data-raw/data-raw.R

In evanamiesgalonski/speciesdemo: What the Package Does (One Line, Title Case)

library(readr)
library(dplyr)
library(sf)
library(mapview)
library(stringr)
library(rmapshaper)
library(ggplot2)
library(tidyverse)
library(magrittr)

# species data
# clean species data
bc_species <- readr::read_tsv("/Users/evanamies-galonski/Documents/gin thesis/bcsee_export.tsv")
names(bc_species) <- gsub(" ", "", names(bc_species))

# conservation status (red/blue list) function
bc_species %<>% mutate(COSEWIC = str_replace(COSEWIC, "\\(", ""),
                     COSEWIC = str_replace(COSEWIC, "\\)", "")) %>%
  separate(COSEWIC, c("COSEWIC", "Implemented Date"),
                       sep =" ", extra = "merge") %>%
  mutate(`Implemented Date` = lubridate::parse_date_time(`Implemented Date`, "m y"))

# cosewic status abbrevations changed
bc_species <- mutate(bc_species,
                     `COSEWIC Status` = case_when(COSEWIC == "E" ~ "Endangered",
                                                  COSEWIC == "XT" ~ "Extirpated",
                                                  COSEWIC == "T" ~ "Threatened",
                                                  COSEWIC == "X" ~ "Extinct",
                                                  COSEWIC == "SC" ~ "Special Concern",
                                                  COSEWIC == "NAR" ~ "Not At Risk",
                                                  COSEWIC == "DD" ~ "Data Deficient",
                                                  COSEWIC == "E/T" ~ "Endangered/Threatened",
                                                  TRUE ~ "No Status"))

# Dropping columns
bc_species %<>% select(-c(ScientificNameSynonyms, EnglishNameSynonyms, GlobalStatusReviewDate, ProvStatusChangeDate,
                          ProvStatusReviewDate, COSEWICComments, ProvincialFRPA, GOERT, MBCA, SARAComments,
                          BreedingBird, MappingStatus, X46, CDCMaps, COSEWIC))


# ecosections
ecosections <- select(bc_species, ScientificName, Ecosection)

# this gets ecosections for each ScientificName
ecosections <- do.call("rbind", lapply(1:nrow(ecosections), function(x){
  data <- ecosections[x,]
  splits <- strsplit(data$Ecosection, ";")[[1]]
  data <- data.frame(ScientificName = rep(data$ScientificName, length(splits)),
                     Ecosection = splits, stringsAsFactors = FALSE)
}))

# Loading maps used in analysis
ecosection_map <- sf::st_read("~/Documents/gin thesis/ERC_ECOSEC_polygon.shp")

# ecosection_map2 <- bcmaps::ecosections()
bc_boundary <- bcmaps::bc_bound()

ecosection_simple <- ms_simplify(ecosection_map)

usethis::use_data(bc_species, overwrite = TRUE)

usethis::use_data(ecosection_simple, ecosections, bc_boundary,
                  overwrite = TRUE, internal = TRUE)