From c06b628c1212f201aa76e5f04e0a47f1ebef1563 Mon Sep 17 00:00:00 2001 From: Matt Strimas-Mackey Date: Fri, 3 Jan 2025 07:00:42 -0800 Subject: [PATCH] cran release --- DESCRIPTION | 2 +- R/auk-version.r | 6 +- README.md | 2 +- _pkgdown.yml | 2 + auk.Rproj | 1 + docs/404.html | 48 ++-- docs/CONDUCT.html | 16 +- docs/CONTRIBUTING.html | 16 +- docs/LICENSE.html | 16 +- docs/articles/auk.html | 142 +++++------ docs/articles/development.html | 20 +- docs/articles/index.html | 16 +- docs/authors.html | 24 +- docs/index.html | 20 +- docs/news/index.html | 16 +- docs/pkgdown.yml | 10 +- docs/reference/Rplot001.png | Bin 1011 -> 0 bytes docs/reference/auk-package.html | 18 +- docs/reference/auk.html | 8 + docs/reference/auk_bbox.html | 32 +-- docs/reference/auk_bcr.html | 34 +-- docs/reference/auk_breeding.html | 28 +-- docs/reference/auk_clean.html | 38 +-- docs/reference/auk_complete.html | 28 +-- docs/reference/auk_country.html | 34 +-- docs/reference/auk_county.html | 34 +-- docs/reference/auk_date.html | 36 +-- docs/reference/auk_distance.html | 34 +-- docs/reference/auk_duration.html | 32 +-- docs/reference/auk_ebd.html | 36 +-- docs/reference/auk_ebd_version.html | 28 +-- docs/reference/auk_exotic.html | 34 +-- docs/reference/auk_extent.html | 32 +-- docs/reference/auk_filter.auk_ebd.html | 8 + docs/reference/auk_filter.auk_sampling.html | 8 + docs/reference/auk_filter.html | 56 ++--- docs/reference/auk_get_awk_path.html | 22 +- docs/reference/auk_get_ebd_path.html | 24 +- docs/reference/auk_last_edited.html | 30 +-- docs/reference/auk_observer.html | 32 +-- docs/reference/auk_project.html | 32 +-- docs/reference/auk_protocol.html | 32 +-- docs/reference/auk_rollup.html | 32 +-- docs/reference/auk_sampling.html | 30 +-- docs/reference/auk_select.html | 38 +-- docs/reference/auk_set_awk_path.html | 32 +-- docs/reference/auk_set_ebd_path.html | 32 +-- docs/reference/auk_species.html | 36 +-- docs/reference/auk_split.html | 40 +-- docs/reference/auk_state.html | 34 +-- docs/reference/auk_time.html | 32 +-- docs/reference/auk_unique.html | 36 +-- docs/reference/auk_version.html | 28 +-- docs/reference/auk_year.html | 36 +-- docs/reference/auk_zerofill.auk_ebd.html | 8 + docs/reference/auk_zerofill.character.html | 8 + docs/reference/auk_zerofill.data.frame.html | 8 + docs/reference/auk_zerofill.html | 54 ++-- docs/reference/bcr_codes.html | 18 +- docs/reference/collapse_zerofill.html | 8 + docs/reference/ebird_species.html | 34 +-- docs/reference/ebird_states.html | 18 +- docs/reference/ebird_taxonomy.html | 18 +- docs/reference/filter_repeat_visits.html | 40 +-- docs/reference/format_unmarked_occu.html | 46 ++-- docs/reference/get_ebird_taxonomy.html | 32 +-- docs/reference/index.html | 16 +- docs/reference/process_barcharts.html | 26 +- docs/reference/read_ebd.auk_ebd.html | 8 + docs/reference/read_ebd.character.html | 8 + docs/reference/read_ebd.html | 46 ++-- docs/reference/read_sampling.auk_ebd.html | 8 + .../reference/read_sampling.auk_sampling.html | 8 + docs/reference/read_sampling.character.html | 8 + docs/reference/read_sampling.html | 8 + docs/reference/reexports.html | 16 +- docs/reference/valid_protocols.html | 18 +- docs/sitemap.xml | 232 +++++------------- 78 files changed, 1082 insertions(+), 1105 deletions(-) delete mode 100644 docs/reference/Rplot001.png create mode 100644 docs/reference/auk.html create mode 100644 docs/reference/auk_filter.auk_ebd.html create mode 100644 docs/reference/auk_filter.auk_sampling.html create mode 100644 docs/reference/auk_zerofill.auk_ebd.html create mode 100644 docs/reference/auk_zerofill.character.html create mode 100644 docs/reference/auk_zerofill.data.frame.html create mode 100644 docs/reference/collapse_zerofill.html create mode 100644 docs/reference/read_ebd.auk_ebd.html create mode 100644 docs/reference/read_ebd.character.html create mode 100644 docs/reference/read_sampling.auk_ebd.html create mode 100644 docs/reference/read_sampling.auk_sampling.html create mode 100644 docs/reference/read_sampling.character.html create mode 100644 docs/reference/read_sampling.html diff --git a/DESCRIPTION b/DESCRIPTION index 5f4595a..c2dbc7b 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -54,4 +54,4 @@ VignetteBuilder: Encoding: UTF-8 LazyData: true Roxygen: list(markdown = TRUE) -RoxygenNote: 7.3.1 +RoxygenNote: 7.3.2 diff --git a/R/auk-version.r b/R/auk-version.r index 0027cdf..d6ffa2d 100644 --- a/R/auk-version.r +++ b/R/auk-version.r @@ -21,7 +21,7 @@ #' @examples #' auk_version() auk_version <- function() { - list(auk_version = "auk 0.7.0", - ebd_version = as.Date("2023-10-25", "%Y-%m-%d"), - taxonomy_version = 2023) + list(auk_version = "auk 0.8.0", + ebd_version = as.Date("2024-10-29", "%Y-%m-%d"), + taxonomy_version = 2024) } diff --git a/README.md b/README.md index 2c72ae5..3099dc0 100644 --- a/README.md +++ b/README.md @@ -212,7 +212,7 @@ defined, the filtering is actually conducted using `auk_filter()`. auk_complete() ebd #> Input - #> EBD: /private/var/folders/mg/qh40qmqd7376xn8qxd6hm5lwjyy0h2/T/RtmpBEc62Y/temp_libpath324735beea83/auk/extdata/ebd-sample.txt + #> EBD: /private/var/folders/wf/y1p0nztd2ps95ppplsl5bjjr0000gs/T/Rtmp7EtevZ/temp_libpathb9796963586e/auk/extdata/ebd-sample.txt #> #> Output #> Filters not executed diff --git a/_pkgdown.yml b/_pkgdown.yml index 31c5cd2..d08fbef 100644 --- a/_pkgdown.yml +++ b/_pkgdown.yml @@ -1,3 +1,5 @@ +url: https://cornelllabofornithology.github.io/auk/ + navbar: structure: left: [intro, reference, articles, cheatsheet, tutorials, news] diff --git a/auk.Rproj b/auk.Rproj index 21a4da0..fe8abe2 100644 --- a/auk.Rproj +++ b/auk.Rproj @@ -1,4 +1,5 @@ Version: 1.0 +ProjectId: 75beeb8f-7a35-4a34-aa86-8e874912f531 RestoreWorkspace: Default SaveWorkspace: Default diff --git a/docs/404.html b/docs/404.html index cbc6c2a..f52b69a 100644 --- a/docs/404.html +++ b/docs/404.html @@ -6,26 +6,26 @@ Page not found (404) • auk - - - - - - + + + + + + - - + + - - - + + + - +
@@ -46,20 +46,20 @@ - +
@@ -113,16 +113,16 @@

Page not found (404)

-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.1.

- - + + diff --git a/docs/CONDUCT.html b/docs/CONDUCT.html index 5fadc0e..7d2f1bc 100644 --- a/docs/CONDUCT.html +++ b/docs/CONDUCT.html @@ -1,9 +1,9 @@ -Contributor Covenant Code of Conduct • aukContributor Covenant Code of Conduct • auk - +
- +
@@ -118,15 +118,15 @@

Attribution -

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.1.

- - + + diff --git a/docs/CONTRIBUTING.html b/docs/CONTRIBUTING.html index de9b9c2..ed616f1 100644 --- a/docs/CONTRIBUTING.html +++ b/docs/CONTRIBUTING.html @@ -1,9 +1,9 @@ -CONTRIBUTING • aukCONTRIBUTING • auk - +
- +
@@ -105,15 +105,15 @@

Thanks for contributing!
-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.1.

- - + + diff --git a/docs/LICENSE.html b/docs/LICENSE.html index 63a95d8..48e7b5d 100644 --- a/docs/LICENSE.html +++ b/docs/LICENSE.html @@ -1,9 +1,9 @@ -GNU General Public License • aukGNU General Public License • auk - +
- +
@@ -274,15 +274,15 @@

How to Apply These Terms

-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.1.

- - + + diff --git a/docs/articles/auk.html b/docs/articles/auk.html index 0747fe3..6d1eeb5 100644 --- a/docs/articles/auk.html +++ b/docs/articles/auk.html @@ -18,15 +18,13 @@ - - - +
- +
@@ -101,6 +99,8 @@

Introduction to auk

+
## Error in get(paste0(generic, ".", class), envir = get_method_env()) : 
+##   object 'type_sum.accel' not found

eBird is an online tool for recording bird observations. Since its inception, nearly 500 million records of bird sightings (i.e. combinations of location, date, time, @@ -140,7 +140,7 @@

Quick start
+
 library(auk)
 # path to the ebird data file, here a sample included in the package
 # in practice, provide path to ebd, e.g. input_file <- "data/ebd_relFeb-2018.txt"
@@ -159,7 +159,7 @@ 
Quick startread_ebd()

 
For those not familiar with the pipe operator (%>%),
 the above code could be rewritten:

-
+
 input_file <- system.file("extdata/ebd-sample.txt", package = "auk")
 output_file <- "ebd_filtered_grja.txt"
 ebd <- auk_ebd(input_file)
@@ -242,7 +242,7 @@ 
Example data
+
 library(auk)
 library(dplyr)
 system.file("extdata/ebd-sample.txt", package = "auk")

@@ -252,7 +252,7 @@ 
Example data
+
 # ebd
 system.file("extdata/zerofill-ex_ebd.txt", package = "auk")
 # sampling event data
@@ -340,12 +340,12 @@ 
The auk_ebd objectauk_ebd object, use auk_ebd():

-
+
 ebd <- system.file("extdata/ebd-sample.txt", package = "auk") %>% 
   auk_ebd()
 ebd
 #> Input 
-#>   EBD: /private/var/folders/mg/qh40qmqd7376xn8qxd6hm5lwjyy0h2/T/RtmpBEc62Y/temp_libpath32473f2f276e/auk/extdata/ebd-sample.txt 
+#>   EBD: /private/var/folders/wf/y1p0nztd2ps95ppplsl5bjjr0000gs/T/Rtmp7EtevZ/temp_libpathb97949a13185/auk/extdata/ebd-sample.txt 
 #> 
 #> Output 
 #>   Filters not executed
@@ -432,7 +432,7 @@ 
Defining filtersauk_ebd object, in order to define the filters. Once the
 filters have been defined, the filtering is actually conducted using
 auk_filter().

-
+
 ebd_filters <- ebd %>% 
   # species: common and scientific names can be mixed
   auk_species(species = c("Canada Jay", "Cyanocitta cristata")) %>%
@@ -451,7 +451,7 @@ 
Defining filters  auk_complete()
 ebd_filters
 #> Input 
-#>   EBD: /private/var/folders/mg/qh40qmqd7376xn8qxd6hm5lwjyy0h2/T/RtmpBEc62Y/temp_libpath32473f2f276e/auk/extdata/ebd-sample.txt 
+#>   EBD: /private/var/folders/wf/y1p0nztd2ps95ppplsl5bjjr0000gs/T/Rtmp7EtevZ/temp_libpathb97949a13185/auk/extdata/ebd-sample.txt 
 #> 
 #> Output 
 #>   Filters not executed
@@ -491,7 +491,7 @@ 
Executing filters
+
 output_file <- "ebd_filtered_blja-grja.txt"
 ebd_jays <- system.file("extdata/ebd-sample.txt", package = "auk") %>% 
   auk_ebd() %>% 
@@ -509,7 +509,7 @@ 
Readingread_ebd() uses stringsAsFactors = FALSE,
 quote = "", sets column classes, and converts variable
 names to snake_case.

-
+
 system.file("extdata/ebd-sample.txt", package = "auk") %>% 
   read_ebd() %>% 
   glimpse()
@@ -523,22 +523,22 @@ 
Reading#> $ taxon_concept_id          <chr> "avibase-361B447A", "avibase-361B447A", "avi…
 #> $ common_name               <chr> "Green Jay", "Green Jay", "Canada Jay", "Can…
 #> $ scientific_name           <chr> "Cyanocorax yncas", "Cyanocorax yncas", "Per…
-#> $ exotic_code               <chr> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, …
+#> $ exotic_code               <chr> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, …
 #> $ observation_count         <chr> "2", "6", "1", "1", "X", "3", "4", "3", "6",…
-#> $ breeding_code             <chr> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, …
-#> $ breeding_category         <chr> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, …
-#> $ behavior_code             <chr> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, …
-#> $ age_sex                   <chr> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, …
+#> $ breeding_code             <chr> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, …
+#> $ breeding_category         <chr> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, …
+#> $ behavior_code             <chr> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, …
+#> $ age_sex                   <chr> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, …
 #> $ country                   <chr> "United States", "United States", "Canada", …
 #> $ country_code              <chr> "US", "US", "CA", "CA", "MX", "MX", "CA", "U…
 #> $ state                     <chr> "Texas", "Texas", "British Columbia", "Briti…
 #> $ state_code                <chr> "US-TX", "US-TX", "CA-BC", "CA-BC", "MX-NLE"…
 #> $ county                    <chr> "Zapata", "Starr", "Northern Rockies", "Nort…
 #> $ county_code               <chr> "US-TX-505", "US-TX-427", "CA-BC-NR", "CA-BC…
-#> $ iba_code                  <chr> NA, NA, NA, NA, "MX_69", NA, NA, NA, NA, NA,…
+#> $ iba_code                  <chr> NA, NA, NA, NA, "MX_69", NA, NA, NA, NA, NA,…
 #> $ bcr_code                  <int> 36, 36, 6, 6, 48, 36, 13, 10, 36, 48, 48, 8,…
-#> $ usfws_code                <chr> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, …
-#> $ atlas_block               <chr> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, …
+#> $ usfws_code                <chr> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, …
+#> $ atlas_block               <chr> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, …
 #> $ locality                  <chr> "Zapata Library / City Park (LTC 085)", "Fal…
 #> $ locality_id               <chr> "L846015", "L128962", "L343808", "L343808", …
 #> $ locality_type             <chr> "H", "H", "H", "H", "H", "H", "H", "H", "H",…
@@ -552,24 +552,24 @@ 
Reading#> $ protocol_code             <chr> "P22", "P22", "P21", "P21", "P22", "P22", "P…
 #> $ project_code              <chr> "EBIRD", "EBIRD", "EBIRD", "EBIRD", "EBIRD",…
 #> $ duration_minutes          <int> 30, 60, 60, 90, 90, 90, 90, 35, 60, 60, 75, …
-#> $ effort_distance_km        <dbl> 1.609, 3.219, NA, NA, 1.000, 1.500, NA, 3.21…
-#> $ effort_area_ha            <dbl> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, 4.04…
+#> $ effort_distance_km        <dbl> 1.609, 3.219, NA, NA, 1.000, 1.500, NA, 3.21…
+#> $ effort_area_ha            <dbl> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, 4.04…
 #> $ number_observers          <int> 2, 2, 13, 13, 7, 2, 2, 5, 4, 5, 5, 2, 5, 10,…
 #> $ all_species_reported      <lgl> TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TR…
 #> $ group_identifier          <chr> "G1131664", "G1131665", "G1158137", "G115813…
 #> $ has_media                 <lgl> FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FA…
 #> $ approved                  <lgl> TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TR…
 #> $ reviewed                  <lgl> FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FA…
-#> $ reason                    <chr> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, …
-#> $ trip_comments             <chr> NA, NA, "BCFO extension trip", "BCFO extensi…
-#> $ species_comments          <chr> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, …

+#> $ reason                    <chr> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, …
+#> $ trip_comments             <chr> NA, NA, "BCFO extension trip", "BCFO extensi…
+#> $ species_comments          <chr> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, …

 
auk_filter() returns an auk_ebd object with
 the output file paths stored in it. This auk_ebd object can
 then be passed directly to auk_read(), allowing for a
 complete pipeline. For example, we can create an auk_ebd
 object, define filters, filter with AWK, and read in the results all at
 once.

-
+
 output_file <- "ebd_filtered_blja-grja.txt"
 ebd_df <- system.file("extdata/ebd-sample.txt", package = "auk") %>% 
   auk_ebd() %>% 
@@ -585,7 +585,7 @@ 
Saving the AWK commandawk_file. In addition, by setting
 execute = FALSE the AWK script will be generated but not
 run.

-
+
 awk_script <- system.file("extdata/ebd-sample.txt", package = "auk") %>% 
   auk_ebd() %>% 
   auk_species(species = c("Canada Jay", "Cyanocitta cristata")) %>% 
@@ -647,7 +647,7 @@ 
Group checklistsread_ebd() automatically runs auk_unique(),
 however, we can use unique = FALSE then manually run
 auk_unique().

