average.spec: average replicate spectra within a directory of spectra files

In serbinsh/R-FieldSpectra: Functions for processing field spectroscopy data. Current supported instruments include ADS FieldSpec, Spectral Evolution, and Spectra Vista Corporation

average replicate spectra within a directory of spectra files

Description

Function to average replicate spectra within a directory of spectra files

Usage

average.spec(
  file.dir = NULL,
  out.dir = NULL,
  spec.type = "Reflectance",
  start.wave = NULL,
  end.wave = NULL,
  step.size = NULL,
  bias.threshold = NULL,
  outlier.cutoff = 2,
  suffix.length = NULL,
  output.file.ext = NULL,
  metadata.file = NULL,
  image = FALSE,
  settings.file = NULL
)

Arguments

file.dir	Directory of spectra files to process
out.dir	Output directory for processed spectra files
spec.type	Option to set what type of spectra to average. Options: Reflectance, Transmittance. Can be set with abbreviations: e.g. "Refl" or "Tran" Default is "Reflectance"
start.wave	Starting wavelength of spectra files. Not needed if specified in XML settings file.
end.wave	Ending wavelength of spectra files. Not needed if specified in XML settings file.
step.size	Resolution of spectra files. E.g. 1 for 1nm, 5 for 5nm. Not needed if specified in XML settings file.
bias.threshold	Reflectance/transmittance cutoff to remove spectra with anartificial bias (shift) due to improper spectral collection
outlier.cutoff	[Optional] Set upper/lower standard deviation cutoff to identify statistical Refl/Trans outliers within individual sample sets. Set as outlier.cutoff*Sample Sdev, e.g. 2.0*Sdev. Default 2.0
suffix.length	Length of auto numbering attached to ASD file names. This number of characters will be removed from the filename when averaged.
output.file.ext	Optional setting to set file extension of output files. Defaults to .csv
metadata.file	Option to select custom metadata file for use in processing. If not set then the information is either read from default metadata file, the settings file or at the function call. Need to set this as the full qualified path to the spectral metadata file is using a custom file/location
image	Logical. Whether to produce .png images of each spectrum (TRUE) or not (FALSE). Default is FALSE. Useful for diagnosing spectral observations during processing.
settings.file	Settings file used for spectral processing options (OPTIONAL). Contains information related to the spectra collection instrument, output directories, and processing options such as applying a jump correction to the spectra files. Options in the settings file take precedent over options selected in the function call.
spec.dataframe	Option to return a data frame with the converted spectra files

Author(s)

Shawn P. Serbin

Examples

## Not run: 
average.spec()
average.spec(file.dir,out.dir, start.wave=350,end.wave=2500,step.size=1,bias.threshold=0.06,
suffix.length=5,output.file.ext=".csv",spec.dataframe = TRUE,)

## End(Not run)
 

serbinsh/R-FieldSpectra documentation built on March 31, 2022, 10:08 p.m.