rm(list = ls())
library(rspecan)
sethere()
data_name <- "ecosis_cedarcreek_biodiversity"
data_longname <- "2014 Cedar Creek ESR Grassland Biodiversity Experiment: Leaf-level Contact Data: Trait Predictions"
ecosis_file <- "raw_data/2014-cedar-creek-esr-grassland-biodiversity-experiment--leaf-level-contact-data--trait-predictions.csv"
dat_full <- read_csv(ecosis_file) %>%
mutate(spectra_id = sprintf("%s_%03d", data_name, ID))
############################################################
# Process spectra
############################################################
wave_rxp <- "^[[:digit:]]+$"
spectra_colname <- "spectra_id"
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 = spectra_id,
instrument = paste(`Instrument Manufacturer`, `Instrument Model`),
spectra_type = `Measurement Quantity`,
LMA = `LMA g m2`,
LMA_unit = "g m-2",
Cmass = `C`,
Cmass_unit = "%",
Nmass = N,
Nmass_unit = "%",
CN_ratio = `C:N`,
lignin = Lignin,
lignin_unit = "%",
cellulose = `Cell`,
cellulose_unit = "%",
fiber = Fiber,
fiber_unit = "%",
chlorophyll = `Chl g m2`,
chlorophyll_unit = "g m2",
USDA_code = toupper(`USDA Symbol`),
latitude = 45.402,
longitude = -93.199
)
############################################################
# 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)
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