-
+
 # read in an ebd file and don't automatically remove duplicates
 ebd_dupes <- system.file("extdata/ebd-sample.txt", package = "auk") %>%
   read_ebd(unique = FALSE)
@@ -655,9 +655,8 @@ 
Group checklistsebd_unique <- auk_unique(ebd_dupes)
 # compare number of rows
 nrow(ebd_dupes)
-#> [1] 400

-
-nrow(ebd_unique)
+#> [1] 400
+nrow(ebd_unique)
 #> [1] 398

 

 

@@ -684,12 +683,10 @@ 
Taxonomic rollup# taxa below species have been rolled up to species
 unique(ebd$category)
 #> [1] "domestic"   "form"       "hybrid"     "intergrade" "slash"     
-#> [6] "spuh"       "species"    "issf"

-
-unique(ebd_ru$category)
-#> [1] "species"

-
-
+#> [6] "spuh"       "species"    "issf"
+unique(ebd_ru$category)
+#> [1] "species"
+
 # yellow-rump warbler subspecies rollup
 # without rollup, there are three observations
 ebd %>%
@@ -702,9 +699,8 @@ 
Taxonomic rollup#> 1 S44943108    intergrade Yellow-rumpe… Yellow-rumped Warbler… 1                
 #> 2 S129851825   species    Yellow-rumpe… NA                     1                
 #> 3 S129851825   issf       Yellow-rumpe… Yellow-rumped Warbler… 1                
-#> 4 S129851825   issf       Yellow-rumpe… Yellow-rumped Warbler… 2

-
-# with rollup, they have been combined
+#> 4 S129851825   issf       Yellow-rumpe… Yellow-rumped Warbler… 2
+# with rollup, they have been combined
 ebd_ru %>%
   filter(common_name == "Yellow-rumped Warbler") %>%
   select(checklist_id, category, common_name, observation_count)
@@ -745,7 +741,7 @@ 
Filtering
+
 # to produce zero-filled data, provide an EBD and sampling event data file
 f_ebd <- system.file("extdata/zerofill-ex_ebd.txt", package = "auk")
 f_smp <- system.file("extdata/zerofill-ex_sampling.txt", package = "auk")
@@ -755,8 +751,8 @@ 
Filteringauk_complete()
 filters
 #> Input 
-#>   EBD: /private/var/folders/mg/qh40qmqd7376xn8qxd6hm5lwjyy0h2/T/RtmpBEc62Y/temp_libpath32473f2f276e/auk/extdata/zerofill-ex_ebd.txt 
-#>   Sampling events: /private/var/folders/mg/qh40qmqd7376xn8qxd6hm5lwjyy0h2/T/RtmpBEc62Y/temp_libpath32473f2f276e/auk/extdata/zerofill-ex_sampling.txt 
+#>   EBD: /private/var/folders/wf/y1p0nztd2ps95ppplsl5bjjr0000gs/T/Rtmp7EtevZ/temp_libpathb97949a13185/auk/extdata/zerofill-ex_ebd.txt 
+#>   Sampling events: /private/var/folders/wf/y1p0nztd2ps95ppplsl5bjjr0000gs/T/Rtmp7EtevZ/temp_libpathb97949a13185/auk/extdata/zerofill-ex_sampling.txt 
 #> 
 #> Output 
 #>   Filters not executed
@@ -782,14 +778,14 @@ 
Filteringauk_filter() to
 actually run AWK. Output files must be provided for both the EBD and
 sampling event data.

-
+
 ## ebd_sed_filtered <- auk_filter(filters, 
 ##                                file = "ebd-filtered.txt",
 ##                                file_sampling = "sampling-filtered.txt")
 ebd_sed_filtered
 #> Input 
-#>   EBD: /private/var/folders/mg/qh40qmqd7376xn8qxd6hm5lwjyy0h2/T/RtmpBEc62Y/temp_libpath32473f2f276e/auk/extdata/zerofill-ex_ebd.txt 
-#>   Sampling events: /private/var/folders/mg/qh40qmqd7376xn8qxd6hm5lwjyy0h2/T/RtmpBEc62Y/temp_libpath32473f2f276e/auk/extdata/zerofill-ex_sampling.txt 
+#>   EBD: /private/var/folders/wf/y1p0nztd2ps95ppplsl5bjjr0000gs/T/Rtmp7EtevZ/temp_libpathb97949a13185/auk/extdata/zerofill-ex_ebd.txt 
+#>   Sampling events: /private/var/folders/wf/y1p0nztd2ps95ppplsl5bjjr0000gs/T/Rtmp7EtevZ/temp_libpathb97949a13185/auk/extdata/zerofill-ex_sampling.txt 
 #> 
 #> Output 
 #>   EBD: ebd-filtered.txt 
@@ -819,7 +815,7 @@ 
Reading and zero-filling
 
The filtered datasets can now be combined into a zero-filled,
 presence-absence dataset using auk_zerofill().

-
+
 ## ebd_zf <- auk_zerofill(ebd_sed_filtered)
 ebd_zf
 #> Zero-filled EBD: 131 unique checklists, for 1 species.

@@ -836,7 +832,7 @@ 
Reading and zero-fillingebd_zf$observations contains the species counts and a
 binary presence-absence variable
 
-
+
 head(ebd_zf$observations)
 #> # A tibble: 6 × 8
 #>   checklist_id scientific_name     breeding_code breeding_category behavior_code
@@ -848,9 +844,8 @@ 
Reading and zero-filling#> 5 S10006786    Todiramphus chloris NA            NA                NA           
 #> 6 S10011787    Todiramphus chloris NA            NA                NA           
 #> # ℹ 3 more variables: age_sex <chr>, observation_count <chr>,
-#> #   species_observed <lgl>

-
-glimpse(ebd_zf$sampling_events)
+#> #   species_observed <lgl>
+glimpse(ebd_zf$sampling_events)
 #> Rows: 131
 #> Columns: 31
 #> $ checklist_id              <chr> "S9843037", "S34396450", "S9589770", "S16642…
@@ -859,12 +854,12 @@ 
Reading and zero-filling#> $ country_code              <chr> "SG", "SG", "SG", "SG", "SG", "SG", "SG", "S…
 #> $ state                     <chr> "Singapore", "Singapore", "Singapore", "Sing…
 #> $ state_code                <chr> "SG-", "SG-", "SG-", "SG-", "SG-", "SG-", "S…
-#> $ county                    <chr> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, …
-#> $ county_code               <chr> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, …
-#> $ iba_code                  <chr> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, …
-#> $ bcr_code                  <int> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, …
-#> $ usfws_code                <chr> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, …
-#> $ atlas_block               <chr> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, …
+#> $ county                    <chr> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, …
+#> $ county_code               <chr> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, …
+#> $ iba_code                  <chr> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, …
+#> $ bcr_code                  <int> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, …
+#> $ usfws_code                <chr> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, …
+#> $ atlas_block               <chr> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, …
 #> $ locality                  <chr> "Pulau Ubin", "Pulau Ubin", "Pulau Ubin", "P…
 #> $ locality_id               <chr> "L1055540", "L1055540", "L1055540", "L105554…
 #> $ locality_type             <chr> "H", "H", "H", "H", "H", "H", "H", "H", "H",…
@@ -878,24 +873,23 @@ 
Reading and zero-filling#> $ protocol_code             <chr> "P22", "P22", "P22", "P22", "P21", "P22", "P…
 #> $ project_code              <chr> "EBIRD", "EBIRD", "EBIRD_CAN", "EBIRD_AU", "…
 #> $ duration_minutes          <int> 300, 180, 300, 510, 23, 195, 150, 105, 190, …
-#> $ effort_distance_km        <dbl> 1.609, 4.000, 3.000, 10.000, NA, 3.000, 3.00…
-#> $ effort_area_ha            <dbl> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, …
+#> $ effort_distance_km        <dbl> 1.609, 4.000, 3.000, 10.000, NA, 3.000, 3.00…
+#> $ effort_area_ha            <dbl> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, …
 #> $ number_observers          <int> 2, 2, 6, 1, 2, 3, 12, 3, 1, 1, 3, 3, 2, 1, 1…
 #> $ all_species_reported      <lgl> TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TR…
-#> $ group_identifier          <chr> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, …
-#> $ trip_comments             <chr> "With Ailin Chuah on day trip", NA, NA, "Spe…

+#> $ group_identifier          <chr> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, …
+#> $ trip_comments             <chr> "With Ailin Chuah on day trip", NA, NA, "Spe…

 
This format is efficient for storage because the checklist
 information isn’t duplicated, however, a single flat data frame is often
 required for analysis. To collapse the two data frames together use
 collapse_zerofill(), or call auk_zerofill()
 with collapse = TRUE.

-
+
 ## ebd_zf_df <- auk_zerofill(ebd_filtered, collapse = TRUE)
 ebd_zf_df <- collapse_zerofill(ebd_zf)
 class(ebd_zf_df)
-#> [1] "tbl_df"     "tbl"        "data.frame"

-
-ebd_zf_df
+#> [1] "tbl_df"     "tbl"        "data.frame"
+ebd_zf_df
 #> # A tibble: 131 × 38
 #>    checklist_id last_edited_date    country country_code state state_code county
 #>    <chr>        <chr>               <chr>   <chr>        <chr> <chr>      <chr> 
@@ -938,9 +932,7 @@ 
References
 
-        
-

+      

 
 

 
@@ -953,16 +945,16 @@ 
References
   

-
Site built with pkgdown 2.0.9.

+
Site built with pkgdown 2.1.1.

 

 
       
 

 
-  
 
 
-  
+
+
 
   
 
diff --git a/docs/articles/development.html b/docs/articles/development.html
index ebf7e6d..3b64115 100644
--- a/docs/articles/development.html
+++ b/docs/articles/development.html
@@ -18,15 +18,13 @@
 
 
 
-
-
 
 
 
-    
+
 
     

       

 
 
-      
+
 
       

   

@@ -395,9 +393,7 @@ 
CRAN submission
 
-        
-

+      

 
 

 
@@ -410,16 +406,16 @@ 
CRAN submission
   

-
Site built with pkgdown 2.0.9.

+
Site built with pkgdown 2.1.1.

 

 
       
 

 
-  
 
 
-  
+
+
 
   
 
diff --git a/docs/articles/index.html b/docs/articles/index.html
index 0ee129f..5601957 100644
--- a/docs/articles/index.html
+++ b/docs/articles/index.html
@@ -1,9 +1,9 @@
 
-Articles • aukArticles • auk
-    
+
 
     

       

   

 

 
-      
+
 
       

   

@@ -80,15 +80,15 @@ 
All vignettes

 

 
 

-  
Site built with pkgdown 2.0.9.

+  
Site built with pkgdown 2.1.1.

 

 
       

 
-  
 
 
-  
+
+
 
   
 
diff --git a/docs/authors.html b/docs/authors.html
index 18bc0dd..86c1dab 100644
--- a/docs/authors.html
+++ b/docs/authors.html
@@ -1,9 +1,9 @@
 
-Authors and Citation • aukAuthors and Citation • auk
-    
+
 
     

       

   

 

 
-      
+
 
       

   

@@ -63,21 +63,21 @@
         
Authors and Citation

       

 
-      
+
       

@@ -109,15 +109,15 @@ 
Citation

 

 
 

-  
Site built with pkgdown 2.0.9.

+  
Site built with pkgdown 2.1.1.

 

 
       

 
-  
 
 
-  
+
+
 
   
 
diff --git a/docs/index.html b/docs/index.html
index f8278c7..16a53fb 100644
--- a/docs/index.html
+++ b/docs/index.html
@@ -19,14 +19,14 @@
 
 
 
-
+
 
 
 
-    
+
 
     

       

 
 
-      
+
 
       

   

@@ -115,7 +115,7 @@ 
Installation
 
Vignette
 

-
Full details on using auk to produce both presence-only and presence-absence data are outlined in the vignette.

+
Full details on using auk to produce both presence-only and presence-absence data are outlined in the vignette.

 

 

 
Cheatsheet
@@ -231,7 +231,7 @@ 
Filtering  auk_complete()
 ebd
 #> Input 
-#>   EBD: /private/var/folders/mg/qh40qmqd7376xn8qxd6hm5lwjyy0h2/T/RtmpBEc62Y/temp_libpath324735beea83/auk/extdata/ebd-sample.txt 
+#>   EBD: /private/var/folders/wf/y1p0nztd2ps95ppplsl5bjjr0000gs/T/Rtmp7EtevZ/temp_libpathb9796963586e/auk/extdata/ebd-sample.txt 
 #> 
 #> Output 
 #>   Filters not executed
@@ -415,16 +415,16 @@ 
Dev status

 
 

   

-
Site built with pkgdown 2.0.9.

+
Site built with pkgdown 2.1.1.

 

 
       
 

 
-  
 
 
-  
+
+
 
   
 
diff --git a/docs/news/index.html b/docs/news/index.html
index df4ca3c..4798d35 100644
--- a/docs/news/index.html
+++ b/docs/news/index.html
@@ -1,9 +1,9 @@
 
-Changelog • aukChangelog • auk
-    
+
 
     

       

   

 

 
-      
+
 
       

   

@@ -249,15 +249,15 @@ 
auk 0.0.12017-
 

 
 

-  
Site built with pkgdown 2.0.9.

+  
Site built with pkgdown 2.1.1.

 

 
       

 
-  
 
 
-  
+
+
 
   
 
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
index 858ba76..a03d95e 100644
--- a/docs/pkgdown.yml
+++ b/docs/pkgdown.yml
@@ -1,8 +1,10 @@
-pandoc: 3.1.11
-pkgdown: 2.0.9
+pandoc: '3.2'
+pkgdown: 2.1.1
 pkgdown_sha: ~
 articles:
   auk: auk.html
   development: development.html
-last_built: 2024-10-29T14:22Z
-
+last_built: 2025-01-03T06:03Z
+urls:
+  reference: https://cornelllabofornithology.github.io/auk/reference
+  article: https://cornelllabofornithology.github.io/auk/articles
diff --git a/docs/reference/Rplot001.png b/docs/reference/Rplot001.png
deleted file mode 100644
index 17a358060aed2a86950757bbd25c6f92c08c458f..0000000000000000000000000000000000000000
GIT binary patch
literal 0
HcmV?d00001

literal 1011
zcmeAS@N?(olHy`uVBq!ia0y~yV0-|=9Be?5+AI5}0x7m6Z+90U4Fo@(ch>_c&H|6f
zVg?3oArNM~bhqvg0|WD9PZ!6KiaBo&GBN^{G%5UFpXcEKVvd5*5Eu=C0SJK)8A6*F
U7`aXvEC5;V>FVdQ&MBb@00SN#Z2$lO

diff --git a/docs/reference/auk-package.html b/docs/reference/auk-package.html
index 45fd673..7b0ecf0 100644
--- a/docs/reference/auk-package.html
+++ b/docs/reference/auk-package.html
@@ -1,10 +1,10 @@
 
 auk: eBird Data Extraction and Processing in R — auk-package • auk
-    
+
 
     

       

   

 

 
-      
+
 
       

   

@@ -74,7 +74,7 @@ 
auk: eBird Data Extraction and Processing in R

     
@@ -98,15 +98,15 @@ 
Author

 

 
 

-  
Site built with pkgdown 2.0.9.

+  
Site built with pkgdown 2.1.1.

 

 
       

 
-  
 
 
-  
+
+
 
   
 
diff --git a/docs/reference/auk.html b/docs/reference/auk.html
new file mode 100644
index 0000000..3a10f2a
--- /dev/null
+++ b/docs/reference/auk.html
@@ -0,0 +1,8 @@
+
+  
+    
+    
+    
+  
+
+
diff --git a/docs/reference/auk_bbox.html b/docs/reference/auk_bbox.html
index ca6d55e..a29cb3b 100644
--- a/docs/reference/auk_bbox.html
+++ b/docs/reference/auk_bbox.html
@@ -1,11 +1,11 @@
 
 Filter the eBird data by spatial bounding box — auk_bbox • auk
-    
+
 
     

       

   

 

 
-      
+
 
       

   

@@ -78,12 +78,14 @@ 
Filter the eBird data by spatial bounding box

 
     

     
Arguments

-    
x

+
+
+
x

 
auk_ebd or auk_sampling object; reference to file created by
 auk_ebd() or auk_sampling().

 
 
-
bbox

+
bbox

 
numeric or sf or Raster* object; spatial bounding box
 expressed as the range of latitudes and longitudes in decimal degrees:
 c(lng_min, lat_min, lng_max, lat_max). Note that longitudes in the
@@ -95,9 +97,7 @@ 
Arguments

 

     

     
Value

-    
-
-
An auk_ebd object.

+    
An auk_ebd object.

     

     

     
Details

@@ -106,7 +106,7 @@ 
Details

     

     

     
See also

-    
Other filter: 
+    
Other filter:
 auk_bcr(),
 auk_breeding(),
 auk_complete(),
@@ -135,7 +135,7 @@ 
Examples

   auk_ebd() %>%
   auk_bbox(bbox = c(-125, 37, -120, 52))
 #> Input 
-#>   EBD: /private/var/folders/mg/qh40qmqd7376xn8qxd6hm5lwjyy0h2/T/RtmpBEc62Y/temp_libpath32473f2f276e/auk/extdata/ebd-sample.txt 
+#>   EBD: /private/var/folders/wf/y1p0nztd2ps95ppplsl5bjjr0000gs/T/Rtmp7EtevZ/temp_libpathb97949a13185/auk/extdata/ebd-sample.txt 
 #> 
 #> Output 
 #>   Filters not executed
@@ -163,7 +163,7 @@ 
Examples

 ebd <- auk_ebd(system.file("extdata/ebd-sample.txt", package = "auk"))
 auk_bbox(ebd, bbox = c(-125, 37, -120, 52))
 #> Input 
-#>   EBD: /private/var/folders/mg/qh40qmqd7376xn8qxd6hm5lwjyy0h2/T/RtmpBEc62Y/temp_libpath32473f2f276e/auk/extdata/ebd-sample.txt 
+#>   EBD: /private/var/folders/wf/y1p0nztd2ps95ppplsl5bjjr0000gs/T/Rtmp7EtevZ/temp_libpathb97949a13185/auk/extdata/ebd-sample.txt 
 #> 
 #> Output 
 #>   Filters not executed
@@ -200,15 +200,15 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.0.9.

+  
Site built with pkgdown 2.1.1.

 

 
       

 
-  
 
 
-  
+
+
 
   
 
diff --git a/docs/reference/auk_bcr.html b/docs/reference/auk_bcr.html
index 79a3e8b..d787892 100644
--- a/docs/reference/auk_bcr.html
+++ b/docs/reference/auk_bcr.html
@@ -4,11 +4,11 @@
 BCRs are ecologically distinct regions in North America with similar bird
 communities, habitats, and resource management issues. This function only
 defines the filter and, once all filters have been defined, auk_filter()
-should be used to call AWK and perform the filtering.">
-    
+
 
     

       

   

 

 
-      
+
 
       

   

@@ -84,17 +84,19 @@ 
Filter the eBird data by Bird Conservation Region

 
     

     
Arguments

-    
x

+
+
+
x

 
auk_ebd or auk_sampling object; reference to file created by
 auk_ebd() or auk_sampling().

 
 
-
bcr

+
bcr

 
integer; BCRs to filter by. BCRs are identified by an integer,
 from 1 to 66, that can be looked up in the bcr_codes table.

 
 
-
replace

+
replace

 
logical; multiple calls to auk_bcr() are additive,
 unless replace = FALSE, in which case the previous list of states to
 filter by will be removed and replaced by that in the current call.

@@ -102,9 +104,7 @@ 
Arguments

 

     

     
Value

-    
-
-
An auk_ebd object.

+    
An auk_ebd object.

     

     

     
Details

@@ -113,7 +113,7 @@ 
Details

     

     

     
See also

-    
Other filter: 
+    
Other filter:
 auk_bbox(),
 auk_breeding(),
 auk_complete(),
@@ -147,7 +147,7 @@ 
Examples

   auk_ebd() %>%
   auk_bcr(bcr = 24)
 #> Input 
-#>   EBD: /private/var/folders/mg/qh40qmqd7376xn8qxd6hm5lwjyy0h2/T/RtmpBEc62Y/temp_libpath32473f2f276e/auk/extdata/ebd-sample.txt 
+#>   EBD: /private/var/folders/wf/y1p0nztd2ps95ppplsl5bjjr0000gs/T/Rtmp7EtevZ/temp_libpathb97949a13185/auk/extdata/ebd-sample.txt 
 #> 
 #> Output 
 #>   Filters not executed
@@ -175,7 +175,7 @@ 
Examples

 ebd <- auk_ebd(system.file("extdata/ebd-sample.txt", package = "auk"))
 auk_bcr(ebd, bcr = 24)
 #> Input 
-#>   EBD: /private/var/folders/mg/qh40qmqd7376xn8qxd6hm5lwjyy0h2/T/RtmpBEc62Y/temp_libpath32473f2f276e/auk/extdata/ebd-sample.txt 
+#>   EBD: /private/var/folders/wf/y1p0nztd2ps95ppplsl5bjjr0000gs/T/Rtmp7EtevZ/temp_libpathb97949a13185/auk/extdata/ebd-sample.txt 
 #> 
 #> Output 
 #>   Filters not executed
@@ -212,15 +212,15 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.0.9.

