_names_path = TRUE,
  run_names_ext = FALSE,
  metadata = NULL,
  na.strings = c("NA", ""),
  extension,
  names_to_col,
  ...
)

Arguments

files

A vector of filepaths (relative to current working directory) where each one is a widemeasures set of data

filetype

(optional) the type(s) of the files. Options include:

"csv", "xls", or "xlsx".

"tbl" or "table" to use read.table to read the file, "csv2" to use read.csv2, "delim" to use read.delim, or "delim2" to use read.delim2.

If none provided, read_wides will infer filetype(s) from the extension(s) in files. When extension is not "csv", "xls", or "xlsx", will use "table".

startrow, endrow, startcol, endcol

(optional) the rows and columns where the data are located in files.

Can be a vector or list the same length as files, or a single value that applies to all files. Values can be numeric or a string that will be automatically converted to numeric by from_excel.

If not provided, data is presumed to begin on the first row and column of the file(s) and end on the last row and column of the file(s).

header

logical for whether there is a header in the data. If FALSE columns are simply numbered. If TRUE, the first row of the data (startrow if specified) is used as the column names

sheet

The sheet of the input files where data is located (if input files are .xls or .xlsx). If not specified defaults to the first sheet

run_names

Names to give the widemeasures read in. By default uses the file names if not specified

run_names_header

Should the run names (provided in run_names or inferred from files) be added as a column to the widemeasures? If run_names_header is NULL, they will not be. If run_names_header is a string, that string will be the column header for the column where the names will be stored

run_names_dot

If run_names are inferred from filenames, should the leading './' (if any) be retained

run_names_path

If run_names are inferred from filenames, should the path (if any) be retained

run_names_ext

If run_names are inferred from filenames, should the file extension (if any) be retained

metadata

(optional) non-spectrophotometric data that should be associated with each read widemeasures. A named list where each item in the list is either: a vector of length 2, or a list containing two vectors.

In the former case, each vector should provide the row and column where the metadata is located in all of the blockmeasures input files.

In the latter case, the first vector should provide the rows where the metadata is located in each of the corresponding input files, and the second vector should provide the columns where the metadata is located in each of the corresponding input files. (This case is typically used when reading multiple blocks from a single file.)

na.strings

A character vector of strings which are to be interpreted as NA values by utils::read.csv, readxl::read_xls, readxl::read_xlsx, or utils::read.table

extension

Allowed for backward compatibility; filetype is now the preferred argument name.

names_to_col

Allowed for backward compatibility; run_names_header is now the preferred argument name.

...

Other arguments passed to utils::read.csv, readxl::read_xls, readxl::read_xlsx, or utils::read.table

Details

startrow, endrow, startcol, endcol, timecol, sheet and filetype can either be a single value that applies for all files or vectors or lists the same length as files,

Value

A dataframe containing a single widemeasures, or A list of widemeasures named by filename