scripts/process.ecosis_spectral_variation_leafcanopy.R

In ashiklom/rspecan: Leaf reflectance spectra analysis

rm(list = ls())
library(rspecan)
sethere()

data_name <- "ecosis_spectral_variation_leafcanopy"
data_longname <- "Spectral Variation Between Leaf-level and Canopy-level Measurements"
ecosis_file <- "raw_data/spectral-variation-between-leaf-level-and-canopy-level-measurements.csv"

dat_full <- read_csv(ecosis_file) %>%
  # Keep only single plants
  filter(`# of Plants` == 1)

############################################################
# Process spectra
############################################################
wave_rxp <- "^[[:digit:]]+$"
spectra_colname <- "idstr"

spectra <- dat2specmat(dat_full, spectra_colname, wave_rxp)
str(spectra)

wl <- getwl(spectra)
if (FALSE) {
  matplot(wl, spectra, type = "l")
}

wl_prospect <- wl >= 400 & wl <= 2500
wl_bad <- FALSE
wl_keep <- wl_prospect & !wl_bad

data_wl_inds <- which(wl_keep)
wl_kept <- wl[wl_keep]
prospect_wl_inds <- which(prospect_wl %in% wl_kept)

############################################################
# Process metadata
############################################################
dat_sub <- dat_full %>%
  select(-matches(wave_rxp))

dat <- dat_sub %>%
  transmute(
    data_name = !!data_name,
    spectra_id = idstr,
    spectra_type = "reflectance",
    N_fertilization_treatment = `Fertilization Treatment`,
    USDA_code = Species
  )

############################################################
# Store results
############################################################

store_path <- file.path(processed_dir, paste0(data_name, ".rds"))

datalist <- list(
  data_name = data_name,
  data_longname = data_longname,
  data_filename = ecosis_file,
  self_filename = store_path,
  metadata = dat,
  spectra = spectra,
  data_wl_inds = data_wl_inds,
  prospect_wl_inds = prospect_wl_inds
)

check_datalist(datalist)

submit_df <- dat %>%
  filter(spectra_type == "reflectance") %>%
  select(data_name, spectra_id)

saveRDS(datalist, store_path)
write_submit_file(submit_df, data_name)