+  
Site built with pkgdown 2.1.1.

 

 
       

 
-  
 
 
-  
+
+
 
   
 
diff --git a/docs/reference/auk_breeding.html b/docs/reference/auk_breeding.html
index 1d7eb12..f7eb906 100644
--- a/docs/reference/auk_breeding.html
+++ b/docs/reference/auk_breeding.html
@@ -3,11 +3,11 @@
 observations, for example, if nesting building behaviour is observed. Use
 this filter to select only those observations with an associated breeding
 code. This function only defines the filter and, once all filters have been
-defined, auk_filter() should be used to call AWK and perform the filtering.">
-    
+
 
     

       

   

 

 
-      
+
 
       

   

@@ -82,20 +82,20 @@ 
Filter to only include observations with breeding codes

 
     

     
Arguments

-    
x

+
+
+
x

 
auk_ebd object; reference to basic dataset file created by
 auk_ebd().

 
 

     

     
Value

-    
-
-
An auk_ebd object.

+    
An auk_ebd object.

     

     

     
See also

-    
Other filter: 
+    
Other filter:
 auk_bbox(),
 auk_bcr(),
 auk_complete(),
@@ -123,7 +123,7 @@ 
Examples

   auk_ebd() %>%
   auk_breeding()
 #> Input 
-#>   EBD: /private/var/folders/mg/qh40qmqd7376xn8qxd6hm5lwjyy0h2/T/RtmpBEc62Y/temp_libpath32473f2f276e/auk/extdata/ebd-sample.txt 
+#>   EBD: /private/var/folders/wf/y1p0nztd2ps95ppplsl5bjjr0000gs/T/Rtmp7EtevZ/temp_libpathb97949a13185/auk/extdata/ebd-sample.txt 
 #> 
 #> Output 
 #>   Filters not executed
@@ -160,15 +160,15 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.0.9.

+  
Site built with pkgdown 2.1.1.

 

 
       

 
-  
 
 
-  
+
+
 
   
 
diff --git a/docs/reference/auk_clean.html b/docs/reference/auk_clean.html
index b5a79c6..854846f 100644
--- a/docs/reference/auk_clean.html
+++ b/docs/reference/auk_clean.html
@@ -1,10 +1,10 @@
 
 Clean an eBird data file (Deprecated) — auk_clean • auk
-    
+
 
     

       

   

 

 
-      
+
 
       

   

@@ -76,23 +76,25 @@ 
Clean an eBird data file (Deprecated)

 
     

     
Arguments

-    
f_in

+
+
+
f_in

 
character; input file. If file is not found as specified, it will
 be looked for in the directory specified by the EBD_PATH environment
 variable.

 
 
-
f_out

+
f_out

 
character; output file.

 
 
-
sep

+
sep

 
character; the input field separator, the basic dataset is tab
 separated by default. Must only be a single character and space delimited
 is not allowed since spaces appear in many of the fields.

 
 
-
remove_text

+
remove_text

 
logical; whether all free text entry columns should be
 removed. These columns include comments, location names, and observer
 names. These columns cause import errors due to special characters and
@@ -101,27 +103,25 @@ 
Arguments

 to a significant reduction in file size.

 
 
-
overwrite

+
overwrite

 
logical; overwrite output file if it already exists.

 
 

     

     
Value

-    
-
-
If AWK ran without errors, the output filename is returned, however,
+    
If AWK ran without errors, the output filename is returned, however,
 if an error was encountered the exit code is returned.

     

     

     
See also

-    
Other text: 
+    
Other text:
 auk_select(),
 auk_split()

     

 
     

     
Examples

-    
if (FALSE) {
+    
if (FALSE) { # \dontrun{
 # get the path to the example data included in the package
 f <- system.file("extdata/ebd-sample.txt", package = "auk")
 # output to a temp file for example
@@ -132,7 +132,7 @@ 
Examples

 # clean file to remove problem rows
 # note: this function is deprecated and no longer does anything
 auk_clean(f, f_out)
-}
+} # }
 

     

   

@@ -147,15 +147,15 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.0.9.

+  
Site built with pkgdown 2.1.1.

 

 
       

 
-  
 
 
-  
+
+
 
   
 
diff --git a/docs/reference/auk_complete.html b/docs/reference/auk_complete.html
index 62c06ff..6049e25 100644
--- a/docs/reference/auk_complete.html
+++ b/docs/reference/auk_complete.html
@@ -4,11 +4,11 @@
 checklists are the most valuable for scientific uses since they provide
 presence and absence data.This function only defines the filter and, once all
 filters have been defined, auk_filter() should be used to call AWK and
-perform the filtering.">
-    
+
 
     

       

   

 

 
-      
+
 
       

   

@@ -84,16 +84,16 @@ 
Filter out incomplete checklists from the eBird data

 
     

     
Arguments

-    
x

+
+
+
x

 
auk_ebd or auk_sampling object; reference to file created by
 auk_ebd() or auk_sampling().

 
 

     

     
Value

-    
-
-
An auk_ebd object.

+    
An auk_ebd object.

     

     

     
Details

@@ -102,7 +102,7 @@ 
Details

     

     

     
See also

-    
Other filter: 
+    
Other filter:
 auk_bbox(),
 auk_bcr(),
 auk_breeding(),
@@ -130,7 +130,7 @@ 
Examples

   auk_ebd() %>%
   auk_complete()
 #> Input 
-#>   EBD: /private/var/folders/mg/qh40qmqd7376xn8qxd6hm5lwjyy0h2/T/RtmpBEc62Y/temp_libpath32473f2f276e/auk/extdata/ebd-sample.txt 
+#>   EBD: /private/var/folders/wf/y1p0nztd2ps95ppplsl5bjjr0000gs/T/Rtmp7EtevZ/temp_libpathb97949a13185/auk/extdata/ebd-sample.txt 
 #> 
 #> Output 
 #>   Filters not executed
@@ -167,15 +167,15 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.0.9.

+  
Site built with pkgdown 2.1.1.

 

 
       

 
-  
 
 
-  
+
+
 
   
 
diff --git a/docs/reference/auk_country.html b/docs/reference/auk_country.html
index 2172810..77b138c 100644
--- a/docs/reference/auk_country.html
+++ b/docs/reference/auk_country.html
@@ -2,11 +2,11 @@
 Filter the eBird data by country — auk_country • auk
-    
+
 
     

       

   

 

 
-      
+
 
       

   

@@ -80,12 +80,14 @@ 
Filter the eBird data by country

 
     

     
Arguments

-    
x

+
+
+
x

 
auk_ebd or auk_sampling object; reference to file created by
 auk_ebd() or auk_sampling().

 
 
-
country

+
country

 
character; countries to filter by. Countries can either be
 expressed as English names or
 ISO 2-letter country codes.
@@ -93,7 +95,7 @@ 
Arguments

 countrycode, so there is some flexibility in names.

 
 
-
replace

+
replace

 
logical; multiple calls to auk_country() are additive,
 unless replace = FALSE, in which case the previous list of countries to
 filter by will be removed and replaced by that in the current call.

@@ -101,9 +103,7 @@ 
Arguments

 

     

     
Value

-    
-
-
An auk_ebd object.

+    
An auk_ebd object.

     

     

     
Details

@@ -112,7 +112,7 @@ 
Details

     

     

     
See also

-    
Other filter: 
+    
Other filter:
 auk_bbox(),
 auk_bcr(),
 auk_breeding(),
@@ -143,7 +143,7 @@ 
Examples

   auk_ebd() %>%
   auk_country(country)
 #> Input 
-#>   EBD: /private/var/folders/mg/qh40qmqd7376xn8qxd6hm5lwjyy0h2/T/RtmpBEc62Y/temp_libpath32473f2f276e/auk/extdata/ebd-sample.txt 
+#>   EBD: /private/var/folders/wf/y1p0nztd2ps95ppplsl5bjjr0000gs/T/Rtmp7EtevZ/temp_libpathb97949a13185/auk/extdata/ebd-sample.txt 
 #> 
 #> Output 
 #>   Filters not executed
@@ -171,7 +171,7 @@ 
Examples

 ebd <- auk_ebd(system.file("extdata/ebd-sample.txt", package = "auk"))
 auk_country(ebd, country)
 #> Input 
-#>   EBD: /private/var/folders/mg/qh40qmqd7376xn8qxd6hm5lwjyy0h2/T/RtmpBEc62Y/temp_libpath32473f2f276e/auk/extdata/ebd-sample.txt 
+#>   EBD: /private/var/folders/wf/y1p0nztd2ps95ppplsl5bjjr0000gs/T/Rtmp7EtevZ/temp_libpathb97949a13185/auk/extdata/ebd-sample.txt 
 #> 
 #> Output 
 #>   Filters not executed
@@ -208,15 +208,15 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.0.9.

+  
Site built with pkgdown 2.1.1.

 

 
       

 
-  
 
 
-  
+
+
 
   
 
diff --git a/docs/reference/auk_county.html b/docs/reference/auk_county.html
index 897d78c..b175e80 100644
--- a/docs/reference/auk_county.html
+++ b/docs/reference/auk_county.html
@@ -2,11 +2,11 @@
 Filter the eBird data by county — auk_county • auk
-    
+
 
     

       

   

 

 
-      
+
 
       

   

@@ -80,12 +80,14 @@ 
Filter the eBird data by county

 
     

     
Arguments

-    
x

+
+
+
x

 
auk_ebd or auk_sampling object; reference to file created by
 auk_ebd() or auk_sampling().

 
 
-
county

+
county

 
character; counties to filter by. eBird uses county codes
 consisting of three parts, the 2-letter ISO country code, a 1-3 character
 state code, and a county code, all separated by a dash. For example,
@@ -93,7 +95,7 @@ 
Arguments

 county code is to find the corresponding explore region page and look at the URL.

 
 
-
replace

+
replace

 
logical; multiple calls to auk_county() are additive,
 unless replace = FALSE, in which case the previous list of states to
 filter by will be removed and replaced by that in the current call.

@@ -101,9 +103,7 @@ 
Arguments

 

     

     
Value

-    
-
-
An auk_ebd object.

+    
An auk_ebd object.

     

     

     
Details

@@ -115,7 +115,7 @@ 
Details

     

     

     
See also

-    
Other filter: 
+    
Other filter:
 auk_bbox(),
 auk_bcr(),
 auk_breeding(),
@@ -144,7 +144,7 @@ 
Examples

   auk_ebd() %>%
   auk_county("US-NY-109")
 #> Input 
-#>   EBD: /private/var/folders/mg/qh40qmqd7376xn8qxd6hm5lwjyy0h2/T/RtmpBEc62Y/temp_libpath32473f2f276e/auk/extdata/ebd-sample.txt 
+#>   EBD: /private/var/folders/wf/y1p0nztd2ps95ppplsl5bjjr0000gs/T/Rtmp7EtevZ/temp_libpathb97949a13185/auk/extdata/ebd-sample.txt 
 #> 
 #> Output 
 #>   Filters not executed
@@ -172,7 +172,7 @@ 
Examples

 ebd <- auk_ebd(system.file("extdata/ebd-sample.txt", package = "auk"))
 auk_county(ebd, "US-NY-109")
 #> Input 
-#>   EBD: /private/var/folders/mg/qh40qmqd7376xn8qxd6hm5lwjyy0h2/T/RtmpBEc62Y/temp_libpath32473f2f276e/auk/extdata/ebd-sample.txt 
+#>   EBD: /private/var/folders/wf/y1p0nztd2ps95ppplsl5bjjr0000gs/T/Rtmp7EtevZ/temp_libpathb97949a13185/auk/extdata/ebd-sample.txt 
 #> 
 #> Output 
 #>   Filters not executed
@@ -209,15 +209,15 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.0.9.

+  
Site built with pkgdown 2.1.1.

 

 
       

 
-  
 
 
-  
+
+
 
   
 
diff --git a/docs/reference/auk_date.html b/docs/reference/auk_date.html
index ab2d075..699a19b 100644
--- a/docs/reference/auk_date.html
+++ b/docs/reference/auk_date.html
@@ -2,11 +2,11 @@
 Filter the eBird data by date — auk_date • auk
-    
+
 
     

       

   

 

 
-      
+
 
       

   

@@ -80,12 +80,14 @@ 
Filter the eBird data by date

 
     

     
Arguments

-    
x

+
+
+
x

 
auk_ebd or auk_sampling object; reference to file created by
 auk_ebd() or auk_sampling().

 
 
-
date

+
date

 
character or date; date range to filter by, provided either as a
 character vector in the format "2015-12-31" or a vector of Date objects.
 To filter on a range of dates, regardless of year, use "*" in place of
@@ -94,9 +96,7 @@ 
Arguments

 

     

     
Value

-    
-
-
An auk_ebd object.

+    
An auk_ebd object.

     

     

     
Details

@@ -109,7 +109,7 @@ 
Details

     

     

     
See also

-    
Other filter: 
+    
Other filter:
 auk_bbox(),
 auk_bcr(),
 auk_breeding(),
@@ -137,7 +137,7 @@ 
Examples

   auk_ebd() %>%
   auk_date(date = c("2010-01-01", "2010-12-31"))
 #> Input 
-#>   EBD: /private/var/folders/mg/qh40qmqd7376xn8qxd6hm5lwjyy0h2/T/RtmpBEc62Y/temp_libpath32473f2f276e/auk/extdata/ebd-sample.txt 
+#>   EBD: /private/var/folders/wf/y1p0nztd2ps95ppplsl5bjjr0000gs/T/Rtmp7EtevZ/temp_libpathb97949a13185/auk/extdata/ebd-sample.txt 
 #> 
 #> Output 
 #>   Filters not executed
@@ -165,7 +165,7 @@ 
Examples

 ebd <- auk_ebd(system.file("extdata/ebd-sample.txt", package = "auk"))
 auk_date(ebd, date = c("2010-01-01", "2010-12-31"))
 #> Input 
-#>   EBD: /private/var/folders/mg/qh40qmqd7376xn8qxd6hm5lwjyy0h2/T/RtmpBEc62Y/temp_libpath32473f2f276e/auk/extdata/ebd-sample.txt 
+#>   EBD: /private/var/folders/wf/y1p0nztd2ps95ppplsl5bjjr0000gs/T/Rtmp7EtevZ/temp_libpathb97949a13185/auk/extdata/ebd-sample.txt 
 #> 
 #> Output 
 #>   Filters not executed
@@ -195,7 +195,7 @@ 
Examples

   # may-june records from all years
   auk_date(date = c("*-05-01", "*-06-30"))
 #> Input 
-#>   EBD: /private/var/folders/mg/qh40qmqd7376xn8qxd6hm5lwjyy0h2/T/RtmpBEc62Y/temp_libpath32473f2f276e/auk/extdata/ebd-sample.txt 
+#>   EBD: /private/var/folders/wf/y1p0nztd2ps95ppplsl5bjjr0000gs/T/Rtmp7EtevZ/temp_libpathb97949a13185/auk/extdata/ebd-sample.txt 
 #> 
 #> Output 
 #>   Filters not executed
@@ -225,7 +225,7 @@ 
Examples

   # dec-jan records from all years
   auk_date(date = c("*-12-01", "*-01-31"))
 #> Input 
-#>   EBD: /private/var/folders/mg/qh40qmqd7376xn8qxd6hm5lwjyy0h2/T/RtmpBEc62Y/temp_libpath32473f2f276e/auk/extdata/ebd-sample.txt 
+#>   EBD: /private/var/folders/wf/y1p0nztd2ps95ppplsl5bjjr0000gs/T/Rtmp7EtevZ/temp_libpathb97949a13185/auk/extdata/ebd-sample.txt 
 #> 
 #> Output 
 #>   Filters not executed
@@ -262,15 +262,15 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.0.9.

+  
Site built with pkgdown 2.1.1.

 

 
       

 
-  
 
 
-  
+
+
 
   
 
diff --git a/docs/reference/auk_distance.html b/docs/reference/auk_distance.html
index 4bbd419..a5984f6 100644
--- a/docs/reference/auk_distance.html
+++ b/docs/reference/auk_distance.html
@@ -5,11 +5,11 @@
 perform the filtering. Note that stationary checklists (i.e. point counts)
 have no distance associated with them, however, since these checklists can
 be assumed to have 0 distance they will be kept if 0 is in the range defined
-by distance.">
-    
+
 
     

       

   

 

 
-      
+
 
       

   

@@ -86,27 +86,27 @@ 
Filter eBird data by distance travelled

 
     

     
Arguments

-    
x

+
+
+
x

 
auk_ebd or auk_sampling object; reference to file created by
 auk_ebd() or auk_sampling().

 
 
-
distance

+
distance

 
integer; 2 element vector specifying the range of distances
 to filter by. The default is to accept distances in kilometers, use
 distance_units = "miles" for miles.

 
 
-
distance_units

+
distance_units

 
character; whether distances are provided in kilometers
 (the default) or miles.

 
 

     

     
Value

-    
-
-
An auk_ebd object.

+    
An auk_ebd object.

     

     

     
Details

@@ -115,7 +115,7 @@ 
Details

     

     

     
See also

-    
Other filter: 
+    
Other filter:
 auk_bbox(),
 auk_bcr(),
 auk_breeding(),
@@ -144,7 +144,7 @@ 
Examples

   auk_ebd() %>%
   auk_distance(distance = c(0, 10))
 #> Input 
-#>   EBD: /private/var/folders/mg/qh40qmqd7376xn8qxd6hm5lwjyy0h2/T/RtmpBEc62Y/temp_libpath32473f2f276e/auk/extdata/ebd-sample.txt 
+#>   EBD: /private/var/folders/wf/y1p0nztd2ps95ppplsl5bjjr0000gs/T/Rtmp7EtevZ/temp_libpathb97949a13185/auk/extdata/ebd-sample.txt 
 #> 
 #> Output 
 #>   Filters not executed
@@ -172,7 +172,7 @@ 
Examples

 ebd <- auk_ebd(system.file("extdata/ebd-sample.txt", package = "auk"))
 auk_distance(ebd, distance = c(0, 10))
 #> Input 
-#>   EBD: /private/var/folders/mg/qh40qmqd7376xn8qxd6hm5lwjyy0h2/T/RtmpBEc62Y/temp_libpath32473f2f276e/auk/extdata/ebd-sample.txt 
+#>   EBD: /private/var/folders/wf/y1p0nztd2ps95ppplsl5bjjr0000gs/T/Rtmp7EtevZ/temp_libpathb97949a13185/auk/extdata/ebd-sample.txt 
 #> 
 #> Output 
 #>   Filters not executed
@@ -209,15 +209,15 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.0.9.

+  
Site built with pkgdown 2.1.1.

