README.md

In alkc/spectrawizreader: Lightweight package for reading files produced by Apogee Spectrawiz and Spectrovision

apogreereader

Early development!

This package is still in early development. Function names and such might be subject to change!

The first stable version of this package will (hopefully) be available via CRAN. Until then, follow the instructions below to install the development version.

Hello world!

apogeereader is a package for reading files containing spectral measurements made using the Stellarnet SpectraWiz® Spectroscopy Software and Apogee Instruments, Inc. Spectrovision Spectroradiometer software. It is inspired by the asdreader package (for ASD Fieldspec data) in its basic functionality.

Installation

To install this development version of spectrawizreader, please use the install_github() function from the devtools package, like so:

devtools::install_github("alkc/apogeereader")

Usage

Spectrawiz

Basic file input

# Get path to demo file included in the package:
path_to_spectrawiz_file <- trm_file()

# Read the file into a data.frame
spectral_data <- read_spectrawiz(file)

# Print first five columns:
print(spectral_data[,1:5])

The first column in the data.frame returned by read_spectrawiz is always the filename associated with the input file. To remove it, just subset away the first column:

spectral_data <- spectral_data[,-1]

Getting the wavelengths

The wavelengths are stored in the column names of the data.frame returned by read_spectrawiz().

Use the base function colnames() to extract the wavelengths, followed by as.numeric() to convert the wavelength vector from characters to numbers.

Here is an example:

path_to_spectrawiz_file <- trm_file()
spectral_data <- read_spectrawiz(path_to_spectrawiz_file)

# The first column in spectral_data contains file paths, so we remove it 
# before we extract the colnames
wavelengths <- colnames(spectral_data[,-1])

# The wavelengths are stored as characters in the column names. To convert them
# back to numeric format, use as.numeric():
wavelengths <- as.numeric(wavelengths)

# Done!
# Preview the first six values:
head(wavelengths)
# [1] 339.0 339.5 340.0 340.5 341.0 341.5

Spectrovision

Basic file input

spectrovision_file <- spectrovision_file()
spectral_data <- read_spectrovision(spectrovision_file)

The first column of the resulting data.frame is the timestamp associated with each measurement. If you wish to split the timestamp into separate Date, Time and Sensor for each row them set the split_timestamp argument to TRUE in read_spectrovision:

spectrovision_file <- spectrovision_file()
spectral_data <- read_spectrovision(spectrovision_file, split_timestamp = TRUE)

Merging multiple spectrovision files into a single data.frame

library(purrr)

spectrovision_files <- c(path_to_spectrovision_1, path_to_spectrovision_2, 
path_to_spectrovision_3)

spectral_data <- map_dfr(spectrovision_files, read_spectrovision)

alkc/spectrawizreader documentation built on April 23, 2021, 6:38 a.m.