data-raw/and_vertebrates.R

In adhil0/alohaal:

## code to prepare `and_vertebrates` dataset goes here
# Attach packages
library(usethis)
library(metajam)

# Save link location for the data package:
and_url <- "https://portal.edirepository.org/nis/dataviewer?packageid=knb-lter-and.4027.14&entityid=5b18ded1cd996f5e8d361a9275a600cf"

# Download the data package with metajam
and_download <- download_d1_data(data_url = and_url, path = tempdir())

# Read in data
and_files <- read_d1_files(and_download)
and_vertebrates_raw <- and_files$data
and_vertebrates <- and_vertebrates_raw %>%
  select(YEAR,
         SITECODE,
         SECTION,
         REACH,
         SPECIES,
         LENGTH1,
         LENGTH2,
         WEIGHT,
         SAMPLEDATE) %>%
  mutate(
    SPECIES = recode(
      SPECIES,
      "RHOL" = "Olympic Torrent Salamander",
      "ONCL" = "Coastal Cutthroat Trout",
      "DITE" = "Coastal Giant Salamander"
    ),
    SITECODE = as.factor(SITECODE),
    SECTION = as.factor(SECTION),
    REACH = as.factor(REACH)
  )

#select _>mutate <- recode
  #drop SELECT Year sitecode section reach species length1 length2 weight sampledate

# Save the data as a data object (.Rda) with usethis::use_data() - this code should already exist in the script, just update the dataset name
# NOTE: You could do some wrangling HERE to simplify the dataset before storing the .Rda, but we’ll just use it as read in from metajam today

usethis::use_data(and_vertebrates, overwrite = TRUE)