 

 
       

 
-  
 
 
-  
+
+
 
   
 
diff --git a/docs/reference/auk_duration.html b/docs/reference/auk_duration.html
index 4a0384b..d9d3338 100644
--- a/docs/reference/auk_duration.html
+++ b/docs/reference/auk_duration.html
@@ -4,11 +4,11 @@
 have been defined, auk_filter() should be used to call AWK and perform the
 filtering. Note that checklists with no effort, such as incidental
 observations, will be excluded if this filter is used since they have no
-associated duration information.">
-    
+
 
     

       

   

 

 
-      
+
 
       

   

@@ -84,21 +84,21 @@ 
Filter the eBird data by duration

 
     

     
Arguments

-    
x

+
+
+
x

 
auk_ebd or auk_sampling object; reference to file created by
 auk_ebd() or auk_sampling().

 
 
-
duration

+
duration

 
integer; 2 element vector specifying the range of durations
 in minutes to filter by.

 
 

     

     
Value

-    
-
-
An auk_ebd object.

+    
An auk_ebd object.

     

     

     
Details

@@ -107,7 +107,7 @@ 
Details

     

     

     
See also

-    
Other filter: 
+    
Other filter:
 auk_bbox(),
 auk_bcr(),
 auk_breeding(),
@@ -136,7 +136,7 @@ 
Examples

   auk_ebd() %>%
   auk_duration(duration = c(0, 60))
 #> Input 
-#>   EBD: /private/var/folders/mg/qh40qmqd7376xn8qxd6hm5lwjyy0h2/T/RtmpBEc62Y/temp_libpath32473f2f276e/auk/extdata/ebd-sample.txt 
+#>   EBD: /private/var/folders/wf/y1p0nztd2ps95ppplsl5bjjr0000gs/T/Rtmp7EtevZ/temp_libpathb97949a13185/auk/extdata/ebd-sample.txt 
 #> 
 #> Output 
 #>   Filters not executed
@@ -164,7 +164,7 @@ 
Examples

 ebd <- auk_ebd(system.file("extdata/ebd-sample.txt", package = "auk"))
 auk_duration(ebd, duration = c(0, 60))
 #> Input 
-#>   EBD: /private/var/folders/mg/qh40qmqd7376xn8qxd6hm5lwjyy0h2/T/RtmpBEc62Y/temp_libpath32473f2f276e/auk/extdata/ebd-sample.txt 
+#>   EBD: /private/var/folders/wf/y1p0nztd2ps95ppplsl5bjjr0000gs/T/Rtmp7EtevZ/temp_libpathb97949a13185/auk/extdata/ebd-sample.txt 
 #> 
 #> Output 
 #>   Filters not executed
@@ -201,15 +201,15 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.0.9.

+  
Site built with pkgdown 2.1.1.

 

 
       

 
-  
 
 
-  
+
+
 
   
 
diff --git a/docs/reference/auk_ebd.html b/docs/reference/auk_ebd.html
index 81204be..364d9ab 100644
--- a/docs/reference/auk_ebd.html
+++ b/docs/reference/auk_ebd.html
@@ -1,10 +1,10 @@
 
 Reference to eBird data file — auk_ebd • auk
-    
+
 
     

       

   

 

 
-      
+
 
       

   

@@ -76,13 +76,15 @@ 
Reference to eBird data file

 
     

     
Arguments

-    
file

+
+
+
file

 
character; input file. If file is not found as specified, it will
 be looked for in the directory specified by the EBD_PATH environment
 variable.

 
 
-
file_sampling

+
file_sampling

 
character; optional input sampling event data (i.e.
 checklists) file, required if you intend to zero-fill the data to produce a
 presence-absence data set. This file consists of just effort information
@@ -93,7 +95,7 @@ 
Arguments

 directory specified by the EBD_PATH environment variable.

 
 
-
sep

+
sep

 
character; the input field separator, the eBird data are tab
 separated so this should generally not be modified. Must only be a single
 character and space delimited is not allowed since spaces appear in many of
@@ -102,9 +104,7 @@ 
Arguments

 

     

     
Value

-    
-
-
An auk_ebd object storing the file reference and the desired
+    
An auk_ebd object storing the file reference and the desired
 filters once created with other package functions.

     

     

@@ -127,7 +127,7 @@ 
Details

     

     

     
See also

-    
Other objects: 
+    
Other objects:
 auk_sampling()

     

 
@@ -138,7 +138,7 @@ 
Examples

 f <- system.file("extdata/ebd-sample.txt", package = "auk")
 auk_ebd(f)
 #> Input 
-#>   EBD: /private/var/folders/mg/qh40qmqd7376xn8qxd6hm5lwjyy0h2/T/RtmpBEc62Y/temp_libpath32473f2f276e/auk/extdata/ebd-sample.txt 
+#>   EBD: /private/var/folders/wf/y1p0nztd2ps95ppplsl5bjjr0000gs/T/Rtmp7EtevZ/temp_libpathb97949a13185/auk/extdata/ebd-sample.txt 
 #> 
 #> Output 
 #>   Filters not executed
@@ -166,8 +166,8 @@ 
Examples

 f_cl <- system.file("extdata/zerofill-ex_sampling.txt", package = "auk")
 auk_ebd(f_ebd, file_sampling = f_cl)
 #> Input 
-#>   EBD: /private/var/folders/mg/qh40qmqd7376xn8qxd6hm5lwjyy0h2/T/RtmpBEc62Y/temp_libpath32473f2f276e/auk/extdata/zerofill-ex_ebd.txt 
-#>   Sampling events: /private/var/folders/mg/qh40qmqd7376xn8qxd6hm5lwjyy0h2/T/RtmpBEc62Y/temp_libpath32473f2f276e/auk/extdata/zerofill-ex_sampling.txt 
+#>   EBD: /private/var/folders/wf/y1p0nztd2ps95ppplsl5bjjr0000gs/T/Rtmp7EtevZ/temp_libpathb97949a13185/auk/extdata/zerofill-ex_ebd.txt 
+#>   Sampling events: /private/var/folders/wf/y1p0nztd2ps95ppplsl5bjjr0000gs/T/Rtmp7EtevZ/temp_libpathb97949a13185/auk/extdata/zerofill-ex_sampling.txt 
 #> 
 #> Output 
 #>   Filters not executed
@@ -204,15 +204,15 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.0.9.

+  
Site built with pkgdown 2.1.1.

 

 
       

 
-  
 
 
-  
+
+
 
   
 
diff --git a/docs/reference/auk_ebd_version.html b/docs/reference/auk_ebd_version.html
index 7a77e20..0fc6a4e 100644
--- a/docs/reference/auk_ebd_version.html
+++ b/docs/reference/auk_ebd_version.html
@@ -2,11 +2,11 @@
 Get the EBD version and associated taxonomy version — auk_ebd_version • auk
-    
+
 
     

       

   

 

 
-      
+
 
       

   

@@ -80,12 +80,14 @@ 
Get the EBD version and associated taxonomy version

 
     

     
Arguments

-    
x

+
+
+
x

 
filename of EBD of sampling event data file, auk_ebd object, or
 auk_sampling object.

 
 
-
check_exists

+
check_exists

 
logical; should the file be checked for existence before
 processing. If check_exists = TRUE and the file does not exists, the
 function will raise an error.

@@ -93,16 +95,14 @@ 
Arguments

 

     

     
Value

-    
-
-
A list with two elements:
  • ebd_version: a date object specifying the release date of the EBD.
    • 
+    
    A list with two elements:
    • ebd_version: a date object specifying the release date of the EBD.
      • 
 
    • taxonomy_version: the year of the taxonomy used in this EBD.
      • 
 
    Both elements will be NA if an EBD version cannot be extracted from the
 filename.
    
     

     

     
See also

-    
Other helpers: 
+    
Other helpers:
 auk_version(),
 ebird_species(),
 get_ebird_taxonomy(),
@@ -132,15 +132,15 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.0.9.

+  
Site built with pkgdown 2.1.1.

 

 
       

 
-  
 
 
-  
+
+
 
   
 
diff --git a/docs/reference/auk_exotic.html b/docs/reference/auk_exotic.html
index 4dfffce..5d2403a 100644
--- a/docs/reference/auk_exotic.html
+++ b/docs/reference/auk_exotic.html
@@ -5,11 +5,11 @@
 codes: "" (i.e. no code, meaning it is a native species), "N" (naturalized),
 "P" (provisional), or "X" (escapee). This function only defines the filter
 and, once all filters have been defined, auk_filter() should be used to
-call AWK and perform the filtering.'>
-    
+
 
     

       

   

 

 
-      
+
 
       

   

@@ -86,17 +86,19 @@ 
Filter the eBird data by exotic code

 
     

     
Arguments

-    
x

+
+
+
x

 
auk_ebd or auk_sampling object; reference to file created by
 auk_ebd() or auk_sampling().

 
 
-
exotic_code

+
exotic_code

 
characterr; exotic codes to filter by. Note that an empty
 string (""), meaning no exotic code, is used for native species.

 
 
-
replace

+
replace

 
logical; multiple calls to auk_exotic() are additive,
 unless replace = FALSE, in which case the previous list of states to
 filter by will be removed and replaced by that in the current call.

@@ -104,13 +106,11 @@ 
Arguments

 

     

     
Value

-    
-
-
An auk_ebd object.

+    
An auk_ebd object.

     

     

     
See also

-    
Other filter: 
+    
Other filter:
 auk_bbox(),
 auk_bcr(),
 auk_breeding(),
@@ -138,7 +138,7 @@ 
Examples

 ebd <- auk_ebd(system.file("extdata/ebd-sample.txt", package = "auk"))
 auk_exotic(ebd, exotic_code = "")
 #> Input 
-#>   EBD: /private/var/folders/mg/qh40qmqd7376xn8qxd6hm5lwjyy0h2/T/RtmpBEc62Y/temp_libpath32473f2f276e/auk/extdata/ebd-sample.txt 
+#>   EBD: /private/var/folders/wf/y1p0nztd2ps95ppplsl5bjjr0000gs/T/Rtmp7EtevZ/temp_libpathb97949a13185/auk/extdata/ebd-sample.txt 
 #> 
 #> Output 
 #>   Filters not executed
@@ -165,7 +165,7 @@ 
Examples

 # filter to native and naturalized observations
 auk_exotic(ebd, exotic_code = c("", "N"))
 #> Input 
-#>   EBD: /private/var/folders/mg/qh40qmqd7376xn8qxd6hm5lwjyy0h2/T/RtmpBEc62Y/temp_libpath32473f2f276e/auk/extdata/ebd-sample.txt 
+#>   EBD: /private/var/folders/wf/y1p0nztd2ps95ppplsl5bjjr0000gs/T/Rtmp7EtevZ/temp_libpathb97949a13185/auk/extdata/ebd-sample.txt 
 #> 
 #> Output 
 #>   Filters not executed
@@ -202,15 +202,15 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.0.9.

+  
Site built with pkgdown 2.1.1.

 

 
       

 
-  
 
 
-  
+
+
 
   
 
diff --git a/docs/reference/auk_extent.html b/docs/reference/auk_extent.html
index 390a402..400b310 100644
--- a/docs/reference/auk_extent.html
+++ b/docs/reference/auk_extent.html
@@ -1,9 +1,9 @@
 
-Filter the eBird data by spatial extent — auk_extent • aukFilter the eBird data by spatial extent — auk_extent • auk
-    
+
 
     

       

   

 

 
-      
+
 
       

   

@@ -74,12 +74,14 @@ 
Filter the eBird data by spatial extent

 
     

     
Arguments

-    
x

+
+
+
x

 
auk_ebd or auk_sampling object; reference to file created by
 auk_ebd() or auk_sampling().

 
 
-
extent

+
extent

 
numeric; spatial extent expressed as the range of latitudes and
 longitudes in decimal degrees: c(lng_min, lat_min, lng_max, lat_max).
 Note that longitudes in the Western Hemisphere and latitudes sound of the
@@ -88,13 +90,11 @@ 
Arguments

 

     

     
Value

-    
-
-
An auk_ebd object.

+    
An auk_ebd object.

     

     

     
See also

-    
Other filter: 
+    
Other filter:
 auk_bbox(),
 auk_bcr(),
 auk_breeding(),
@@ -123,7 +123,7 @@ 
Examples

   auk_ebd() %>%
   auk_bbox(bbox = c(-125, 37, -120, 52))
 #> Input 
-#>   EBD: /private/var/folders/mg/qh40qmqd7376xn8qxd6hm5lwjyy0h2/T/RtmpBEc62Y/temp_libpath32473f2f276e/auk/extdata/ebd-sample.txt 
+#>   EBD: /private/var/folders/wf/y1p0nztd2ps95ppplsl5bjjr0000gs/T/Rtmp7EtevZ/temp_libpathb97949a13185/auk/extdata/ebd-sample.txt 
 #> 
 #> Output 
 #>   Filters not executed
@@ -151,7 +151,7 @@ 
Examples

 ebd <- auk_ebd(system.file("extdata/ebd-sample.txt", package = "auk"))
 auk_bbox(ebd, bbox = c(-125, 37, -120, 52))
 #> Input 
-#>   EBD: /private/var/folders/mg/qh40qmqd7376xn8qxd6hm5lwjyy0h2/T/RtmpBEc62Y/temp_libpath32473f2f276e/auk/extdata/ebd-sample.txt 
+#>   EBD: /private/var/folders/wf/y1p0nztd2ps95ppplsl5bjjr0000gs/T/Rtmp7EtevZ/temp_libpathb97949a13185/auk/extdata/ebd-sample.txt 
 #> 
 #> Output 
 #>   Filters not executed
@@ -188,15 +188,15 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.0.9.

+  
Site built with pkgdown 2.1.1.

 

 
       

 
-  
 
 
-  
+
+
 
   
 
diff --git a/docs/reference/auk_filter.auk_ebd.html b/docs/reference/auk_filter.auk_ebd.html
new file mode 100644
index 0000000..03340f0
--- /dev/null
+++ b/docs/reference/auk_filter.auk_ebd.html
@@ -0,0 +1,8 @@
+
+  
+    
+    
+    
+  
+
+
diff --git a/docs/reference/auk_filter.auk_sampling.html b/docs/reference/auk_filter.auk_sampling.html
new file mode 100644
index 0000000..03340f0
--- /dev/null
+++ b/docs/reference/auk_filter.auk_sampling.html
@@ -0,0 +1,8 @@
+
+  
+    
+    
+    
+  
+
+
diff --git a/docs/reference/auk_filter.html b/docs/reference/auk_filter.html
index 5bbf1c6..f138993 100644
--- a/docs/reference/auk_filter.html
+++ b/docs/reference/auk_filter.html
@@ -4,11 +4,11 @@
 creation of the auk_ebd object should be done with auk_ebd() and filters
 can be defined using the various other functions in this package, e.g.
 auk_species() or auk_country(). Note that this function typically takes
-at least a couple hours to run on the full dataset">
-    
+
 
     

       

   

 

 
-      
+
 
       

   

@@ -81,7 +81,7 @@ 
Filter the eBird file using AWK

     

     
auk_filter(x, file, ...)
 
-# S3 method for auk_ebd
+# S3 method for class 'auk_ebd'
 auk_filter(
   x,
   file,
@@ -96,7 +96,7 @@ 
Filter the eBird file using AWK

   ...
 )
 
-# S3 method for auk_sampling
+# S3 method for class 'auk_sampling'
 auk_filter(
   x,
   file,
@@ -112,24 +112,26 @@ 
Filter the eBird file using AWK

 
     

     
Arguments

-    
x

+
+
+
x

 
auk_ebd or auk_sampling object; reference to file created by
 auk_ebd() or auk_sampling().

 
 
-
file

+
file

 
character; output file.

 
 
-
...

+
...

 
arguments passed on to methods.

 
 
-
file_sampling

+
file_sampling

 
character; optional output file for sampling data.

 
 
-
keep

+
keep

 
character; a character vector specifying the names of the columns
 to keep in the output file. Columns should be as they appear in the header
 of the EBD; however, names are not case sensitive and spaces may be
@@ -137,41 +139,39 @@ 
Arguments

 "common_NAME" are all valid.

 
 
-
drop

+
drop

 
character; a character vector of columns to drop in the same
 format as keep. Ignored if keep is supplied.

 
 
-
awk_file

+
awk_file

 
character; output file to optionally save the awk script to.

 
 
-
sep

+
sep

 
character; the input field separator, the eBird file is tab
 separated by default. Must only be a single character and space delimited
 is not allowed since spaces appear in many of the fields.

 
 
-
filter_sampling

+
filter_sampling

 
logical; whether the sampling event data should also
 be filtered.

 
 
-
execute

+
execute

 
logical; whether to execute the awk script, or output it to a
 file for manual execution. If this flag is FALSE, awk_file must be
 provided.

 
 
-
overwrite

+
overwrite

 
logical; overwrite output file if it already exists

 
 

     

     
Value

-    
-
-
An auk_ebd object with the output files set. If execute = FALSE,
+    
An auk_ebd object with the output files set. If execute = FALSE,
 then the path to the AWK script is returned instead.

     

     

@@ -191,13 +191,13 @@ 
Details

     

     

     
Methods (by class)

-    
+
 
  • auk_filter(auk_ebd): auk_ebd object
    • 
 
  • auk_filter(auk_sampling): auk_sampling object
    • 
 

     

     
See also

-    
Other filter: 
+    
Other filter:
 auk_bbox(),
 auk_bcr(),
 auk_breeding(),
@@ -245,14 +245,14 @@ 
Examples

 filters <- auk_complete(filters)
 
 # apply filters
-if (FALSE) {
+if (FALSE) { # \dontrun{
 # output to a temp file for example
 # in practice, provide path to output file
 # e.g. f_out <- "output/ebd_filtered.txt"
 f_out <- tempfile()
 filtered <- auk_filter(filters, file = f_out)
 str(read_ebd(filtered))
-}
+} # }
 

     

   

@@ -267,15 +267,15 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.0.9.

+  
Site built with pkgdown 2.1.1.

 

 
       

 
-  
 
 
-  
+
+
 
   
 
diff --git a/docs/reference/auk_get_awk_path.html b/docs/reference/auk_get_awk_path.html
index fb2a463..cdf58de 100644
--- a/docs/reference/auk_get_awk_path.html
+++ b/docs/reference/auk_get_awk_path.html
@@ -3,11 +3,11 @@
 "/usr/bin/awk"), or highlights if it's not installed. To manually set the
 path to AWK, set the AWK_PATH environment variable in your .Renviron
 file, which can be accomplished with the helper function
-auk_set_awk_path(path).">
-    
+
 
     

       

   

 

 
-      
+
 
       

   

@@ -82,13 +82,11 @@ 
OS specific path to AWK executable

 
     

     
Value

-    
-
-
Path to AWK or NA if AWK wasn't found.

+    
Path to AWK or NA if AWK wasn't found.

     

     

     
See also

-    
Other paths: 
+    
Other paths:
 auk_get_ebd_path(),
 auk_set_awk_path(),
 auk_set_ebd_path()

@@ -112,15 +110,15 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.0.9.

+  
Site built with pkgdown 2.1.1.

