import_file {respR}

Import respirometry system raw data files (DEPRECATED)

Description

Automatically import data from different respirometry hardware and software systems. WARNING: This function is now deprecated and will not be updated. See below.

Usage

import_file(path, export = FALSE)

Arguments

path

string. Path to file.

export

logical. If TRUE, exports the data as a csv to the same directory, as determined by the path parameter.

Details

This function has been deprecated, will not be updated, and will be removed entirely in the next major version of respR (i.e. v3.0, which is not planned for any time soon, so may still be years away).

Note that use of this function to import data is OPTIONAL and in fact NOT RECOMMENDED. respR has an extremely simple input data structure requirement: paired numeric values of time and oxygen amount in any common units in a data.frame. To our knowledge, every oxygen sensor system allows you to export data in a format (e.g. .csv, .txt, .xlsx) which are easy to import into R, and this is a basic skill anyone using R should be comfortable with. import_file was only ever a convenience function intended for those completely new to R. It is ALWAYS better to import files yourself using generic functions such as read.csv(), read.table() or fread() as it gives you much more control and the ability to troubleshoot issues.

For files currently supported, the function extracts data columns, removes redundant rows of metadata, and generally cleans up column names (e.g. removes whitespace and characters which cause text encoding issues) to make the data easier to work with. Files should be sensor system raw output files where possible; files opened and re-saved in a different format will likely fail to import.

Currently tested and working for these files:

• Pyro Firesting

• Pyro Workbench (very experimental - likely to fail and will not be updated further)

• PreSens OXY10

• PreSens OXY4

• PreSens (OxyView generic, including multiplate systems)

• PreSens/Loligo 24-Well Multiplate System (output Excel files)

• MiniDOT

• Loligo AutoResp ('_raw' files output, not metadata files)

• Loligo Witrox (same as AutoResp, without metadata)

• Vernier (raw qmbl, csv, or txt)

• NeoFox

• Qbox Aqua

Files with European numeric formatting (i.e. commas instead of points to denote decimals) are supported, and will be converted to point decimals on import. This is experimental functionality, so please provide feedback for any files for which this might fail.

While the devices listed above are supported, the import functionality is experimental due to limited access to sample files. Users should be aware we have not been able to test every variation of file formats, and should carefully check the imported data, and be prepared to import data using other functions such as read.csv().

More

For additional help, documentation, vignettes, and more visit the respR website at https://januarharianto.github.io/respR/

Value

A data.frame object of all columned data

Examples

## Not run: 
# Import a file
import_file("path/to/file")

# Import a file and export it to same directory as a csv
import_file("path/to/file", export = TRUE)

## End(Not run)