rm(list = ls())
library(rspecan)
sethere()
data_name <- "ecosis_santamonica"
data_longname <- "Santa Monica Mountains vegetation species spectra"
ecosis_file <- "raw_data/santa-monica-mountains-vegetation-species-spectra.csv"
dat_full <- read_csv(ecosis_file)
wave_rxp <- "^[[:digit:]]+$"
dat_sub <- dat_full %>%
select(-matches(wave_rxp))
dat <- dat_sub %>%
transmute(
data_name = !!data_name,
spectra_id = Spectra,
spectra_type = "reflectance",
common_name = `Common Name`,
description = `Description`,
genus = case_when(
!is.na(`Latin genus`) ~ `Latin genus`,
!is.na(`Latin Genus`) ~ `Latin Genus`,
TRUE ~ NA_character_
),
species = case_when(
!is.na(`Latin species`) ~ `Latin species`,
!is.na(`Latin Species`) ~ `Latin Species`,
TRUE ~ NA_character_
),
USDA_code = `USDA Symbol`,
collection_date = lubridate::mdy(`Sample Collection Date`),
target_type = `Surface Type`
)
spectra <- dat2specmat(dat_full, "Spectra", wave_rxp)
str(spectra)
wl <- getwl(spectra)
if (FALSE) {
matplot(wl, spectra, pch = 20, xlim = c(2300, 2400))
}
wl_prospect <- wl >= 400 & wl <= 2500
wl_bad <- wl > 2320
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)
sp_good <- spectra[data_wl_inds, ]
if (FALSE) {
matplot(wl_kept, sp_good, type = "l")
}
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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