# Organize
rm(list = ls())
library(devtools)
devtools::install_github("rscherrer/sagreicolor")
library(pavo)
library(sagreicolor)
# Read spectral data
specs <- readRDS("data/specs.rds")
# Read locality data
locale <- readRDS("data/locale.rds")
# What habitats do we want?
whatHabitats <- c("coastal", "coppice", "mangrove")
# Choose a spot to study
spot <- 2
# Process the spectra into a data frame
specdata <- sagreicolor::process_spectra(specs, locale, spot)
# Reduce to the wanted habitats
specdata <- sagreicolor::subset_habitats(specdata, whatHabitats)
# Remove missing entries from spectral dataset
specs <- sagreicolor::df2rspec(specdata)
# Calculate mean reflectance
specdata$meanrefl <- unlist(summary(specs, 'B2'))
# Calculate cut-on wavelength
specdata$cuton <- unlist(summary(specs, 'H3', wlmin = 450, wlmax = 700))
# Calculate red and UV reflectance
specdata$Red <- unlist(summary(specs, 'S1R'))
specdata$UV <- unlist(summary(specs, 'S1U'))
# Compute Principal Components
dewlaPCA <- sagreicolor::spectral_pca(specdata)
# Save the prcomp object
saveRDS(dewlaPCA, "data/dewlaPCA.rds")
# Bind Principal Components to the data frame
specdata <- cbind(specdata, dewlaPCA$x)
# Save the data
write.csv(specdata, "data/specdata.csv")
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