 

 
       

 
-  
 
 
-  
+
+
 
   
 
diff --git a/docs/reference/auk_get_ebd_path.html b/docs/reference/auk_get_ebd_path.html
index 2d277ba..7227673 100644
--- a/docs/reference/auk_get_ebd_path.html
+++ b/docs/reference/auk_get_ebd_path.html
@@ -1,10 +1,10 @@
 
 Return EBD data path — auk_get_ebd_path • auk
-    
+
 
     

       

   

 

 
-      
+
 
       

   

@@ -76,13 +76,11 @@ 
Return EBD data path

 
     

     
Value

-    
-
-
The path stored in the EBD_PATH environment variable.

+    
The path stored in the EBD_PATH environment variable.

     

     

     
See also

-    
Other paths: 
+    
Other paths:
 auk_get_awk_path(),
 auk_set_awk_path(),
 auk_set_ebd_path()

@@ -91,7 +89,7 @@ 
See also

     

     
Examples

     
auk_get_ebd_path()
-#> [1] "/Users/mes335/data/ebird"
+#> [1] NA
 

     

   

@@ -106,15 +104,15 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.0.9.

+  
Site built with pkgdown 2.1.1.

 

 
       

 
-  
 
 
-  
+
+
 
   
 
diff --git a/docs/reference/auk_last_edited.html b/docs/reference/auk_last_edited.html
index 7cba489..0717f28 100644
--- a/docs/reference/auk_last_edited.html
+++ b/docs/reference/auk_last_edited.html
@@ -3,11 +3,11 @@
 edited dates. Last edited date is typically used to extract just new or
 recently edited data. This function only defines the filter and, once all
 filters have been defined, auk_filter() should be used to call AWK and
-perform the filtering.">
-    
+
 
     

       

   

 

 
-      
+
 
       

   

@@ -82,21 +82,21 @@ 
Filter the eBird data by last edited date

 
     

     
Arguments

-    
x

+
+
+
x

 
auk_ebd or auk_sampling object; reference to file created by
 auk_ebd() or auk_sampling().

 
 
-
date

+
date

 
character or date; date range to filter by, provided either as a
 character vector in the format "2015-12-31" or a vector of Date objects.

 
 

     

     
Value

-    
-
-
An auk_ebd object.

+    
An auk_ebd object.

     

     

     
Details

@@ -105,7 +105,7 @@ 
Details

     

     

     
See also

-    
Other filter: 
+    
Other filter:
 auk_bbox(),
 auk_bcr(),
 auk_breeding(),
@@ -133,7 +133,7 @@ 
Examples

   auk_ebd() %>%
   auk_last_edited(date = c("2010-01-01", "2010-12-31"))
 #> Input 
-#>   EBD: /private/var/folders/mg/qh40qmqd7376xn8qxd6hm5lwjyy0h2/T/RtmpBEc62Y/temp_libpath32473f2f276e/auk/extdata/ebd-sample.txt 
+#>   EBD: /private/var/folders/wf/y1p0nztd2ps95ppplsl5bjjr0000gs/T/Rtmp7EtevZ/temp_libpathb97949a13185/auk/extdata/ebd-sample.txt 
 #> 
 #> Output 
 #>   Filters not executed
@@ -170,15 +170,15 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.0.9.

+  
Site built with pkgdown 2.1.1.

 

 
       

 
-  
 
 
-  
+
+
 
   
 
diff --git a/docs/reference/auk_observer.html b/docs/reference/auk_observer.html
index 9d34c86..9d12c3b 100644
--- a/docs/reference/auk_observer.html
+++ b/docs/reference/auk_observer.html
@@ -2,11 +2,11 @@
 Filter the eBird data by observer — auk_observer • auk
-    
+
 
     

       

   

 

 
-      
+
 
       

   

@@ -80,12 +80,14 @@ 
Filter the eBird data by observer

 
     

     
Arguments

-    
x

+
+
+
x

 
auk_ebd or auk_sampling object; reference to file created by
 auk_ebd() or auk_sampling().

 
 
-
observer_id

+
observer_id

 
character or integer; observers to filter by. Observer IDs
 can be provided either as integer (e.g. 12345) or character with the "obsr"
 prefix as they appear in the EBD (e.g. "obsr12345").

@@ -93,13 +95,11 @@ 
Arguments

 

     

     
Value

-    
-
-
An auk_ebd or `auk_sampling`` object.

+    
An auk_ebd or `auk_sampling“ object.

     

     

     
See also

-    
Other filter: 
+    
Other filter:
 auk_bbox(),
 auk_bcr(),
 auk_breeding(),
@@ -127,7 +127,7 @@ 
Examples

   auk_ebd() %>%
   auk_observer("obsr313215")
 #> Input 
-#>   EBD: /private/var/folders/mg/qh40qmqd7376xn8qxd6hm5lwjyy0h2/T/RtmpBEc62Y/temp_libpath32473f2f276e/auk/extdata/ebd-sample.txt 
+#>   EBD: /private/var/folders/wf/y1p0nztd2ps95ppplsl5bjjr0000gs/T/Rtmp7EtevZ/temp_libpathb97949a13185/auk/extdata/ebd-sample.txt 
 #> 
 #> Output 
 #>   Filters not executed
@@ -155,7 +155,7 @@ 
Examples

 ebd <- auk_ebd(system.file("extdata/ebd-sample.txt", package = "auk"))
 auk_observer(ebd, observer = 313215)
 #> Input 
-#>   EBD: /private/var/folders/mg/qh40qmqd7376xn8qxd6hm5lwjyy0h2/T/RtmpBEc62Y/temp_libpath32473f2f276e/auk/extdata/ebd-sample.txt 
+#>   EBD: /private/var/folders/wf/y1p0nztd2ps95ppplsl5bjjr0000gs/T/Rtmp7EtevZ/temp_libpathb97949a13185/auk/extdata/ebd-sample.txt 
 #> 
 #> Output 
 #>   Filters not executed
@@ -192,15 +192,15 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.0.9.

+  
Site built with pkgdown 2.1.1.

 

 
       

 
-  
 
 
-  
+
+
 
   
 
diff --git a/docs/reference/auk_project.html b/docs/reference/auk_project.html
index 9ae1ae5..c934eff 100644
--- a/docs/reference/auk_project.html
+++ b/docs/reference/auk_project.html
@@ -3,11 +3,11 @@
 Virginia Breeding Bird Survey) and have an associated project code in the
 eBird dataset (e.g. EBIRD_ATL_VA). This function only defines the filter and,
 once all filters have been defined, auk_filter() should be used to call AWK
-and perform the filtering.">
-    
+
 
     

       

   

 

 
-      
+
 
       

   

@@ -82,21 +82,21 @@ 
Filter the eBird data by project code

 
     

     
Arguments

-    
x

+
+
+
x

 
auk_ebd or auk_sampling object; reference to file created by
 auk_ebd() or auk_sampling().

 
 
-
project

+
project

 
character; project code to filter by (e.g. "EBIRD_MEX").
 Multiple codes are accepted.

 
 

     

     
Value

-    
-
-
An auk_ebd object.

+    
An auk_ebd object.

     

     

     
Details

@@ -105,7 +105,7 @@ 
Details

     

     

     
See also

-    
Other filter: 
+    
Other filter:
 auk_bbox(),
 auk_bcr(),
 auk_breeding(),
@@ -133,7 +133,7 @@ 
Examples

   auk_ebd() %>%
   auk_project("EBIRD_MEX")
 #> Input 
-#>   EBD: /private/var/folders/mg/qh40qmqd7376xn8qxd6hm5lwjyy0h2/T/RtmpBEc62Y/temp_libpath32473f2f276e/auk/extdata/ebd-sample.txt 
+#>   EBD: /private/var/folders/wf/y1p0nztd2ps95ppplsl5bjjr0000gs/T/Rtmp7EtevZ/temp_libpathb97949a13185/auk/extdata/ebd-sample.txt 
 #> 
 #> Output 
 #>   Filters not executed
@@ -161,7 +161,7 @@ 
Examples

 ebd <- auk_ebd(system.file("extdata/ebd-sample.txt", package = "auk"))
 auk_project(ebd, "EBIRD_MEX")
 #> Input 
-#>   EBD: /private/var/folders/mg/qh40qmqd7376xn8qxd6hm5lwjyy0h2/T/RtmpBEc62Y/temp_libpath32473f2f276e/auk/extdata/ebd-sample.txt 
+#>   EBD: /private/var/folders/wf/y1p0nztd2ps95ppplsl5bjjr0000gs/T/Rtmp7EtevZ/temp_libpathb97949a13185/auk/extdata/ebd-sample.txt 
 #> 
 #> Output 
 #>   Filters not executed
@@ -198,15 +198,15 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.0.9.

+  
Site built with pkgdown 2.1.1.

 

 
       

 
-  
 
 
-  
+
+
 
   
 
diff --git a/docs/reference/auk_protocol.html b/docs/reference/auk_protocol.html
index 808f97e..1ebce96 100644
--- a/docs/reference/auk_protocol.html
+++ b/docs/reference/auk_protocol.html
@@ -2,11 +2,11 @@
 Filter the eBird data by protocol — auk_protocol • auk
-    
+
 
     

       

   

 

 
-      
+
 
       

   

@@ -80,12 +80,14 @@ 
Filter the eBird data by protocol

 
     

     
Arguments

-    
x

+
+
+
x

 
auk_ebd or auk_sampling object; reference to file created by
 auk_ebd() or auk_sampling().

 
 
-
protocol

+
protocol

 
character. Many protocols exist in the database, however, the
 most commonly used are:
  • Stationary
    • 
 
  • Traveling
    • 
@@ -98,9 +100,7 @@ 
    Arguments
    
 

     

     
Value

-    
-
-
An auk_ebd object.

+    
An auk_ebd object.

     

     

     
Details

@@ -109,7 +109,7 @@ 
Details

     

     

     
See also

-    
Other filter: 
+    
Other filter:
 auk_bbox(),
 auk_bcr(),
 auk_breeding(),
@@ -137,7 +137,7 @@ 
Examples

   auk_ebd() %>%
   auk_protocol("Stationary")
 #> Input 
-#>   EBD: /private/var/folders/mg/qh40qmqd7376xn8qxd6hm5lwjyy0h2/T/RtmpBEc62Y/temp_libpath32473f2f276e/auk/extdata/ebd-sample.txt 
+#>   EBD: /private/var/folders/wf/y1p0nztd2ps95ppplsl5bjjr0000gs/T/Rtmp7EtevZ/temp_libpathb97949a13185/auk/extdata/ebd-sample.txt 
 #> 
 #> Output 
 #>   Filters not executed
@@ -165,7 +165,7 @@ 
Examples

 ebd <- auk_ebd(system.file("extdata/ebd-sample.txt", package = "auk"))
 auk_protocol(ebd, "Stationary")
 #> Input 
-#>   EBD: /private/var/folders/mg/qh40qmqd7376xn8qxd6hm5lwjyy0h2/T/RtmpBEc62Y/temp_libpath32473f2f276e/auk/extdata/ebd-sample.txt 
+#>   EBD: /private/var/folders/wf/y1p0nztd2ps95ppplsl5bjjr0000gs/T/Rtmp7EtevZ/temp_libpathb97949a13185/auk/extdata/ebd-sample.txt 
 #> 
 #> Output 
 #>   Filters not executed
@@ -202,15 +202,15 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.0.9.

+  
Site built with pkgdown 2.1.1.

 

 
       

 
-  
 
 
-  
+
+
 
   
 
diff --git a/docs/reference/auk_rollup.html b/docs/reference/auk_rollup.html
index 6c80ecf..33df3f4 100644
--- a/docs/reference/auk_rollup.html
+++ b/docs/reference/auk_rollup.html
@@ -7,11 +7,11 @@
 up to the species level. In the resulting EBD data.frame,
 category will be "species" for all records and the subspecies fields will
 be dropped. By default, read_ebd() calls ebd_rollup() when importing an
-eBird data file.'>
-    
+
 
     

       

   

 

 
-      
+
 
       

   

@@ -90,27 +90,27 @@ 
Roll up eBird taxonomy to species

 
     

     
Arguments

-    
x

+
+
+
x

 
data.frame; data frame of eBird data, typically as imported by
 read_ebd()

 
 
-
taxonomy_version

+
taxonomy_version

 
integer; the version (i.e. year) of the taxonomy. In
 most cases, this should be left empty to use the version of the taxonomy
 included in the package. See get_ebird_taxonomy().

 
 
-
drop_higher

+
drop_higher

 
logical; whether to remove taxa above species during the
 rollup process, e.g. "spuhs" like "duck sp.".

 
 

     

     
Value

-    
-
-
A data frame of the eBird data with taxonomic rollup applied.

+    
A data frame of the eBird data with taxonomic rollup applied.

     

     

     
Details

@@ -133,7 +133,7 @@ 
Details

 (Red-tailed Hawk (Northern), Upland Goose (Bar-breasted)). If the checklist
 contains multiple taxa corresponding to the same species, the lower level
 taxa are rolled up, otherwise these records are left as is.

-
  • Spuh:  Genus or identification at broad level -- e.g., duck sp.,
+
  • Spuh:  Genus or identification at broad level – e.g., duck sp.,
 dabbling duck sp.. Dropped by auk_rollup().
    • 
 
  • Slash: Identification to Species-pair e.g., American Black
 Duck/Mallard). Dropped by auk_rollup().
    • 
@@ -156,7 +156,7 @@ 
    References
    
     
    
     
    
     
    See also
    
-    
    Other pre: 
+    
    Other pre:
 auk_unique()
    
     
    
 
@@ -226,15 +226,15 @@ 
    Examples
    
 
    
 
 
    
-  
    Site built with pkgdown 2.0.9.
    
+  
    Site built with pkgdown 2.1.1.
    
 
    
 
       
    
 
-  
 
 
-  
+
+
 
   
 
diff --git a/docs/reference/auk_sampling.html b/docs/reference/auk_sampling.html
index 1a88a0c..1eb797c 100644
--- a/docs/reference/auk_sampling.html
+++ b/docs/reference/auk_sampling.html
@@ -2,11 +2,11 @@
 Reference to eBird sampling event file — auk_sampling • auk
-    
+
 
     
    
       
    
   
    
 
    
 
-      
+
 
       
    
   
    
@@ -80,12 +80,14 @@ 
    Reference to eBird sampling event file
    
 
     
    
     
    Arguments
    
-    
    file
    
+
+
+
    file
    
 
    character; input sampling event data file, which contains
 checklist data from eBird.
    
 
 
-
    sep
    
+
    sep
    
 
    character; the input field separator, the eBird data are tab
 separated so this should generally not be modified. Must only be a single
 character and space delimited is not allowed since spaces appear in many of
@@ -94,9 +96,7 @@ 
    Arguments
    
 
    
     
    
     
    Value
    
-    
-
-
    An auk_sampling object storing the file reference and the desired
+    
    An auk_sampling object storing the file reference and the desired
 filters once created with other package functions.
    
     
    
     
    
@@ -110,7 +110,7 @@ 
    Details
    
     
    
     
    
     
    See also
    
-    
    Other objects: 
+    
    Other objects:
 auk_ebd()
    
     
    
 
@@ -122,7 +122,7 @@ 
    Examples
    
 f <- system.file("extdata/zerofill-ex_sampling.txt", package = "auk")
 auk_sampling(f)
 #> Input 
-#>   Sampling events: /private/var/folders/mg/qh40qmqd7376xn8qxd6hm5lwjyy0h2/T/RtmpBEc62Y/temp_libpath32473f2f276e/auk/extdata/zerofill-ex_sampling.txt 
+#>   Sampling events: /private/var/folders/wf/y1p0nztd2ps95ppplsl5bjjr0000gs/T/Rtmp7EtevZ/temp_libpathb97949a13185/auk/extdata/zerofill-ex_sampling.txt 
 #> 
 #> Output 
 #>   Filters not executed
@@ -155,15 +155,15 @@ 
    Examples
    
 
    
 
 
    
-  
    Site built with pkgdown 2.0.9.
    
+  
    Site built with pkgdown 2.1.1.
    
 
    
 
       
    
 
-  
 
 
-  
+
+
 
   
 
diff --git a/docs/reference/auk_select.html b/docs/reference/auk_select.html
index 245f89a..03edab1 100644
--- a/docs/reference/auk_select.html
+++ b/docs/reference/auk_select.html
@@ -1,10 +1,10 @@
 
 Select a subset of columns — auk_select • auk
-    
+
 
     
    
       
    
   
    
 
    
 
-      
+
 
       
    
   
    
@@ -76,12 +76,14 @@ 
    Select a subset of columns
    
 
     
    
     
    Arguments
    
-    
    x
    
+
+
+
    x
    
 
    auk_ebd or auk_sampling object; reference to file created by
 auk_ebd() or auk_sampling().
    
 
 
-
    select
    
+
    select
    
 
    character; a character vector specifying the names of the
 columns to select. Columns should be as they appear in the header of the
 EBD; however, names are not case sensitive and spaces may be replaced by
@@ -89,36 +91,34 @@ 
    Arguments
    
 all valid.
    
 
 
-
    file
    
+
    file
    
 
    character; output file.
    
 
 
-
    sep
    
+
    sep
    
 
    character; the input field separator, the eBird file is tab
 separated by default. Must only be a single character and space delimited
 is not allowed since spaces appear in many of the fields.
    
 
 
-
    overwrite
    
+
    overwrite
    
 
    logical; overwrite output file if it already exists
    
 
 
    
     
    
     
    Value
    
-    
-
-
    Invisibly returns the filename of the output file.
    
+    
    Invisibly returns the filename of the output file.
    
     
    
     
    
     
    See also
    
-    
    Other text: 
+    
    Other text:
 auk_clean(),
 auk_split()
    
     
    
 
     
    
     
    Examples
    
-    
    if (FALSE) {
+    
    if (FALSE) { # \dontrun{
 # select a minimal set of columns
 out_file <- tempfile()
 ebd <- auk_ebd(system.file("extdata/ebd-sample.txt", package = "auk"))
@@ -128,7 +128,7 @@ 
    Examples
    
           "observer_id")
 selected <- auk_select(ebd, select = cols, file = out_file)
 str(read_ebd(selected))
-}
+} # }
 
    
     
    
   
    
@@ -143,15 +143,15 @@ 
    Examples
    
 
    
 
 
    
-  
    Site built with pkgdown 2.0.9.
    
+  
    Site built with pkgdown 2.1.1.
    
 
    
 
       
    
 
-  
 
 
-  
+
+
 
   
 
diff --git a/docs/reference/auk_set_awk_path.html b/docs/reference/auk_set_awk_path.html
index 3f0bf32..a976861 100644
--- a/docs/reference/auk_set_awk_path.html
+++ b/docs/reference/auk_set_awk_path.html
@@ -5,11 +5,11 @@
 should NOT set AWK_PATH, only do so if you have installed AWK in
 non-standard location and auk cannot find it. This function first looks
 for for an .Renviron location defined by R_ENVIRON_USER, then defaults to
-~/.Renviron.">
-    
+
 
     
    
       
    
   
    
 
    
 
-      
+
 
       
    
   
    
@@ -86,26 +86,26 @@ 
    Set a custom path to AWK executable
    
 
     
    
     
    Arguments
    
-    
    path
    
+
+
+
    path
    
 
    character; path to the AWK executable on your system, e.g.
 "C:/cygwin64/bin/gawk.exe" or "/usr/bin/awk".
    
