data-raw/ems-vmv-codes.R

In bcgov/wqbc: Tidy Water Quality Data and Calculate Thresholds for British Columbia

library(dplyr)
library(magrittr)
library(readr)
library(devtools)
library(tidyr)
library(rems)
library(canwqdata)

vmv_codes <- canwqdata::wq_params() %>%
  select(VMV_CODE,
    VMV_VARIABLE_CODE = NATIONAL_VARIABLE_CODE,
    VMV_VARIABLE = VARIABLE_COMMON_NAME,
    VMV_VARIABLE_TYPE = VARIABLE_TYPE,
    VMV_UNIT = MEASUREMENT_UNIT,
    VMV_UNIT_NAME = DESCRIPTION,
    VMV_METHOD_CODE = NATIONAL_METHOD_CODE,
    VMV_METHOD_TITLE = METHOD_TITLE
  ) %>%
  mutate_all(stringr::str_trim, side = "both") %>%
  distinct()

ems_codes <- rems::ems_parameters %>%
  select(
    EMS_CODE = PARAMETER_CODE,
    EMS_VARIABLE = PARAMETER,
    EMS_UNIT = UNIT,
    EMS_UNIT_CODE = UNIT_CODE,
    EMS_METHOD_CODE = ANALYTICAL_METHOD_CODE,
    EMS_METHOD_TITLE = ANALYTICAL_METHOD,
    EMS_MDL = METHOD_DETECTION_LIMIT
  ) %>%
  mutate_all(stringr::str_trim, side = "both") %>%
  distinct()

## Ensure codes have consistent leading zeros etc.
vmv_ems_xwalk <- read_csv("data-raw/VMV_to_EMS.csv",
  col_types = cols(.default = col_character())
) %>%
  filter(OTHER_SYSTEM_NAME == "EMS") %>%
  separate(OTHER_SYSTEM_CODE, c("EMS_CODE", "EMS_METHOD_CODE"), 4) %>%
  select(
    VMV_CODE = vmv_code,
    VMV_METHOD_CODE = method_code,
    EMS_CODE,
    EMS_METHOD_CODE,
    EMS_UNIT_CODE = OTHER_SYSTEM_UNIT_CODE
  ) %>%
  mutate_all(stringr::str_trim, side = "both") %>%
  distinct()

# VMV_CODE should be unique but include VMV_METHOD_CODE for completeness.
# The combination of EMS_CODE, EMS_METHOD_CODE, and EMS_UNIT_CODE should be
# unique.
vmv_ems <- left_join(ems_codes, vmv_ems_xwalk,
  by = c(
    "EMS_CODE",
    "EMS_METHOD_CODE",
    "EMS_UNIT_CODE"
  )
) %>%
  left_join(vmv_codes, by = c("VMV_CODE", "VMV_METHOD_CODE")) %>%
  select(
    EMS_CODE,
    EMS_VARIABLE,
    EMS_UNIT,
    EMS_UNIT_CODE,
    EMS_METHOD_CODE,
    EMS_METHOD_TITLE,
    EMS_MDL,
    VMV_CODE,
    VMV_VARIABLE_CODE,
    VMV_VARIABLE,
    VMV_VARIABLE_TYPE,
    VMV_UNIT,
    VMV_UNIT_NAME,
    VMV_METHOD_CODE,
    VMV_METHOD_TITLE
  )

use_data(ems_codes, vmv_ems, vmv_codes, overwrite = TRUE)