update arguments for read_importentero for easier input

R/read_importentero.R

@@ -1,12 +1,8 @@
 #' Download Enterococcus data from the Water Quality Portal
 #'
-#' @param args a list of arguments to pass to Water Quality Portal. See \code{examples} for detail on how to use. Must contain the following fields:
-#' \describe{
-#'  \item{\code{siteid}}{character, vector of stations}
-#'  \item{\code{characteristicName}}{character, vector to select 'Characteristic Names' from WQP}
-#'  \item{\code{startDateLo}}{date, start date for data to download}
-#'  \item{\code{startDateHi}}{date, end date for data to download}
-#' }
+#' @param stas character, a vector of stations.  If \code{NULL}, defaults to all stations in \code{\link{catchprecip}}.
+#' @param startDate character, starting date of observations as YYYY-MM-DD
+#' @param endDate character, ending date of observations as YYYY-MM-DD
 #'
 #' @details Retrieves Enterococcus sample data from selected stations and date range from the Water Quality Portal, \url{https://www.waterqualitydata.us}
 #'
@@ -33,30 +29,35 @@
 #'
 #' @examples
 #' \dontrun{
-#' # set up list of args
+#' # stations to download
 #' stations <- c('21FLHILL_WQX-101',
 #' '21FLHILL_WQX-102',
 #' '21FLHILL_WQX-103')
-#' entero_names <- c('Enterococci',
-#'                   'Enterococcus')
-#' startDate <- as.Date('2023-01-01')
-#' endDate <- as.Date('2023-02-01')
-#'
-#' args <- list(
-#'   siteid = stations,
-#'   characteristicName = entero_names,
-#'   startDateLo = format(startDate, '%m-%d-%Y'),
-#'   startDateHi = format(endDate, '%m-%d-%Y')
-#' )
 #'
 #' # download and read the data
-#' entero_in <- read_importentero(args = args)
+#' entero_in <- read_importentero(stas = stations, startDate = '2023-01-01', endDate = '2023-02-01')
+#'
 #' head(entero_in)
 #'
 #' }
+read_importentero <- function(stas = NULL, startDate, endDate){
+
+  # default to all stations if not specified
+  if(is.null(stas))
+    stations <- unique(catchprecip$station)
+
+  entero_names <- c('Enterococci',
+                    'Enterococcus')
+  startDate <- as.Date(startDate)
+  endDate <- as.Date(endDate)
+
+  args <- list(
+    siteid = stations,
+    characteristicName = entero_names,
+    startDateLo = format(startDate, '%m-%d-%Y'),
+    startDateHi = format(endDate, '%m-%d-%Y')
+  )
 
-read_importentero <- function(args){
-  # args should be a list of sites, characteristic names, and start/end dates
 
   # generate the parts
   # a weakness here is building the '&' into everything but siteid -

data-raw/enterodata-raw.R

@@ -2,21 +2,7 @@
 # although apparently data collection only started in 2000 at the earliest of these stations
 library(here)
 
-stations <- unique(catchprecip$station)
-entero_names <- c('Enterococci',
-                  'Enterococcus')
-startDate <- as.Date('1995-01-01')
-endDate <- as.Date('2023-12-31')
-
-args <- list(
-  siteid = stations,
-  characteristicName = entero_names,
-  startDateLo = format(startDate, '%m-%d-%Y'),
-  startDateHi = format(endDate, '%m-%d-%Y')
-)
-# date format has to be mm-dd-yyyy
-
-enterodata <- read_importentero(args = args) %>%
+enterodata <- read_importentero(startDate = '1995-01-01', endDate = '2023-12-31') %>%
   dplyr::select(-qualifier,
                 -LabComments)
 

tests/testthat/test-read_importentero.R

@@ -25,16 +25,10 @@ test_that("read_importentero works correctly", {
   mock_read_csv <- mock(return_value = mock_data)
   stub(read_importentero, "read.csv", mock_read_csv)
 
-  # Prepare arguments
-  args <- list(
-    siteid = c("21FLHILL_WQX-101", "21FLHILL_WQX-102"),
-    characteristicName = c("Enterococci", "Enterococcus"),
-    startDateLo = "01-01-2023",
-    startDateHi = "12-31-2023"
-  )
+  stations <- c("21FLHILL_WQX-101", "21FLHILL_WQX-102")
 
   # Call the function with mocked dependencies
-  result <- read_importentero(args)
+  result <- read_importentero(stas = stations, startDate = "2023-01-01", endDate = "2023-12-31")
 
   # Define expected output
   expected_output <- data.frame(