 
 
-
    overwrite
    
+
    overwrite
    
 
    logical; should the existing AWK_PATH be overwritten if it
 has already been set in .Renviron.
    
 
 
    
     
    
     
    Value
    
-    
-
-
    Edits .Renviron, sets AWK_PATH for the current session, then
+    
    Edits .Renviron, sets AWK_PATH for the current session, then
 returns the EBD path invisibly.
    
     
    
     
    
     
    See also
    
-    
    Other paths: 
+    
    Other paths:
 auk_get_awk_path(),
 auk_get_ebd_path(),
 auk_set_ebd_path()
    
@@ -113,9 +113,9 @@ 
    See also
    
 
     
    
     
    Examples
    
-    
    if (FALSE) {
+    
    if (FALSE) { # \dontrun{
 auk_set_awk_path("/usr/bin/awk")
-}
+} # }
 
    
     
    
   
    
@@ -130,15 +130,15 @@ 
    Examples
    
 
    
 
 
    
-  
    Site built with pkgdown 2.0.9.
    
+  
    Site built with pkgdown 2.1.1.
    
 
    
 
       
    
 
-  
 
 
-  
+
+
 
   
 
diff --git a/docs/reference/auk_set_ebd_path.html b/docs/reference/auk_set_ebd_path.html
index 6f52bb5..51c6103 100644
--- a/docs/reference/auk_set_ebd_path.html
+++ b/docs/reference/auk_set_ebd_path.html
@@ -6,11 +6,11 @@
 path every time. This will increase the portability of your code. Use this
 function to set EBD_PATH in your .Renviron file; it is also possible to
 manually edit the file. This function first looks for for an .Renviron
-location defined by R_ENVIRON_USER, then defaults to ~/.Renviron.">
-    
+
 
     
    
       
    
   
    
 
    
 
-      
+
 
       
    
   
    
@@ -88,26 +88,26 @@ 
    Set the path to EBD text files
    
 
     
    
     
    Arguments
    
-    
    path
    
+
+
+
    path
    
 
    character; directory where the EBD text files are stored, e.g.
 "/home/matt/ebd".
    
 
 
-
    overwrite
    
+
    overwrite
    
 
    logical; should the existing EBD_PATH be overwritten if it
 has already been set in .Renviron.
    
 
 
    
     
    
     
    Value
    
-    
-
-
    Edits .Renviron, sets EBD_PATH for the current session, then
+    
    Edits .Renviron, sets EBD_PATH for the current session, then
 returns the EBD path invisibly.
    
     
    
     
    
     
    See also
    
-    
    Other paths: 
+    
    Other paths:
 auk_get_awk_path(),
 auk_get_ebd_path(),
 auk_set_awk_path()
    
@@ -115,9 +115,9 @@ 
    See also
    
 
     
    
     
    Examples
    
-    
    if (FALSE) {
+    
    if (FALSE) { # \dontrun{
 auk_set_ebd_path("/home/matt/ebd")
-}
+} # }
 
    
     
    
   
    
@@ -132,15 +132,15 @@ 
    Examples
    
 
    
 
 
    
-  
    Site built with pkgdown 2.0.9.
    
+  
    Site built with pkgdown 2.1.1.
    
 
    
 
       
    
 
-  
 
 
-  
+
+
 
   
 
diff --git a/docs/reference/auk_species.html b/docs/reference/auk_species.html
index 92ed826..264abe0 100644
--- a/docs/reference/auk_species.html
+++ b/docs/reference/auk_species.html
@@ -1,11 +1,11 @@
 
 Filter the eBird data by species — auk_species • auk
-    
+
 
     
    
       
    
   
    
 
    
 
-      
+
 
       
    
   
    
@@ -78,23 +78,25 @@ 
    Filter the eBird data by species
    
 
     
    
     
    Arguments
    
-    
    x
    
+
+
+
    x
    
 
    auk_ebd object; reference to object created by auk_ebd().
    
 
 
-
    species
    
+
    species
    
 
    character; species to filter by, provided as scientific or
 English common names, or a mixture of both. These names must match the
 official eBird Taxomony (ebird_taxonomy).
    
 
 
-
    taxonomy_version
    
+
    taxonomy_version
    
 
    integer; the version (i.e. year) of the taxonomy. In
 most cases, this should be left empty to use the version of the taxonomy
 included in the package. See get_ebird_taxonomy().
    
 
 
-
    replace
    
+
    replace
    
 
    logical; multiple calls to auk_species() are additive,
 unless replace = FALSE, in which case the previous list of species to
 filter by will be removed and replaced by that in the current call.
    
@@ -102,9 +104,7 @@ 
    Arguments
    
 
    
     
    
     
    Value
    
-    
-
-
    An auk_ebd object.
    
+    
    An auk_ebd object.
    
     
    
     
    
     
    Details
    
@@ -117,7 +117,7 @@ 
    Details
    
     
    
     
    
     
    See also
    
-    
    Other filter: 
+    
    Other filter:
 auk_bbox(),
 auk_bcr(),
 auk_breeding(),
@@ -147,7 +147,7 @@ 
    Examples
    
   auk_ebd() %>%
   auk_species(species)
 #> Input 
-#>   EBD: /private/var/folders/mg/qh40qmqd7376xn8qxd6hm5lwjyy0h2/T/RtmpBEc62Y/temp_libpath32473f2f276e/auk/extdata/ebd-sample.txt 
+#>   EBD: /private/var/folders/wf/y1p0nztd2ps95ppplsl5bjjr0000gs/T/Rtmp7EtevZ/temp_libpathb97949a13185/auk/extdata/ebd-sample.txt 
 #> 
 #> Output 
 #>   Filters not executed
@@ -175,7 +175,7 @@ 
    Examples
    
 ebd <- auk_ebd(system.file("extdata/ebd-sample.txt", package = "auk"))
 auk_species(ebd, species)
 #> Input 
-#>   EBD: /private/var/folders/mg/qh40qmqd7376xn8qxd6hm5lwjyy0h2/T/RtmpBEc62Y/temp_libpath32473f2f276e/auk/extdata/ebd-sample.txt 
+#>   EBD: /private/var/folders/wf/y1p0nztd2ps95ppplsl5bjjr0000gs/T/Rtmp7EtevZ/temp_libpathb97949a13185/auk/extdata/ebd-sample.txt 
 #> 
 #> Output 
 #>   Filters not executed
@@ -212,15 +212,15 @@ 
    Examples
    
 
    
 
 
    
-  
    Site built with pkgdown 2.0.9.
    
+  
    Site built with pkgdown 2.1.1.
    
 
    
 
       
    
 
-  
 
 
-  
+
+
 
   
 
diff --git a/docs/reference/auk_split.html b/docs/reference/auk_split.html
index 76fd491..206e513 100644
--- a/docs/reference/auk_split.html
+++ b/docs/reference/auk_split.html
@@ -2,11 +2,11 @@
 Split an eBird data file by species — auk_split • auk
-    
+
 
     
    
       
    
   
    
 
    
 
-      
+
 
       
    
   
    
@@ -87,43 +87,43 @@ 
    Split an eBird data file by species
    
 
     
    
     
    Arguments
    
-    
    file
    
+
+
+
    file
    
 
    character; input file.
    
 
 
-
    species
    
+
    species
    
 
    character; species to filter and split by, provided as
 scientific or English common names, or a mixture of both. These names must
 match the official eBird Taxomony (ebird_taxonomy).
    
 
 
-
    prefix
    
+
    prefix
    
 
    character; a file and directory prefix. For example, if
 splitting by species "A" and "B" and prefix = "data/ebd_", the resulting
 files will be "data/ebd_A.txt" and "data/ebd_B.txt".
    
 
 
-
    taxonomy_version
    
+
    taxonomy_version
    
 
    integer; the version (i.e. year) of the taxonomy. In
 most cases, this should be left empty to use the version of the taxonomy
 included in the package. See get_ebird_taxonomy().
    
 
 
-
    sep
    
+
    sep
    
 
    character; the input field separator, the eBird file is tab
 separated by default. Must only be a single character and space delimited
 is not allowed since spaces appear in many of the fields.
    
 
 
-
    overwrite
    
+
    overwrite
    
 
    logical; overwrite output files if they already exists.
    
 
 
    
     
    
     
    Value
    
-    
-
-
    A vector of output filenames, one for each species.
    
+    
    A vector of output filenames, one for each species.
    
     
    
     
    
     
    Details
    
@@ -136,14 +136,14 @@ 
    Details
    
     
    
     
    
     
    See also
    
-    
    Other text: 
+    
    Other text:
 auk_clean(),
 auk_select()
    
     
    
 
     
    
     
    Examples
    
-    
    if (FALSE) {
+    
    if (FALSE) { # \dontrun{
 species <- c("Canada Jay", "Cyanocitta stelleri")
 # get the path to the example data included in the package
 # in practice, provide path to a filtered ebd file
@@ -154,7 +154,7 @@ 
    Examples
    
 # e.g. prefix <- "output/ebd_"
 prefix <- file.path(tempdir(), "ebd_")
 species_files <- auk_split(f, species = species, prefix = prefix)
-}
+} # }
 
    
     
    
   
    
@@ -169,15 +169,15 @@ 
    Examples
    
 
    
 
 
    
-  
    Site built with pkgdown 2.0.9.
    
+  
    Site built with pkgdown 2.1.1.
    
 
    
 
       
    
 
-  
 
 
-  
+
+
 
   
 
diff --git a/docs/reference/auk_state.html b/docs/reference/auk_state.html
index 9730642..a12f753 100644
--- a/docs/reference/auk_state.html
+++ b/docs/reference/auk_state.html
@@ -2,11 +2,11 @@
 Filter the eBird data by state — auk_state • auk
-    
+
 
     
    
       
    
   
    
 
    
 
-      
+
 
       
    
   
    
@@ -80,12 +80,14 @@ 
    Filter the eBird data by state
    
 
     
    
     
    Arguments
    
-    
    x
    
+
+
+
    x
    
 
    auk_ebd or auk_sampling object; reference to file created by
 auk_ebd() or auk_sampling().
    
 
 
-
    state
    
+
    state
    
 
    character; states to filter by. eBird uses 4 to 6 character
 state codes consisting of two parts, the 2-letter ISO country code and a
 1-3 character state code, separated by a dash. For example, "US-NY"
@@ -93,7 +95,7 @@ 
    Arguments
    
 ebird_states for look up state codes.
    
 
 
-
    replace
    
+
    replace
    
 
    logical; multiple calls to auk_state() are additive,
 unless replace = FALSE, in which case the previous list of states to
 filter by will be removed and replaced by that in the current call.
    
@@ -101,9 +103,7 @@ 
    Arguments
    
 
    
     
    
     
    Value
    
-    
-
-
    An auk_ebd object.
    
+    
    An auk_ebd object.
    
     
    
     
    
     
    Details
    
@@ -114,7 +114,7 @@ 
    Details
    
     
    
     
    
     
    See also
    
-    
    Other filter: 
+    
    Other filter:
 auk_bbox(),
 auk_bcr(),
 auk_breeding(),
@@ -156,7 +156,7 @@ 
    Examples
    
   auk_ebd() %>%
   auk_state(states)
 #> Input 
-#>   EBD: /private/var/folders/mg/qh40qmqd7376xn8qxd6hm5lwjyy0h2/T/RtmpBEc62Y/temp_libpath32473f2f276e/auk/extdata/ebd-sample.txt 
+#>   EBD: /private/var/folders/wf/y1p0nztd2ps95ppplsl5bjjr0000gs/T/Rtmp7EtevZ/temp_libpathb97949a13185/auk/extdata/ebd-sample.txt 
 #> 
 #> Output 
 #>   Filters not executed
@@ -184,7 +184,7 @@ 
    Examples
    
 ebd <- auk_ebd(system.file("extdata/ebd-sample.txt", package = "auk"))
 auk_state(ebd, states)
 #> Input 
-#>   EBD: /private/var/folders/mg/qh40qmqd7376xn8qxd6hm5lwjyy0h2/T/RtmpBEc62Y/temp_libpath32473f2f276e/auk/extdata/ebd-sample.txt 
+#>   EBD: /private/var/folders/wf/y1p0nztd2ps95ppplsl5bjjr0000gs/T/Rtmp7EtevZ/temp_libpathb97949a13185/auk/extdata/ebd-sample.txt 
 #> 
 #> Output 
 #>   Filters not executed
@@ -221,15 +221,15 @@ 
    Examples
    
 
    
 
 
    
-  
    Site built with pkgdown 2.0.9.
    
+  
    Site built with pkgdown 2.1.1.
    
 
    
 
       
    
 
-  
 
 
-  
+
+
 
   
 
diff --git a/docs/reference/auk_time.html b/docs/reference/auk_time.html
index cc95aaf..672cb80 100644
--- a/docs/reference/auk_time.html
+++ b/docs/reference/auk_time.html
@@ -2,11 +2,11 @@
 Filter the eBird data by checklist start time — auk_time • auk
-    
+
 
     
    
       
    
   
    
 
    
 
-      
+
 
       
    
   
    
@@ -80,21 +80,21 @@ 
    Filter the eBird data by checklist start time
    
 
     
    
     
    Arguments
    
-    
    x
    
+
+
+
    x
    
 
    auk_ebd or auk_sampling object; reference to file created by
 auk_ebd() or auk_sampling().
    
 
 
-
    start_time
    
+
    start_time
    
 
    character; 2 element character vector giving the range of
 times in 24 hour format, e.g. "06:30" or "16:22".
    
 
 
    
     
    
     
    Value
    
-    
-
-
    An auk_ebd object.
    
+    
    An auk_ebd object.
    
     
    
     
    
     
    Details
    
@@ -103,7 +103,7 @@ 
    Details
    
     
    
     
    
     
    See also
    
-    
    Other filter: 
+    
    Other filter:
 auk_bbox(),
 auk_bcr(),
 auk_breeding(),
@@ -132,7 +132,7 @@ 
    Examples
    
   auk_ebd() %>%
   auk_time(start_time = c("06:00", "08:00"))
 #> Input 
-#>   EBD: /private/var/folders/mg/qh40qmqd7376xn8qxd6hm5lwjyy0h2/T/RtmpBEc62Y/temp_libpath32473f2f276e/auk/extdata/ebd-sample.txt 
+#>   EBD: /private/var/folders/wf/y1p0nztd2ps95ppplsl5bjjr0000gs/T/Rtmp7EtevZ/temp_libpathb97949a13185/auk/extdata/ebd-sample.txt 
 #> 
 #> Output 
 #>   Filters not executed
@@ -160,7 +160,7 @@ 
    Examples
    
 ebd <- auk_ebd(system.file("extdata/ebd-sample.txt", package = "auk"))
 auk_time(ebd, start_time = c("06:00", "08:00"))
 #> Input 
-#>   EBD: /private/var/folders/mg/qh40qmqd7376xn8qxd6hm5lwjyy0h2/T/RtmpBEc62Y/temp_libpath32473f2f276e/auk/extdata/ebd-sample.txt 
+#>   EBD: /private/var/folders/wf/y1p0nztd2ps95ppplsl5bjjr0000gs/T/Rtmp7EtevZ/temp_libpathb97949a13185/auk/extdata/ebd-sample.txt 
 #> 
 #> Output 
 #>   Filters not executed
@@ -197,15 +197,15 @@ 
    Examples
    
 
    
 
 
    
-  
    Site built with pkgdown 2.0.9.
    
+  
    Site built with pkgdown 2.1.1.
    
 
    
 
       
    
 
-  
 
 
-  
+
+
 
   
 
diff --git a/docs/reference/auk_unique.html b/docs/reference/auk_unique.html
index 8da08f1..9e1e94b 100644
--- a/docs/reference/auk_unique.html
+++ b/docs/reference/auk_unique.html
@@ -4,11 +4,11 @@
 these duplicates from the eBird Basic Dataset (EBD) or the EBD sampling event
 data (with checklists_only = TRUE), creating a set of unique bird
 observations. This function is called automatically by read_ebd() and
-read_sampling().">
-    
+
 
     
    
       
    
   
    
 
    
 
-      
+
 
       
    
   
    
@@ -91,16 +91,18 @@ 
    Remove duplicate group checklists
    
 
     
    
     
    Arguments
    
-    
    x
    
+
+
+
    x
    
 
    data.frame; the EBD data frame, typically as imported by
 read_ebd().
    
 
 
-
    group_id
    
+
    group_id
    
 
    character; the name of the group ID column.
    
 
 
-
    checklist_id
    
+
    checklist_id
    
 
    character; the name of the checklist ID column, each
 checklist within a group will get a unique value for this field. The record
 with the lowest checklist_id will be picked as the unique record within
@@ -108,7 +110,7 @@ 
    Arguments
    
 full list of the checklist IDs that went into this group checklist.
    
 
 
-
    species_id
    
+
    species_id
    
 
    character; the name of the column identifying species
 uniquely. This is required to ensure that removing duplicates is done
 independently for each species. Note that this will not treat sub-species
@@ -117,7 +119,7 @@ 
    Arguments
    
 column's name to this argument.
    
 
 
-
    observer_id
    
+
    observer_id
    
 
    character; the name of the column identifying the owner
 of this instance of the group checklist. In the output dataset, the full
 list of observer IDs will be stored (comma separated) in the new
@@ -125,7 +127,7 @@ 
    Arguments
    
 comma separated checklist IDs.
    
 
 
-
    checklists_only
    
+
    checklists_only
    
 
    logical; whether the dataset provided only contains
 checklist information as with the sampling event data file. If this
 argument is TRUE, then the species_id argument is ignored and removing
@@ -134,9 +136,7 @@ 
    Arguments
    
 
    
     
    
     
    Value
    
-    
-
-
    A data frame with unique observations, and an additional field,
+    
    A data frame with unique observations, and an additional field,
 checklist_id, which is a combination of the sampling event and group IDs.
    
     
    
     
    
@@ -152,7 +152,7 @@ 
    Details
    
     
    
     
    
     
    See also
    
-    
    Other pre: 
+    
    Other pre:
 auk_rollup()
    
     
    
 
@@ -181,15 +181,15 @@ 
    Examples
    
 
    
 
 
    
-  
    Site built with pkgdown 2.0.9.
    
+  
    Site built with pkgdown 2.1.1.
    
