proximetricsR (version 0.6.5)

proximate_write_data: Write NIRWise PLUS readable tab-separated files

Description

This function writes tab-separated value files in a readable NIRWise PLUS software format. These files contain visible and Near-Infrared absorbance spectra along with response variables and metainformation (e.g. sample ID, date, comments, etc).

Usage

proximate_write_data(x, 
                     file, 
                     id, 
                     spc, 
                     spc_round = 8, 
                     barcode = "", 
                     properties = NULL, 
                     note = "", 
                     recipe = "", 
                     created, 
                     snr)

Value

Invisibly returns NULL. Called for its side effect of writing a tab-separated value file to file.

Arguments

x

a data.frame of spectral data and metadata, for which the tab separated value file should be generated. See details.

file

a character for the path (and name) in which the tsv will be saved.

id

a vector of characters of length equal to the number of observations in x or of length 1. Each entry gives an observation a specific ID. If length is 1, this entry is recycled for every observation.

spc

either a character or a vector of integers. Specifies where the spectra can be found inside x. Default is "spc".

spc_round

an integer. To how many decimal places should the spectra be rounded? Defaults to 8 decimal places.

barcode

a vector of characters of length equal to the number of observations in x or of length 1. Each entry specifies the barcode for each observation; if length is 1, the entry is recycled for every observation. Default is an empty character.

properties

a vector of characters of arbitrary length. Which properties in x are to be added to the tsv? Note that any missing reference values for the properties are set to 0. Default is NULL.

note

a vector of characters of length equal to the number of observations in x or of length 1. The vector corresponds to the notes for each observation, or, if the vector is of length one, to all notes of all observations. Defaults to an empty character.

recipe

a vector of characters of length equal to the number of observations in x or of length 1. This vector corresponds to the recipe for each observation, or, if the vector is of length one, to all recipes of all observations. Defaults to an empty character.

created

a vector of characters of length equal to the number of observations in x. This vector should contain the date and time of when each observation was measured. If not provided and not contained in x, this parameter will be set to the current date and time of the system.

snr

a vector of characters, corresponding to the serial number of the device on which the measurement was taken. If not provided and not found in x, this parameter will be set to a vector of character of length equal to the number of rows in x, where each individual character is given by 0000000000.

Author

Leonardo Ramirez-Lopez

Details

This function creates a tab separated value file, which is readable by both NIRWise PLUS software and the proximate_read_data function.

The main usage is to transform an already given data file into a format which is readable by NIRWise PLUS. Therefore, if some data of the given object x is already of the correct form, one can pass the corresponding values simply by passing the specific row of x to this function; for example, by passing note = x$Note.

Examples

# \donttest{
data("NIRcannabis")
filename <- file.path(tempdir(), "NIRcannabis.tsv")

proximate_write_data(
  x = NIRcannabis,
  file = filename,
  id = NIRcannabis$ID,
  spc = "spc",
  spc_round = 8,
  barcode = NIRcannabis$Barcode,
  properties = c("CBDA", "THCA", "CBD", "THC"),
  note = NIRcannabis$Note,
  recipe = NIRcannabis$Recipe,
  created = NIRcannabis$Begin
)

# Since we do not change anything, the following produces the same tsv:
proximate_write_data(
  x = NIRcannabis,
  file = filename,
  properties = c("CBDA", "THCA", "CBD", "THC")
)
# Delete the file
file.remove(filename)
# }