added basic DEM formatting

data-raw/fun_DEM.R

@@ -0,0 +1,132 @@
+################################### HEADER ###################################
+#  TITLE: fun_DEM.R
+#  DESCRIPTION: Formats numerical data for DEM
+#  AUTHOR(S): Mariel Sorlien
+#  DATE LAST UPDATED: 2023-03-30
+#  GIT REPO:
+#  R version 4.2.0 (2022-04-22 ucrt) x86_64
+##############################################################################.
+
+library(lubridate)
+library(tidyverse)
+library(writexl)
+
+################################# FUNCTION ###################################
+
+brc_format_DEM <- function(sites_db, data_num_db, keep_ecoli=FALSE, min_year, 
+                           max_year, output_path) {
+
+  RI_towns = c('Burrillville', 'Central Falls', 'Cumberland', 'Glocester',
+               'Lincoln', 'North Smithfield', 'Pawtucket', 'Scituate',
+               'Woonsocket')
+
+  # Format, filter site data ----
+  df_sites <- readRDS(sites_db) %>%
+    # Select only RI sites
+    filter(TOWN %in% RI_towns) %>%
+    # Add STATE column
+    mutate(STATE = 'RI') %>%
+    # Select columns
+    select(SITE_NUMBER, BRC_CODE, SITE_NAME, LATITUDE, LONGITUDE,
+           WATERBODY_NAME, TOWN, STATE, HUC12_NUM, HUC_NAME) %>%
+    # Tweak column names
+    rename(HUC12_NAME=HUC_NAME) %>%
+    # Tweak HUC12_NUM, ensure starts with zero
+    mutate(HUC12_NUM=ifelse(nchar(HUC12_NUM)<12, paste0("0", HUC12_NUM),
+                            HUC12_NUM)) %>%
+    # Replace NA with -999999
+    replace(is.na(.), -999999) %>%
+    mutate(SITE_NUMBER = case_when(SITE_NUMBER=='NA' ~ '-999999',
+                                   TRUE ~ SITE_NUMBER))
+
+  # Process numeric data ----
+  # * Read in data ----
+  df_data_num <- readRDS(data_num_db) %>%
+      rename(BRC_CODE = SITE_BRC_CODE)
+
+  # * Drop E. coli data ----
+  if(keep_ecoli==FALSE){
+    df_data_num <- df_data_num %>%
+      filter(!grepl('E. coli', PARAMETER))
+  }
+
+  # * Drop all non-RI data ----
+  df_merge <- merge(x=df_data_num, y=df_sites, by='BRC_CODE')
+
+  # * Add columns ----
+  df_data_num <- df_merge %>%
+    # Set DATE_TIME to datetime format
+    mutate(DATE_TIME = ymd_hm(DATE_TIME, tz = "America/New_York")) %>%
+    # Filter for date range, only RI data
+    filter(lubridate::year(DATE_TIME) >= min_year,
+           lubridate::year(DATE_TIME) <= max_year) %>%
+    # Drop extra columns
+    select(BRC_CODE, DATE_TIME, PARAMETER, RESULT, UNITS) %>%
+    # Add column for "Sample Type"
+    mutate(SAMPLE_TYPE = case_when(grepl('Replicate', PARAMETER) ~ 'Replicate',
+                                   grepl('Field Blank', PARAMETER) ~ 'Field Blank',
+                                   grepl('Lab Blank', PARAMETER) ~ 'Lab Blank',
+                                   grepl('Blank', PARAMETER) ~ 'Blank',
+                                   TRUE ~ 'Grab')) %>%
+    # Drop 'replicate', 'field blank', 'lab blank' from PARAMETER strings
+    # Case sensitive!
+    mutate(PARAMETER = str_replace_all(PARAMETER,
+                                       c("Replicate" = "",
+                                         "Field Blank" = "",
+                                         "Lab Blank" = "",
+                                         "Blank" = ""))) %>%
+    # Drop trailing blank spaces
+    mutate(PARAMETER = str_trim(PARAMETER))
+
+  # * Format columns ----
+  df_data_DEM <- df_data_num %>%
+    # Rename columns
+    rename('Station Name' = BRC_CODE, 'Sample Type'= SAMPLE_TYPE, 
+           Parameter = PARAMETER, Concentration = RESULT, Unit = UNITS) %>%
+    # Add date, time columns
+    mutate(Date = format(DATE_TIME, format="%m/%d/%Y")) %>%
+    mutate_at("Date", as.character) %>%
+    mutate(Time = format(DATE_TIME, format="%H:%M %Z")) %>%
+    mutate_at("Time", as.character) %>%
+    # Add columns
+    mutate('Sample Media' = 'Water',
+           'Depth' = '',
+           'Qualifier Code' = '',
+           'Detection Limit' = '',
+           'Detection Limit Unit' = Unit,
+           'Quantitation Level' = '',
+           'Quantitation Level Unit' = Unit,
+           'Lab Name' = '',
+           'Analytical Method Number' = '',
+           'Sediment Particle Size' = '',
+           'Particle Size Unit' = '',
+           'Fish Sample Type' = '',
+           'Fish Taxa' = '',
+           'Comments' = '') %>%
+    # Arrange columns, drop extra columns
+    select('Station Name', Date, Time, 'Sample Type', 'Sample Media', Depth,
+           Parameter, Concentration, Unit, 'Qualifier Code', 'Detection Limit',
+           'Detection Limit Unit', 'Quantitation Level', 
+           'Quantitation Level Unit', 'Lab Name', 'Analytical Method Number',
+           'Sediment Particle Size', 'Particle Size Unit', 'Fish Sample Type',
+           'Fish Taxa', Comments) %>%
+    # Sort
+    arrange(Date, Time, 'Station Name', Parameter)
+
+  # Save output ----
+  data_list <- list(CHEM_Template = df_data_DEM,
+                    BRC_Sites = df_sites)
+
+  for (i in 1:length(data_list)) {
+    fileName <- paste0(output_path, names(data_list)[i], ".csv")
+    write.csv(data_list[[i]], fileName, row.names=FALSE)
+  }
+
+}
+
+brc_format_DEM(sites_db='data-raw/sites_db.rds',
+                   data_num_db='data-raw/data_num_db.rds',
+                   keep_ecoli=FALSE,
+                   min_year=2017,
+                   max_year=2022,
+                   output_path='')