 
    
 
       
    
 
-  
 
 
-  
+
+
 
   
 
diff --git a/docs/reference/auk_version.html b/docs/reference/auk_version.html
index caf19df..0723852 100644
--- a/docs/reference/auk_version.html
+++ b/docs/reference/auk_version.html
@@ -5,11 +5,11 @@
 eBird taxonomy included in the packages. The EBD is update quarterly, in
 March, June, September, and December, while the taxonomy is updated annually
 in August or September. To ensure proper functioning, always use the latest
-version of the auk package and the EBD.">
-    
+
 
     
    
       
    
   
    
 
    
 
-      
+
 
       
    
   
    
@@ -86,9 +86,7 @@ 
    Versions of auk, the EBD, and the eBird taxonomy
    
 
     
    
     
    Value
    
-    
-
-
    A list with three elements:
    • auk_version: the version of auk, e.g. "auk 0.4.1".
      • 
+    
      A list with three elements:
      • auk_version: the version of auk, e.g. "auk 0.4.1".
        • 
 
      • ebd_version: a date object specifying the release date of the EBD
 version that this auk version is designed to work with.
        • 
 
      • taxonomy_version: the year of the taxonomy built in to this version of
@@ -96,7 +94,7 @@ 
        Value
        
 
    
     
    
     
    See also
    
-    
    Other helpers: 
+    
    Other helpers:
 auk_ebd_version(),
 ebird_species(),
 get_ebird_taxonomy(),
@@ -107,13 +105,13 @@ 
    See also
    
     
    Examples
    
     
    auk_version()
 #> $auk_version
-#> [1] "auk 0.7.0"
+#> [1] "auk 0.8.0"
 #> 
 #> $ebd_version
-#> [1] "2023-10-25"
+#> [1] "2024-10-29"
 #> 
 #> $taxonomy_version
-#> [1] 2023
+#> [1] 2024
 #> 
 
    
     
    
@@ -129,15 +127,15 @@ 
    Examples
    
 
    
 
 
    
-  
    Site built with pkgdown 2.0.9.
    
+  
    Site built with pkgdown 2.1.1.
    
 
    
 
       
    
 
-  
 
 
-  
+
+
 
   
 
diff --git a/docs/reference/auk_year.html b/docs/reference/auk_year.html
index 18ceabf..54a5c14 100644
--- a/docs/reference/auk_year.html
+++ b/docs/reference/auk_year.html
@@ -2,11 +2,11 @@
 Filter the eBird data to a set of years — auk_year • auk
-    
+
 
     
    
       
    
   
    
 
    
 
-      
+
 
       
    
   
    
@@ -80,16 +80,18 @@ 
    Filter the eBird data to a set of years
    
 
     
    
     
    Arguments
    
-    
    x
    
+
+
+
    x
    
 
    auk_ebd or auk_sampling object; reference to file created by
 auk_ebd() or auk_sampling().
    
 
 
-
    year
    
+
    year
    
 
    integer; years to filter to.
    
 
 
-
    replace
    
+
    replace
    
 
    logical; multiple calls to auk_year() are additive,
 unless replace = FALSE, in which case the previous list of years to
 filter by will be removed and replaced by that in the current call.
    
@@ -97,9 +99,7 @@ 
    Arguments
    
 
    
     
    
     
    Value
    
-    
-
-
    An auk_ebd object.
    
+    
    An auk_ebd object.
    
     
    
     
    
     
    Details
    
@@ -115,7 +115,7 @@ 
    Details
    
     
    
     
    
     
    See also
    
-    
    Other filter: 
+    
    Other filter:
 auk_bbox(),
 auk_bcr(),
 auk_breeding(),
@@ -146,7 +146,7 @@ 
    Examples
    
   auk_ebd() %>%
   auk_year(year = years)
 #> Input 
-#>   EBD: /private/var/folders/mg/qh40qmqd7376xn8qxd6hm5lwjyy0h2/T/RtmpBEc62Y/temp_libpath32473f2f276e/auk/extdata/ebd-sample.txt 
+#>   EBD: /private/var/folders/wf/y1p0nztd2ps95ppplsl5bjjr0000gs/T/Rtmp7EtevZ/temp_libpathb97949a13185/auk/extdata/ebd-sample.txt 
 #> 
 #> Output 
 #>   Filters not executed
@@ -174,7 +174,7 @@ 
    Examples
    
 ebd <- auk_ebd(system.file("extdata/ebd-sample.txt", package = "auk"))
 auk_year(ebd, years)
 #> Input 
-#>   EBD: /private/var/folders/mg/qh40qmqd7376xn8qxd6hm5lwjyy0h2/T/RtmpBEc62Y/temp_libpath32473f2f276e/auk/extdata/ebd-sample.txt 
+#>   EBD: /private/var/folders/wf/y1p0nztd2ps95ppplsl5bjjr0000gs/T/Rtmp7EtevZ/temp_libpathb97949a13185/auk/extdata/ebd-sample.txt 
 #> 
 #> Output 
 #>   Filters not executed
@@ -204,7 +204,7 @@ 
    Examples
    
   auk_year(year = c(2010, 2012)) %>% 
   auk_date(date = c("*-05-01", "*-06-30"))
 #> Input 
-#>   EBD: /private/var/folders/mg/qh40qmqd7376xn8qxd6hm5lwjyy0h2/T/RtmpBEc62Y/temp_libpath32473f2f276e/auk/extdata/ebd-sample.txt 
+#>   EBD: /private/var/folders/wf/y1p0nztd2ps95ppplsl5bjjr0000gs/T/Rtmp7EtevZ/temp_libpathb97949a13185/auk/extdata/ebd-sample.txt 
 #> 
 #> Output 
 #>   Filters not executed
@@ -241,15 +241,15 @@ 
    Examples
    
 
    
 
 
    
-  
    Site built with pkgdown 2.0.9.
    
+  
    Site built with pkgdown 2.1.1.
    
 
    
 
       
    
 
-  
 
 
-  
+
+
 
   
 
diff --git a/docs/reference/auk_zerofill.auk_ebd.html b/docs/reference/auk_zerofill.auk_ebd.html
new file mode 100644
index 0000000..66b309d
--- /dev/null
+++ b/docs/reference/auk_zerofill.auk_ebd.html
@@ -0,0 +1,8 @@
+
+  
+    
+    
+    
+  
+
+
diff --git a/docs/reference/auk_zerofill.character.html b/docs/reference/auk_zerofill.character.html
new file mode 100644
index 0000000..66b309d
--- /dev/null
+++ b/docs/reference/auk_zerofill.character.html
@@ -0,0 +1,8 @@
+
+  
+    
+    
+    
+  
+
+
diff --git a/docs/reference/auk_zerofill.data.frame.html b/docs/reference/auk_zerofill.data.frame.html
new file mode 100644
index 0000000..66b309d
--- /dev/null
+++ b/docs/reference/auk_zerofill.data.frame.html
@@ -0,0 +1,8 @@
+
+  
+    
+    
+    
+  
+
+
diff --git a/docs/reference/auk_zerofill.html b/docs/reference/auk_zerofill.html
index 6a40580..359e1cd 100644
--- a/docs/reference/auk_zerofill.html
+++ b/docs/reference/auk_zerofill.html
@@ -3,11 +3,11 @@
 file, to produce a zero-filled, presence-absence dataset. The EBD contains
 bird sightings and the sampling event data is a set of all checklists, they
 can be combined to infer absence data by assuming any species not reported on
-a checklist was had a count of zero.">
-    
+
 
     
    
       
    
   
    
 
    
 
-      
+
 
       
    
   
    
@@ -79,7 +79,7 @@ 
    Read and zero-fill an eBird data file
    
     
    
     
    auk_zerofill(x, ...)
 
-# S3 method for data.frame
+# S3 method for class 'data.frame'
 auk_zerofill(
   x,
   sampling_events,
@@ -93,7 +93,7 @@ 
    Read and zero-fill an eBird data file
    
   ...
 )
 
-# S3 method for character
+# S3 method for class 'character'
 auk_zerofill(
   x,
   sampling_events,
@@ -108,7 +108,7 @@ 
    Read and zero-fill an eBird data file
    
   ...
 )
 
-# S3 method for auk_ebd
+# S3 method for class 'auk_ebd'
 auk_zerofill(
   x,
   species,
@@ -127,7 +127,9 @@ 
    Read and zero-fill an eBird data file
    
 
     
    
     
    Arguments
    
-    
    x
    
+
+
+
    x
    
 
    filename, data.frame of eBird observations, or auk_ebd object
 with associated output files as created by auk_filter(). If a filename is
 provided, it must point to the EBD and the sampling_events argument must
@@ -137,11 +139,11 @@ 
    Arguments
    
 auk_unique() to ensure duplicate group checklists have been removed.
    
 
 
-
    ...
    
+
    ...
    
 
    additional arguments passed to methods.
    
 
 
-
    sampling_events
    
+
    sampling_events
    
 
    character or data.frame; filename for the sampling
 event data or a data.frame of the same data. If a data.frame is
 provided it should have been imported with read_sampling(), to ensure the
@@ -150,53 +152,51 @@ 
    Arguments
    
 removed.
    
 
 
-
    species
    
+
    species
    
 
    character; species to include in zero-filled dataset, provided
 as scientific or English common names, or a mixture of both. These names
 must match the official eBird Taxomony (ebird_taxonomy). To include all
 species, leave this argument blank.
    
 
 
-
    taxonomy_version
    
+
    taxonomy_version
    
 
    integer; the version (i.e. year) of the taxonomy. In
 most cases, this should be left empty to use the version of the taxonomy
 included in the package. See get_ebird_taxonomy().
    
 
 
-
    collapse
    
+
    collapse
    
 
    logical; whether to call collapse_zerofill() to return a
 data frame rather than an auk_zerofill object.
    
 
 
-
    unique
    
+
    unique
    
 
    logical; should auk_unique() be run on the input data if it
 hasn't already.
    
 
 
-
    rollup
    
+
    rollup
    
 
    logical; should auk_rollup() be run on the input data if it
 hasn't already.
    
 
 
-
    drop_higher
    
+
    drop_higher
    
 
    logical; whether to remove taxa above species during the
 rollup process, e.g. "spuhs" like "duck sp.". See auk_rollup().
    
 
 
-
    complete
    
+
    complete
    
 
    logical; if TRUE (the default) all checklists are required
 to be complete prior to zero-filling.
    
 
 
-
    sep
    
+
    sep
    
 
    character; single character used to separate fields within a row.
    
 
 
    
     
    
     
    Value
    
-    
-
-
    By default, an auk_zerofill object, or a data frame if collapse = TRUE.
    
+    
    By default, an auk_zerofill object, or a data frame if collapse = TRUE.
    
     
    
     
    
     
    Details
    
@@ -222,7 +222,7 @@ 
    Details
    
     
    
     
    
     
    Methods (by class)
    
-    
+
 
    • auk_zerofill(data.frame): EBD data frame.
      • 
 
    • auk_zerofill(character): Filename of EBD.
      • 
 
    • auk_zerofill(auk_ebd): auk_ebd object output from auk_filter(). Must
@@ -231,7 +231,7 @@ 
      Methods (by class)
      
 
    
     
    
     
    See also
    
-    
    Other import: 
+    
    Other import:
 read_ebd()
    
     
    
 
@@ -264,15 +264,15 @@ 
    Examples
    
 
    
 
 
    
-  
    Site built with pkgdown 2.0.9.
    
+  
    Site built with pkgdown 2.1.1.
    
 
    
 
       
    
 
-  
 
 
-  
+
+
 
   
 
diff --git a/docs/reference/bcr_codes.html b/docs/reference/bcr_codes.html
index 1f492ae..8314b7d 100644
--- a/docs/reference/bcr_codes.html
+++ b/docs/reference/bcr_codes.html
@@ -2,11 +2,11 @@
 BCR Codes — bcr_codes • auk
-    
+
 
     
    
       
    
   
    
 
    
 
-      
+
 
       
    
   
    
@@ -85,7 +85,7 @@ 
    Format
    
 
    
     
    
     
    See also
    
-    
    Other data: 
+    
    Other data:
 ebird_states,
 ebird_taxonomy,
 valid_protocols
    
@@ -103,15 +103,15 @@ 
    See also
    
 
    
 
 
    
-  
    Site built with pkgdown 2.0.9.
    
+  
    Site built with pkgdown 2.1.1.
    
 
    
 
       
    
 
-  
 
 
-  
+
+
 
   
 
diff --git a/docs/reference/collapse_zerofill.html b/docs/reference/collapse_zerofill.html
new file mode 100644
index 0000000..66b309d
--- /dev/null
+++ b/docs/reference/collapse_zerofill.html
@@ -0,0 +1,8 @@
+
+  
+    
+    
+    
+  
+
+
diff --git a/docs/reference/ebird_species.html b/docs/reference/ebird_species.html
index 4e7846c..4261255 100644
--- a/docs/reference/ebird_species.html
+++ b/docs/reference/ebird_species.html
@@ -1,11 +1,11 @@
 
 Lookup species in eBird taxonomy — ebird_species • auk
-    
+
 
     
    
       
    
   
    
 
    
 
-      
+
 
       
    
   
    
@@ -82,19 +82,21 @@ 
    Lookup species in eBird taxonomy
    
 
     
    
     
    Arguments
    
-    
    x
    
+
+
+
    x
    
 
    character; species to look up, provided as scientific or
 English common names, or a mixture of both. Case insensitive.
    
 
 
-
    type
    
+
    type
    
 
    character; whether to return scientific names (scientific),
 English common names (common), or 6-letter eBird species codes (code).
 Alternatively, use all to return a data frame with the all the taxonomy
 information.
    
 
 
-
    taxonomy_version
    
+
    taxonomy_version
    
 
    integer; the version (i.e. year) of the taxonomy.
 Leave empty to use the version of the taxonomy included in the package.
 See get_ebird_taxonomy().
    
@@ -102,15 +104,13 @@ 
    Arguments
    
 
    
     
    
     
    Value
    
-    
-
-
    Character vector of species identified by scientific name, common
+    
    Character vector of species identified by scientific name, common
 name, or species code. If type = "all" a data frame of the taxonomy of
 the requested species is returned.
    
     
    
     
    
     
    See also
    
-    
    Other helpers: 
+    
    Other helpers:
 auk_ebd_version(),
 auk_version(),
 get_ebird_taxonomy(),
@@ -128,10 +128,10 @@ 
    Examples
    
 #> [4] NA                    
 
 # use taxonomy_version to query older taxonomy versions
-if (FALSE) {
+if (FALSE) { # \dontrun{
 ebird_species("Cordillera Azul Antbird")
 ebird_species("Cordillera Azul Antbird", taxonomy_version = 2017)
-}
+} # }
 
    
     
    
   
    
@@ -146,15 +146,15 @@ 
    Examples
    
 
    
 
 
    
-  
    Site built with pkgdown 2.0.9.
    
+  
    Site built with pkgdown 2.1.1.
    
 
    
 
       
    
 
-  
 
 
-  
+
+
 
   
 
diff --git a/docs/reference/ebird_states.html b/docs/reference/ebird_states.html
index 77ddf63..a90b57d 100644
--- a/docs/reference/ebird_states.html
+++ b/docs/reference/ebird_states.html
@@ -3,11 +3,11 @@
 consisting of two parts, the 2-letter ISO country code and a 1-3 character
 state code, separated by a dash. For example, "US-NY" corresponds to New
 York State in the United States. These state codes are required to filter by
-state using auk_state().'>
-    
+
 
     
    
       
    
   
    
 
    
 
-      
+
 
       
    
   
    
@@ -94,7 +94,7 @@ 
    Details
    
     
    
     
    
     
    See also
    
-    
    Other data: 
+    
    Other data:
 bcr_codes,
 ebird_taxonomy,
 valid_protocols
    
@@ -112,15 +112,15 @@ 
    See also
    
 
    
 
 
    
-  
    Site built with pkgdown 2.0.9.
    
+  
    Site built with pkgdown 2.1.1.
    
 
    
 
       
    
 
-  
 
 
-  
+
+
 
   
 
diff --git a/docs/reference/ebird_taxonomy.html b/docs/reference/ebird_taxonomy.html
index 47c8af0..600b11c 100644
--- a/docs/reference/ebird_taxonomy.html
+++ b/docs/reference/ebird_taxonomy.html
@@ -4,11 +4,11 @@
 slash (e.g. American Black Duck/Mallard). This taxonomy is based on the
 Clements Checklist, which is updated annually, typically in the late summer.
 Non-ASCII characters (e.g. those with accents) have been converted to ASCII
-equivalents in this data frame.">
-    
+
 
     
    
       
    
   
    
 
    
 
-      
+
 
       
    
   
    
@@ -100,7 +100,7 @@ 
    Format
    
     
    
     
    
     
    See also
    
-    
    Other data: 
+    
    Other data:
 bcr_codes,
 ebird_states,
 valid_protocols
    
@@ -118,15 +118,15 @@ 
    See also
    
 
    
 
 
    
-  
    Site built with pkgdown 2.0.9.
    
+  
    Site built with pkgdown 2.1.1.
    
 
    
 
       
    
 
-  
 
 
-  
+
+
 
   
 
diff --git a/docs/reference/filter_repeat_visits.html b/docs/reference/filter_repeat_visits.html
index 74120b4..3da966d 100644
--- a/docs/reference/filter_repeat_visits.html
+++ b/docs/reference/filter_repeat_visits.html
@@ -6,11 +6,11 @@
 protocol; however, subsets of the data can be extracted to produce data
 suitable for hierarchical modeling. This function extracts a subset of
 observation data that have a desired number of repeat visits within a period
-of closure.">
-    
+
 
     
    
       
    
   
    
 
    
 
-      
+
 
       
    
   
    
@@ -97,7 +97,9 @@ 
    Filter observations to repeat visits for hierarchical modeling
    
 
     
    
     
    Arguments
    
-    
    x
    
+
+
+
    x
    
 
    data.frame; observation data, e.g. data from the eBird Basic
 Dataset (EBD) zero-filled with auk_zerofill(). This function will also
 work with an auk_zerofill object, in which case it will be converted to
@@ -105,41 +107,41 @@ 
    Arguments
    
 Note that these data must for a single species.
    
 
 
-
    min_obs
    
+
    min_obs
    
 
    integer; minimum number of observations required for each
 site.
    
 
 
-
    max_obs
    
+
    max_obs
    
 
    integer; maximum number of observations allowed for each site.
    
 
 
-
    annual_closure
    
+
    annual_closure
    
 
    logical; whether the entire year should be treated as
 the period of closure (the default). This can be useful, for example, if
 the data have been subset to a period of closure prior to calling
 filter_repeat_visits().
    
 
 
-
    n_days
    
+
    n_days
    
 
    integer; number of days defining the temporal length of
 closure. If annual_closure = TRUE closure periods will be split at year
 boundaries. If annual_closure = FALSE the closure periods will ignore
 year boundaries.
    
 
 
-
    date_var
    
+
    date_var
    
 
    character; column name of the variable in x containing the
 date. This column should either be in Date format or convertible to
 Date format with as.Date().
    
 
 
-
    site_vars
    
+
    site_vars
    
 
    character; names of one of more columns in x that define a
 site, typically the location (e.g. latitude/longitude) and observer ID.
    
 
 
-
    ll_digits
    
+
    ll_digits
    
 
    integer; the number of digits to round latitude and longitude
 to. If latitude and/or longitude are used as site_vars, it's usually best
 to round them prior to identifying sites, otherwise locations that are only
@@ -151,9 +153,7 @@ 
    Arguments
    
 
    
     
    
     
    Value
    
-    
-
-
    A data.frame filtered to only retain observations from sites with
+    
    A data.frame filtered to only retain observations from sites with
 the allowed number of observations within the period of closure. The
 results will be sorted such that sites are together and in chronological
 order. The following variables are added to the data frame:
    • site: a unique identifier for each "site" corresponding to all the
@@ -178,7 +178,7 @@ 
      Details
      
     
    
     
    
     
    See also
    
-    
    Other modeling: 
+    
    Other modeling:
 format_unmarked_occu()
    
     
    
 
@@ -226,15 +226,15 @@ 
    Examples
    
 
    
 
 
    
-  
    Site built with pkgdown 2.0.9.
    
