R/clean-lvl2.R

In iozeroff/cncpointR: What the Package Does (One Line, Title Case)

# This script cleans lvl2.
library(sf)
library(sp)
library(dplyr)
library(stringr)
library(ggplot2)
library(worrms)

fish <- c("Myxini", "Petromyzontida", "Hyperoartia", "Chondrichthyes", "Actinopterygii",
          "Sarcopterygii")

lvl2 <- lvl2 %>% 
  filter(!is.na(coordinateUncertaintyInMeters) & coordinateUncertaintyInMeters <= 30, # Removes all observations with coordinate uncertainty of value NA or greater than 30.
         class != "Aves", !(class %in% fish), # Filters out bird and fish observations.
         !is.na(species)) # Filters NA observations.
  

# Creates a test matrix if lvl2 observations are within cnc_area. 
# XXX Should add 30m buffer to cnc_area?
test <- lvl2 %>% 
  st_as_sf(coords = c("decimalLongitude", "decimalLatitude"), # Converts lvl2 to sf object with same crs as cnc_area.
           crs = st_crs(cnc_area)) %>% 
  st_within(y = cnc_area, sparse = FALSE) # Creates matrix of TRUE/FALSE if points are in polygon.

# Filters lvl2 according to test matrix.  
cnc_pts <- lvl2[test[, 1] == 1,]


# Creates a list of the unique species in cnc_pts.
unique_species <- unique(cnc_pts$species)

#--------------------------------------------------------------------------------------------------------------------------
# XXX Functionalize, and look for a way to speed up (might not be possible to speed up, as it's calling to API with limits).
# Initialize an empty vector to hold WORRMS lookup results.
marine_animals_check <- vector(mode = 'numeric')

# For every entry in species...
for (i in 1:length(unique_species)) {
  check <- NULL
  tryCatch(
    expr = {
      worrms::wm_records_name(species[i], fuzzy=FALSE) # Uses species name to query World Registry of Marine Species for a record, and assigns response to empty list value.
      message(paste("Iteration", i, "Successful"))
      check <<- 1 # 1 if no error.
    },
    error = function(e) {
      message(paste("Error caught on iteration", i, ":", e))
      check <<- 0 # 0 if error, meaning not an entry in WORRMS.
    },
    finally = {
      marine_animals_check <<- append(marine_animals_check, check)
    }
  )
}
# XXX It's working, but I don't trust it to work programmatically, at least as of yet.
# XXX If going to functionalize this, will need to get rid of the <<- (global assignment), and figure out how to assign within function.

#--------------------------------------------------------------------------------------------------------------------------
# Filters for marine animals.
marine_animals <- data.frame(species = unique_species, marine = marine_animals_check) %>% 
  filter(marine == 1)

save(marine_animals, file="data/marine-animals.rda")
# Filters lvl2 species to be species not in marine_animals.
lvl2_terra <- lvl2 %>% 
  filter(!(species %in% marine_animals$species))

save(lvl2_terra, file = "data/lvl2_terra.rda")