rm(list = ls())
library(rspecan)
sethere()
data_name <- "ecosis_08"
ecosis_filename <- "ecosis8.csv"
ecosis_file <- dir(ecosis_dir, ecosis_filename, full.names = TRUE)
dat_full <- read_csv(ecosis_file)
wave_rxp <- "^[[:digit:]]+$"
spectra <- dat2specmat(dat_full, "spectra_id", wave_rxp)
stopifnot(
!any(duplicated(colnames(spectra)))
)
wl <- getwl(spectra)
if (FALSE) {
matplot(wl, spectra, type = "l", xlim = c(350, 500))
}
wl_prospect <- wl >= 400 & wl <= 2500
wl_bad <- FALSE
wl_keep <- wl_prospect & !wl_bad
data_wl_inds <- which(wl_keep)
wl_kept <- wl[wl_keep]
prospect_wl_inds <- which(prospect_wl %in% wl_kept)
stopifnot(length(data_wl_inds) == length(prospect_wl_inds))
sp_good <- spectra[data_wl_inds, ]
if (FALSE) {
matplot(wl_kept, sp_good, type = "l")
}
dat_sub <- dat_full %>%
select(-matches(wave_rxp))
dat <- dat_sub %>%
transmute(
data_name = !!data_name,
spectra_id = Spectra,
spectra_type = "reflectance",
collection_date = lubridate::mdy(`Sample Collection Date`),
latitude = `Latitude`,
longitude = `Longitude`,
USDA_code = `USDA Symbol`,
genus = `Latin Genus`,
species = `Latin Species`,
common_name = `Common Name`,
elevation = `Elevation (m)`,
elevation_unit = "m",
description = `Full Description`,
ash = `% Ash`,
ash_unit = "%",
fat = `% Fat`,
fat_unit = "%",
neutral_detergent_fiber = `% Neutral detergent fiber`,
neutral_detergent_fiber_unit = "%",
NSC = `% Non-structural carbohydrate`,
NSC_unit = "%",
protein = `% Protein`,
protein_unit = "%",
LWC = `Relative water content` * 100,
LWC_unit = "%"
)
stopifnot(
!any(duplicated(dat$spectra_id)),
ncol(spectra) == nrow(dat)
)
store_path <- file.path(processed_dir, paste0(data_name, ".rds"))
datalist <- list(
data_name = data_name,
data_filename = ecosis_file,
self_filename = store_path,
metadata = dat,
spectra = spectra,
data_wl_inds = data_wl_inds,
prospect_wl_inds = prospect_wl_inds
)
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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