Raw beach pathogen data from Suffolk County

Usage

entdat

Format

A data.frame object

Examples

if (FALSE) {
library(dplyr)
entdat1 <- read_pepent() %>% 
  filter(lubridate::year(Date) < 2022)

entdat2 <- read_pepent(path = '~/Desktop/Enterodata_2023.xlsx') %>%
  filter(lubridate::year(Date) >= 2022)

entdat <- bind_rows(entdat1, entdat2)

save(entdat, file = 'data/entdat.RData', compress = 'xz')

# or the file can be manually downloaded from here (format is not the same as path input from SCM)
# https://gis.suffolkcountyny.gov/portal/home/item.html?id=e3b344ff82b74762b625cacaa3e9621a
entdat <- read.csv('~/Desktop/Beach_Water_Quality_Data.csv', header = T) |> 
  dplyr::filter(Type %in% c('Enterococcus', 'Enterococci')) %>% 
  dplyr::select(
    Name,
    FieldNum, 
    Date = ColDate, 
    value = Result, 
    status = Character
  ) %>% 
  dplyr::mutate(
    status = gsub('[[:digit:]]+|\\.', '', value), 
    status = ifelse(status == '', '=', status), 
    value = as.numeric(gsub('>|<', '', value)),
    Date = suppressWarnings({dplyr::case_when(
      grepl('\\/', Date) ~ lubridate::mdy(Date), 
      grepl("^[[:digit:]]+$", Date) ~ as.Date(as.numeric(Date), origin = "1899-12-30"),
      T ~ NA
    )}), 
    Name = dplyr::case_when(
      Name == 'Crescent Beach - Shelter Island' ~ 'Crescent Beach - Suffolk', 
      T ~ Name
    )
  ) %>% 
  dplyr::filter(Name %in% beaches$Name) |> 
  dplyr::arrange(Name, FieldNum, Date)

save(entdat, file = 'data/entdat.RData')
}