change to arguments to snake_case. Fix #17

lifewatch · May 10, 2022 · 3b11bcf · 3b11bcf
1 parent 4053472
commit 3b11bcf
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Showing 6 changed files with 38 additions and 38 deletions.
diff --git a/R/eurobis_occurrences.R b/R/eurobis_occurrences.R
@@ -14,10 +14,10 @@
 #' @param geometry a WKT geometry string or sf object with the region of interest. You can draw a polygon interactively 
 #' with \code{\link{eurobis_map_draw}}
 #' @param dasid IMIS dataset unique identifier. See list of available datasets with \code{\link{eurobis_list_datasets}}
-#' @param startdate Start date of occurrences. Format YYYY-MM-DD.
-#' @param enddate End date of occurrences. Format YYYY-MM-DD.
+#' @param start_date Start date of occurrences. Format YYYY-MM-DD.
+#' @param end_date End date of occurrences. Format YYYY-MM-DD.
 #' @param aphiaid WoRMS taxon unique identifier. See \url{https://www.marinespecies.org/} and \url{https://docs.ropensci.org/worrms/}
-#' @param scientificname Taxon name. It is matched with WoRMS on the fly. Ignored if aphiaid is provided.
+#' @param scientific_name Taxon name. It is matched with WoRMS on the fly. Ignored if aphiaid is provided.
 #' @param functional_groups Functional groups available in WoRMS: See \code{eurobis::species_traits}.
 #' @param cites CITES Annex. See \code{eurobis::species_traits}.
 #' @param habitats_directive Habitats Directive Annex. See \code{eurobis::species_traits}.
@@ -46,23 +46,23 @@
 #' 
 #' # Get occurrences from Zostera marina in the ecoregion Alboran Sea (MRGID 21897)
 #' # See also ?eurobis_list_regions
-#' test <- eurobis_occurrences_full(mrgid = 21897, scientificname = "Zostera marina")
+#' test <- eurobis_occurrences_full(mrgid = 21897, scientific_name = "Zostera marina")
 #' 
 #' # Get zooplankton occurrences from the region of your choice
 #' # See ?eurobis_map_mr and ?eurobis::species_traits
 #' my_area <- eurobis_map_draw()
 #' test <- eurobis_occurrences_basic(geometry = my_area, functional_groups = "zooplankton")
 #' 
 #' # Get occurrences from the Continuous Plankton Recorder (dataset id 216) in January 2016
-#' test <- eurobis_occurrences_basic(dasid = 216, startdate = "2016-01-01", enddate = "2016-01-31")
+#' test <- eurobis_occurrences_basic(dasid = 216, start_date = "2016-01-01", end_date = "2016-01-31")
 #' }
 eurobis_occurrences <- function(type,
                                 url = NULL,
                                 mrgid = NULL, 
                                 geometry = NULL, 
                                 dasid = NULL, 
-                                startdate = NULL, enddate = NULL, 
-                                aphiaid = NULL, scientificname = NULL,
+                                start_date = NULL, end_date = NULL, 
+                                aphiaid = NULL, scientific_name = NULL,
                                 functional_groups = NULL, 
                                 cites = NULL, 
                                 habitats_directive = NULL,
@@ -75,16 +75,16 @@ eurobis_occurrences <- function(type,
   if(!is.null(url)){
     viewparams <- extract_viewparams(url)
   }else if(is.null(url)){
-    viewparams <- build_viewparams(mrgid, geometry, dasid, startdate, enddate, aphiaid, 
+    viewparams <- build_viewparams(mrgid, geometry, dasid, start_date, end_date, aphiaid, 
                                    functional_groups, cites, habitats_directive,
                                    iucn_red_list, msdf_indicators)
   }
 
   # Handle Scientific name
-  if(!is.null(aphiaid) & !is.null(scientificname)){
-    warning("Both aphiaid and scientificname provided: Ignoring scientificname")
-  }else if(!is.null(scientificname)){
-    aphiaid <- eurobis_name2id(scientificname)
+  if(!is.null(aphiaid) & !is.null(scientific_name)){
+    warning("Both aphiaid and scientific_name provided: Ignoring scientific_name")
+  }else if(!is.null(scientific_name)){
+    aphiaid <- eurobis_name2id(scientific_name)
   }
 
   # WFS

diff --git a/R/viewparams.R b/R/viewparams.R
@@ -13,20 +13,20 @@ build_encode <- function(query){
 # build_viewparams(polygon = 'POLYGON((-2 52,-2 58,9 58,9 52,-2 52))')
 # build_viewparams(mrgid = 8364, polygon = 'POLYGON((-2 52,-2 58,9 58,9 52,-2 52))')
 # build_viewparams(dasid = 216)
-# build_viewparams(dasid = 216, startdate = "2000-01-01", enddate = "2022-01-31")
+# build_viewparams(dasid = 216, start_date = "2000-01-01", end_date = "2022-01-31")
 # build_viewparams(mrgid = 8364, polygon = 'POLYGON((-2 52,-2 58,9 58,9 52,-2 52))',
-#                  dasid = 216, startdate = "2000-01-01", enddate = "2022-01-31",
+#                  dasid = 216, start_date = "2000-01-01", end_date = "2022-01-31",
 #                  aphiaid = c(104108, 148947))
 build_viewparams <- function(mrgid = NULL, geometry = NULL, dasid = NULL, 
-                             startdate = NULL, enddate = NULL, aphiaid = NULL, 
+                             start_date = NULL, end_date = NULL, aphiaid = NULL, 
                              functional_groups = NULL, cites = NULL, habitats_directive = NULL,
                              iucn_red_list = NULL, msdf_indicators = NULL
                              ){
 
