library(rgdal)
library(dplyr)
# define parameters -----------------------------------------------------------
spp_in_pth <- file.path("data-raw", "shapefiles", "species")
to_remove <- c("OID_",
"Shape_Leng",
"Shape_Area",
"HydroID",
"GridID",
"NextDownID",
"PU_ID")
# load data -------------------------------------------------------------------
fishes <- readOGR(dsn = spp_in_pth, layer = "Fish_Daly_final_agg")
birds <- readOGR(dsn = spp_in_pth, layer = "Birds_Daly_final_agg")
turtles <- readOGR(dsn = spp_in_pth, layer = "Turtles_Daly_final_agg")
eco_g_lookup <- read.table(file.path("data_raw", "Eco_group_lookup.txt"),
sep = ",",
header = TRUE,
stringsAsFactors = FALSE)
# create site-species array ---------------------------------------------------
site_species_array <- cbind(fishes@data[, setdiff(names(fishes@data), to_remove)],
turtles@data[, setdiff(names(turtles@data), to_remove)],
birds@data[, setdiff(names(birds@data), to_remove)])
# remove `mel_sino` and `ARDEO_AU`
site_species_array <- site_species_array[, setdiff(names(site_species_array), c("mel_sino", "ARDEO_AU"))]
site_species_array <- as.matrix(site_species_array)
# create conservation feature array -------------------------------------------
sp_names_df <- data.frame(sp_names = colnames(site_species_array),
area_of_occ = colSums(site_species_array),
target = 0,
spf = 0,
stringsAsFactors = FALSE)
cons_feat_array <- left_join(sp_names_df, eco_g_lookup)
# remove some fields
cons_feat_array <- as.matrix(cons_feat_array[, c("area_of_occ",
"target",
"spf",
"FaunalGroup",
"EcologicalGroup")])
# save internal data files ----------------------------------------------------
devtools::use_data(site_species_array, site_species_array, overwrite = TRUE)
devtools::use_data(cons_feat_array, cons_feat_array, overwrite = TRUE)
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