data-raw/ble_co2.R

In karenezhao/alohakez:

## code to prepare `ble_co2` dataset goes here

# Attach packages
library(usethis)
library(metajam)

# Save link location for the data package:
ble_url <- "https://portal.edirepository.org/nis/dataviewer?packageid=knb-lter-ble.1.7&entityid=a1723e0e5f3c4881f1a7ede1b036aba6"

# Download the data package with metajam
ble_download <- download_d1_data(data_url = ble_url, path = tempdir(), dir_name="ble")

# Read in data
ble_files <- read_d1_files(ble_download)

ble_co2 <- ble_files$data %>%
  janitor::clean_names() %>%
  select(-c(wind_m_s, k_cm_h, fmmol_mmol_m2_day:fgrams_g_m2_day)) %>%             # Gas transfer co-efficient,
  rename(doc = doc_ppm,           # Dissolved organic carbon
         pCO2 = p_co2_uatm) %>%   # Partial pressure of CO2 (uatm)
  mutate(fw_sal = case_when(
    fw_sal == "FW" ~ "Freshwater",
    TRUE ~ fw_sal
  ),
  julian_day = case_when(
    julian_day == 121 ~ 211,
    TRUE ~ julian_day
  ),
  location_notes = case_when(
    location_notes == "-9999.00" ~ "Not applicable",
    TRUE ~ location_notes
  )
  ) %>%
  mutate(across(where(is.numeric), ~na_if(., -9999.00))) #

usethis::use_data(ble_co2, overwrite = TRUE)