data-raw/read.files.r

In aphalo/photobiologyFilters: Spectral Transmittance and Spectral Reflectance Data

# read all available filter data
# assumes that all files with ".txt" are filter-data files
# assumes that all files with exactly four columns have two replicate measurements that need
# to be averaged
# STEPS
# 1) clear the workspace
# 2) read .txt files
# 3) save all the data.frames created into individual Rda file in data folder
library(photobiology)
library(dplyr)
rm(list = ls())
setwd("data-raw")
file.list <- list.files(pattern = '*.txt')
for (file.name in file.list) {
  df.name <- paste(sub(pattern=".txt", replacement="", x=file.name), "spct", sep=".")
  tmp.df <- read.table(file.name, header=TRUE)
  if (ncol(tmp.df) == 4) {
    tmp.df <- transmute(tmp.df, w.length = w.length.1,
                        Tfr = (transmittance.1 + transmittance.2) / 200)
  } else if (ncol(tmp.df) == 2) {
    tmp.df <- transmute(tmp.df, w.length = w.length, Tfr = transmittance / 100)
  } else {
    stop("ncol != 2 || ncol!=4")
  }
  tmp.df <- mutate(tmp.df, Tfr = ifelse(Tfr < 1e-5, 1e-5, Tfr))
  setFilterSpct(tmp.df, Tfr.type = "total")
  assign(df.name, tmp.df)
  save(list=df.name, file=paste("./rda/", df.name, ".rda", sep=""))
}
setwd("./..")

tools::resaveRdaFiles("data", compress="auto")
print(tools::checkRdaFiles("data"))