clarify how weeks are defined, add category

CornellLabofOrnithology · Apr 8, 2024 · 9d188a4 · 9d188a4
1 parent 299fe6f
commit 9d188a4
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Showing 26 changed files with 105 additions and 72 deletions.
diff --git a/R/process_barcharts.R b/R/process_barcharts.R
@@ -24,19 +24,25 @@
 #'   proportion of checklists in the region that reported the species in the
 #'   given week and `n_detections` gives the number of detections. The total
 #'   number of checklists in each week used to estimate detection frequency is
-#'   provided as a data frame stored in the `sample_sizes` attribute.
+#'   provided as a data frame stored in the `sample_sizes` attribute. Note that
+#'   since most months have more than 28 days, the first three weeks have 7
+#'   days, but the final week has between 7-10 days.
 #'   
 #' @export
 #' @family helpers
 #' @examples
 #' # example bar chart data for svalbard
 #' f <- system.file("extdata/barchart-sample.txt", package = "auk")
 #' # import and process barchart data
-#' barchart <- process_barcharts(f)
-#' head(barchart)
+#' barcharts <- process_barcharts(f)
+#' head(barcharts)
 #' 
 #' # the sample sizes for each week can be access with
-#' attr(barchart, "sample_sizes")
+#' attr(barcharts, "sample_sizes")
+#' 
+#' # bar charts include data for non-species taxa
+#' # use category to filter to only species
+#' barcharts[barcharts$category == "species", ]
 process_barcharts <- function(filename) {
   stopifnot(is.character(filename), file.exists(filename))
 
@@ -74,7 +80,7 @@ process_barcharts <- function(filename) {
 
   # add in species codes
   tax <- auk::ebird_taxonomy
-  tax <- tax[, c("species_code", "common_name", "scientific_name")]
+  tax <- tax[, c("species_code", "common_name", "scientific_name", "category")]
   detfrq <- dplyr::inner_join(tax, detfrq, by = "common_name")
 
   # add in num detections

diff --git a/docs/articles/auk.html b/docs/articles/auk.html
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
@@ -4,5 +4,5 @@ pkgdown_sha: ~
 articles:
   auk: auk.html
   development: development.html
-last_built: 2024-04-08T16:16Z
+last_built: 2024-04-08T16:36Z
 
diff --git a/docs/reference/auk_bbox.html b/docs/reference/auk_bbox.html
diff --git a/docs/reference/auk_bcr.html b/docs/reference/auk_bcr.html
diff --git a/docs/reference/auk_breeding.html b/docs/reference/auk_breeding.html
diff --git a/docs/reference/auk_complete.html b/docs/reference/auk_complete.html
diff --git a/docs/reference/auk_country.html b/docs/reference/auk_country.html
diff --git a/docs/reference/auk_county.html b/docs/reference/auk_county.html