   filters <- c(
     build_filter_geo(mrgid, geometry),
     build_filter_dataset(dasid),
-    build_filter_time(startdate, enddate),
+    build_filter_time(start_date, end_date),
     build_filter_traits(functional_groups, cites, habitats_directive, 
                         iucn_red_list, msdf_indicators)
   )
@@ -173,17 +173,17 @@ build_filter_geo <- function(mrgid = NULL, polygon = NULL){
 # build_filter_time(as.Date("2000-01-01"), "2022-01-31")
 # build_filter_time(NULL, "2022-01-31")
 # build_filter_time("2000-01-01", NULL)
-build_filter_time <- function(startdate = NULL, enddate = NULL){
+build_filter_time <- function(start_date = NULL, end_date = NULL){
 
-  dates <- list(startdate, enddate)
+  dates <- list(start_date, end_date)
 
   dates_are_null <- unlist(lapply(dates, is.null))
   if(all(dates_are_null)) return(NULL)
-  if(any(dates_are_null)) stop("Both startdate and enddate must be provided or ignored")
+  if(any(dates_are_null)) stop("Both start_date and end_date must be provided or ignored")
 
   dates_as_date <- lapply(dates, as.Date) 
 
-  if(dates_as_date[[1]] > dates_as_date[[2]]) stop("startdate cannot be smaller than enddate")
+  if(dates_as_date[[1]] > dates_as_date[[2]]) stop("start_date cannot be smaller than end_date")
 
   dates_as_char <- lapply(dates_as_date, as.character)
 

diff --git a/README.md b/README.md
@@ -32,7 +32,7 @@ occ <- eurobis_occurrences("basic", dasid = 8045)
 ```
 
 ```r
-occ2 <- eurobis_occurrences("basic", dasid = 8045, scientificname = "Zostera marina")
+occ2 <- eurobis_occurrences("basic", dasid = 8045, scientific_name = "Zostera marina")
 ```
 
 ```r

diff --git a/man/eurobis_occurrences.Rd b/man/eurobis_occurrences.Rd
diff --git a/tests/testthat/test-viewparams.R b/tests/testthat/test-viewparams.R
@@ -78,7 +78,7 @@ test_that("viewParams are build correctly", {
   # All together
   is_character <- is.character(
     build_viewparams(mrgid = 8364, geometry = wkt, 
-                     dasid = 216, startdate = "2000-01-01", enddate = "2022-01-31", 
+                     dasid = 216, start_date = "2000-01-01", end_date = "2022-01-31", 
                      aphiaid = c(104108, 148947),
                      functional_groups = c("algae", "zooplankton"),
                      cites = "I",

diff --git a/tests/testthat/test-wfsrequest.R b/tests/testthat/test-wfsrequest.R
@@ -14,10 +14,10 @@ test_that("eurobis_occurrences", {
     expect_true(is_sf_df)
   }
 
-  #' test <- eurobis_occurrences("basic", dasid = 8045, scientificname = "Zostera marina")
-  #' test <- eurobis_occurrences("basic", dasid = 8045, scientificname = c("Zostera marina", "foo"))
-  #' test <- eurobis_occurrences("basic", dasid = 8045, scientificname = "foo")
-  #' test <- eurobis_occurrences("basic", dasid = 8045, scientificname = "Zostera marina", aphiaid = 145795)
+  #' test <- eurobis_occurrences("basic", dasid = 8045, scientific_name = "Zostera marina")
+  #' test <- eurobis_occurrences("basic", dasid = 8045, scientific_name = c("Zostera marina", "foo"))
+  #' test <- eurobis_occurrences("basic", dasid = 8045, scientific_name = "foo")
+  #' test <- eurobis_occurrences("basic", dasid = 8045, scientific_name = "Zostera marina", aphiaid = 145795)
 
 })
 
@@ -33,8 +33,8 @@ test_that("sf handler works fine", {
   test_ok <- eurobis_occurrences(
     "basic", 
     geometry = pol_gibraltar,
-    startdate = "1990-01-01",
-    enddate = "1995-12-31",
+    start_date = "1990-01-01",
+    end_date = "1995-12-31",
     functional_groups = "mammals" 
   )
   expect_true(methods::is(test_ok, "sf"))
@@ -44,8 +44,8 @@ test_that("sf handler works fine", {
     eurobis_occurrences(
       "basic", 
       geometry = pol_gibraltar,
-      startdate = "1990-01-01",
-      enddate = "1995-12-31",
+      start_date = "1990-01-01",
+      end_date = "1995-12-31",
       functional_groups = "pisces" 
     )
   )