+  
    Site built with pkgdown 2.1.1.
    
 
    
 
       
    
 
-  
 
 
-  
+
+
 
   
 
diff --git a/docs/reference/format_unmarked_occu.html b/docs/reference/format_unmarked_occu.html
index 252dea6..d772887 100644
--- a/docs/reference/format_unmarked_occu.html
+++ b/docs/reference/format_unmarked_occu.html
@@ -5,11 +5,11 @@
 of several unmarked objects, which can then be used for modeling. This
 function converts data from a format in which each row is an observation
 (e.g. as in the eBird Basic Dataset) to the esoteric format required by
-unmarked::formatWide() in which each row is a site.">
-    
+
 
     
    
       
    
   
    
 
    
 
-      
+
 
       
    
   
    
@@ -73,11 +73,11 @@ 
    Format EBD data for occupancy modeling with unmarked
    
     
    
     
    Prepare a data frame of species observations for ingestion into the package
 unmarked for hierarchical modeling of abundance and occurrence. The
-function unmarked::formatWide() takes a data frame and converts it to one
+function unmarked::formatWide() takes a data frame and converts it to one
 of several unmarked objects, which can then be used for modeling. This
 function converts data from a format in which each row is an observation
 (e.g. as in the eBird Basic Dataset) to the esoteric format required by
-unmarked::formatWide() in which each row is a site.
    
+unmarked::formatWide() in which each row is a site.
    
     
    
 
     
    
@@ -92,13 +92,15 @@ 
    Format EBD data for occupancy modeling with unmarked
    
 
     
    
     
    Arguments
    
-    
    x
    
+
+
+
    x
    
 
    data.frame; observation data, e.g. from the eBird Basic Dataset
 (EBD), for a single species, that has been filtered to those with
 repeat visits by filter_repeat_visits().
    
 
 
-
    site_id
    
+
    site_id
    
 
    character; a unique idenitifer for each "site", typically
 identifying observations from a unique location by the same observer
 within a period of temporal closure. Data output from
@@ -106,13 +108,13 @@ 
    Arguments
    
 requirements.
    
 
 
-
    response
    
+
    response
    
 
    character; the variable that will act as the response in
 modeling efforts, typically a binary variable indicating presence or
 absence or a count of individuals seen.
    
 
 
-
    site_covs
    
+
    site_covs
    
 
    character; the variables that will act as site-level
 covariates, i.e. covariates that vary at the site level, for example,
 latitude/longitude or habitat predictors. If this parameter is missing, it
@@ -120,7 +122,7 @@ 
    Arguments
    
 covariate (obs_covs) or the site_id, is a site-level covariate.
    
 
 
-
    obs_covs
    
+
    obs_covs
    
 
    character; the variables that will act as observation-level
 covariates, i.e. covariates that vary within sites, at the level of
 observations, for example, time or length of observation.
    
@@ -128,9 +130,7 @@ 
    Arguments
    
 
    
     
    
     
    Value
    
-    
-
-
    A data frame that can be processed by unmarked::formatWide().
+    
    A data frame that can be processed by unmarked::formatWide().
 Each row will correspond to a unqiue site and, assuming there are a maximum
 of N observations per site, columns will be as follows:
    1. The unique site identifier, named "site".
      2. 
 
    2. N response columns, one for each observation, named "y.1", ..., "y.N".
      3. 
@@ -149,13 +149,13 @@ 
      Details
      
 output to this function.
      
 
      format_unmarked_occu() is designed to prepare data to be converted into
 an unmarkedFrameOccu object for occupancy modeling with
-unmarked::occu(); however, it can also be used to prepare data for
+unmarked::occu(); however, it can also be used to prepare data for
 conversion to an unmarkedFramePCount object for abundance modeling with
-unmarked::pcount().
      
+unmarked::pcount().
      
     
    
     
    
     
    See also
    
-    
    Other modeling: 
+    
    Other modeling:
 filter_repeat_visits()
    
     
    
 
@@ -178,7 +178,7 @@ 
    Examples
    
                                               "duration_minutes"))
 # create an unmarked object
 if (requireNamespace("unmarked", quietly = TRUE)) {
-  occ_um <- unmarked::formatWide(occ_wide, type = "unmarkedFrameOccu")
+  occ_um <- unmarked::formatWide(occ_wide, type = "unmarkedFrameOccu")
   unmarked::summary(occ_um)
 }
 #> unmarkedFrame Object
@@ -230,7 +230,7 @@ 
    Examples
    
                                               "duration_minutes"))
 # create an unmarked object
 if (requireNamespace("unmarked", quietly = TRUE)) {
-  abd_um <- unmarked::formatWide(abd_wide, type = "unmarkedFrameOccu")
+  abd_um <- unmarked::formatWide(abd_wide, type = "unmarkedFrameOccu")
   unmarked::summary(abd_um)
 }
 #> unmarkedFrame Object
@@ -276,15 +276,15 @@ 
    Examples
    
 
    
 
 
    
-  
    Site built with pkgdown 2.0.9.
    
+  
    Site built with pkgdown 2.1.1.
    
 
    
 
       
    
 
-  
 
 
-  
+
+
 
   
 
diff --git a/docs/reference/get_ebird_taxonomy.html b/docs/reference/get_ebird_taxonomy.html
index 6a200cf..d40b6fe 100644
--- a/docs/reference/get_ebird_taxonomy.html
+++ b/docs/reference/get_ebird_taxonomy.html
@@ -1,9 +1,9 @@
 
-Get eBird taxonomy via the eBird API — get_ebird_taxonomy • aukGet eBird taxonomy via the eBird API — get_ebird_taxonomy • auk
-    
+
 
     
    
       
    
   
    
 
    
 
-      
+
 
       
    
   
    
@@ -74,22 +74,22 @@ 
    Get eBird taxonomy via the eBird API
    
 
     
    
     
    Arguments
    
-    
    version
    
+
+
+
    version
    
 
    integer; the version (i.e. year) of the taxonomy. The eBird
 taxonomy is updated once a year in August. Leave this parameter blank to
 get the current taxonomy.
    
 
 
-
    locale
    
+
    locale
    
 
    character; the locale for the common names,
 defaults to English.
    
 
 
    
     
    
     
    Value
    
-    
-
-
    A data frame of all species in the eBird taxonomy, consisting of the
+    
    A data frame of all species in the eBird taxonomy, consisting of the
 following columns:
    • scientific_name: scientific name.
      • 
 
    • common_name: common name, defaults to English, but different languages
 can be selected using the locale parameter.
      • 
@@ -105,7 +105,7 @@ 
      Value
      
 
    
     
    
     
    See also
    
-    
    Other helpers: 
+    
    Other helpers:
 auk_ebd_version(),
 auk_version(),
 ebird_species(),
@@ -114,9 +114,9 @@ 
    See also
    
 
     
    
     
    Examples
    
-    
    if (FALSE) {
+    
    if (FALSE) { # \dontrun{
 get_ebird_taxonomy()
-}
+} # }
 
    
     
    
   
    
@@ -131,15 +131,15 @@ 
    Examples
    
 
    
 
 
    
-  
    Site built with pkgdown 2.0.9.
    
+  
    Site built with pkgdown 2.1.1.
    
 
    
 
       
    
 
-  
 
 
-  
+
+
 
   
 
diff --git a/docs/reference/index.html b/docs/reference/index.html
index 00317bf..1aae675 100644
--- a/docs/reference/index.html
+++ b/docs/reference/index.html
@@ -1,9 +1,9 @@
 
-Function reference • aukPackage index • auk
-    
+
 
     
    
       
    
   
    
 
    
 
-      
+
 
       
    
   
    
@@ -287,15 +287,15 @@ 
    Helpers 
    pkgdown 2.0.9.
    
+  
    Site built with pkgdown 2.1.1.
    
 
    
 
       
    
 
-  
 
 
-  
+
+
 
   
 
diff --git a/docs/reference/process_barcharts.html b/docs/reference/process_barcharts.html
index bd52661..564ee01 100644
--- a/docs/reference/process_barcharts.html
+++ b/docs/reference/process_barcharts.html
@@ -12,11 +12,11 @@
 link at the bottom right of the page; however, the text file that's
 downloaded is in a challenging format to work with. This function is designed
 to read these text files and return a nicely formatted data frame for use in
-R.">
-    
+
 
     
    
       
    
   
    
 
    
 
-      
+
 
       
    
   
    
@@ -100,16 +100,16 @@ 
    Process eBird bar chart data
    
 
     
    
     
    Arguments
    
-    
    filename
    
+
+
+
    filename
    
 
    character; path to the bar chart data text file downloaded
 from the eBird website.
    
 
 
    
     
    
     
    Value
    
-    
-
-
    This functions returns a data frame in long format where each row
+    
    This functions returns a data frame in long format where each row
 provides data for one species in one week. detection_frequency gives the
 proportion of checklists in the region that reported the species in the
 given week and n_detections gives the number of detections. The total
@@ -120,7 +120,7 @@ 
    Value
    
     
    
     
    
     
    See also
    
-    
    Other helpers: 
+    
    Other helpers:
 auk_ebd_version(),
 auk_version(),
 ebird_species(),
@@ -194,15 +194,15 @@ 
    Examples
    
 
    
 
 
    
-  
    Site built with pkgdown 2.0.9.
    
+  
    Site built with pkgdown 2.1.1.
    
 
    
 
       
    
 
-  
 
 
-  
+
+
 
   
 
diff --git a/docs/reference/read_ebd.auk_ebd.html b/docs/reference/read_ebd.auk_ebd.html
new file mode 100644
index 0000000..2821563
--- /dev/null
+++ b/docs/reference/read_ebd.auk_ebd.html
@@ -0,0 +1,8 @@
+
+  
+    
+    
+    
+  
+
+
diff --git a/docs/reference/read_ebd.character.html b/docs/reference/read_ebd.character.html
new file mode 100644
index 0000000..2821563
--- /dev/null
+++ b/docs/reference/read_ebd.character.html
@@ -0,0 +1,8 @@
+
+  
+    
+    
+    
+  
+
+
diff --git a/docs/reference/read_ebd.html b/docs/reference/read_ebd.html
index 55fadac..3e0e68d 100644
--- a/docs/reference/read_ebd.html
+++ b/docs/reference/read_ebd.html
@@ -1,11 +1,11 @@
 
 Read an EBD file — read_ebd • auk
-    
+
 
     
    
       
    
   
    
 
    
 
-      
+
 
       
    
   
    
@@ -75,41 +75,43 @@ 
    Read an EBD file
    
     
    
     
    read_ebd(x, sep = "\t", unique = TRUE, rollup = TRUE)
 
-# S3 method for character
+# S3 method for class 'character'
 read_ebd(x, sep = "\t", unique = TRUE, rollup = TRUE)
 
-# S3 method for auk_ebd
+# S3 method for class 'auk_ebd'
 read_ebd(x, sep = "\t", unique = TRUE, rollup = TRUE)
 
 read_sampling(x, sep = "\t", unique = TRUE)
 
-# S3 method for character
+# S3 method for class 'character'
 read_sampling(x, sep = "\t", unique = TRUE)
 
-# S3 method for auk_ebd
+# S3 method for class 'auk_ebd'
 read_sampling(x, sep = "\t", unique = TRUE)
 
-# S3 method for auk_sampling
+# S3 method for class 'auk_sampling'
 read_sampling(x, sep = "\t", unique = TRUE)
    
     
    
 
     
    
     
    Arguments
    
-    
    x
    
+
+
+
    x
    
 
    filename or auk_ebd object with associated output
 files as created by auk_filter().
    
 
 
-
    sep
    
+
    sep
    
 
    character; single character used to separate fields within a row.
    
 
 
-
    unique
    
+
    unique
    
 
    logical; should duplicate grouped checklists be removed. If
 unique = TRUE, auk_unique() is called on the EBD before returning.
    
 
 
-
    rollup
    
+
    rollup
    
 
    logical; should taxonomic rollup to species level be applied.
 If rollup = TRUE, auk_rollup() is called on the EBD before returning.
 Note that this process can be time consuming for large files, try turning
@@ -118,9 +120,7 @@ 
    Arguments
    
 
    
     
    
     
    Value
    
-    
-
-
    A data frame of EBD observations. An additional column,
+    
    A data frame of EBD observations. An additional column,
 checklist_id, is added to output files if unique = TRUE, that uniquely
 identifies the checklist from which the observation came. This field is
 equal to sampling_event_identifier for non-group checklists, and
@@ -138,13 +138,13 @@ 
    Details
    
 
    
     
    
     
    Methods (by class)
    
-    
+
 
    • read_ebd(character): Filename of EBD.
      • 
 
    • read_ebd(auk_ebd): auk_ebd object output from auk_filter()
      • 
 
    
     
    
     
    Functions
    
-    
+
 
    • read_sampling(character): Filename of sampling event data file
      • 
 
    • read_sampling(auk_ebd): auk_ebd object output from auk_filter(). Must have
 had a sampling event data file set in the original call to auk_ebd().
      • 
@@ -152,7 +152,7 @@ 
      Functions
      
 
    
     
    
     
    See also
    
-    
    Other import: 
+    
    Other import:
 auk_zerofill()
    
     
    
 
@@ -197,15 +197,15 @@ 
    Examples
    
 
    
 
 
    
-  
    Site built with pkgdown 2.0.9.
    
+  
    Site built with pkgdown 2.1.1.
    
 
    
 
       
    
 
-  
 
 
-  
+
+
 
   
 
diff --git a/docs/reference/read_sampling.auk_ebd.html b/docs/reference/read_sampling.auk_ebd.html
new file mode 100644
index 0000000..2821563
--- /dev/null
+++ b/docs/reference/read_sampling.auk_ebd.html
@@ -0,0 +1,8 @@
+
+  
+    
+    
+    
+  
+
+
diff --git a/docs/reference/read_sampling.auk_sampling.html b/docs/reference/read_sampling.auk_sampling.html
new file mode 100644
index 0000000..2821563
--- /dev/null
+++ b/docs/reference/read_sampling.auk_sampling.html
@@ -0,0 +1,8 @@
+
+  
+    
+    
+    
+  
+
+
diff --git a/docs/reference/read_sampling.character.html b/docs/reference/read_sampling.character.html
new file mode 100644
index 0000000..2821563
--- /dev/null
+++ b/docs/reference/read_sampling.character.html
@@ -0,0 +1,8 @@
+
+  
+    
+    
+    
+  
+
+
diff --git a/docs/reference/read_sampling.html b/docs/reference/read_sampling.html
new file mode 100644
index 0000000..2821563
--- /dev/null
+++ b/docs/reference/read_sampling.html
@@ -0,0 +1,8 @@
+
+  
+    
+    
+    
+  
+
+
diff --git a/docs/reference/reexports.html b/docs/reference/reexports.html
index 7f9f926..ff49e2d 100644
--- a/docs/reference/reexports.html
+++ b/docs/reference/reexports.html
@@ -6,11 +6,11 @@
 %&gt;%
 
 
-">
-    
+
 
     
    
       
    
   
    
 
    
 
-      
+
 
       
    
   
    
@@ -94,15 +94,15 @@ 
    Objects exported from other packages
    
 
    
 
 
    
-  
    Site built with pkgdown 2.0.9.
    
+  
    Site built with pkgdown 2.1.1.
    
 
    
 
       
    
 
-  
 
 
-  
+
+
 
   
 
diff --git a/docs/reference/valid_protocols.html b/docs/reference/valid_protocols.html
index 721381a..38a8bd1 100644
--- a/docs/reference/valid_protocols.html
+++ b/docs/reference/valid_protocols.html
@@ -1,9 +1,9 @@
 
-Valid Protocols — valid_protocols • aukValid Protocols — valid_protocols • auk
-    
+
 
     
    
       
    
   
    
 
    
 
-      
+
 
       
    
   
    
@@ -78,7 +78,7 @@ 
    Format
    
     
    
     
    
     
    See also
    
-    
    Other data: 
+    
    Other data:
 bcr_codes,
 ebird_states,
 ebird_taxonomy
    
@@ -96,15 +96,15 @@ 
    See also
    
 
    
 
 
    
-  
    Site built with pkgdown 2.0.9.
    
+  
    Site built with pkgdown 2.1.1.
    
 
    
 
       
    
 
-  
 
 
-  
+
+
 
   
 
diff --git a/docs/sitemap.xml b/docs/sitemap.xml
index 1fb3fd6..f3cffe6 100644
--- a/docs/sitemap.xml
+++ b/docs/sitemap.xml
@@ -1,174 +1,60 @@
-
-
-  
-    /404.html
-  
-  
-    /CONDUCT.html
-  
-  
-    /CONTRIBUTING.html
-  
-  
-    /LICENSE.html
-  
-  
-    /articles/auk.html
-  
-  
-    /articles/development.html
-  
-  
-    /articles/index.html
-  
-  
-    /authors.html
-  
-  
-    /index.html
-  
-  
-    /news/index.html
-  
-  
-    /reference/auk-package.html
-  
-  
-    /reference/auk_bbox.html
-  
-  
-    /reference/auk_bcr.html
-  
-  
-    /reference/auk_breeding.html
-  
-  
-    /reference/auk_clean.html
-  
-  
-    /reference/auk_complete.html
-  
-  
-    /reference/auk_country.html
-  
-  
-    /reference/auk_county.html
-  
-  
-    /reference/auk_date.html
-  
-  
-    /reference/auk_distance.html
-  
-  
-    /reference/auk_duration.html
-  
-  
-    /reference/auk_ebd.html
-  
-  
-    /reference/auk_ebd_version.html
-  
-  
-    /reference/auk_exotic.html
-  
-  
-    /reference/auk_extent.html
-  
-  
-    /reference/auk_filter.html
-  
-  
-    /reference/auk_get_awk_path.html
-  
-  
-    /reference/auk_get_ebd_path.html
-  
-  
-    /reference/auk_last_edited.html
-  
-  
-    /reference/auk_observer.html
-  
-  
-    /reference/auk_project.html
-  
-  
-    /reference/auk_protocol.html
-  
-  
-    /reference/auk_rollup.html
-  
-  
-    /reference/auk_sampling.html
-  
-  
-    /reference/auk_select.html
-  
-  
-    /reference/auk_set_awk_path.html
-  
-  
-    /reference/auk_set_ebd_path.html
-  
-  
-    /reference/auk_species.html
-  
-  
-    /reference/auk_split.html
-  
-  
-    /reference/auk_state.html
-  
-  
-    /reference/auk_time.html
-  
-  
-    /reference/auk_unique.html
-  
-  
-    /reference/auk_version.html
-  
-  
-    /reference/auk_year.html
-  
-  
-    /reference/auk_zerofill.html
-  
-  
-    /reference/bcr_codes.html
-  
-  
-    /reference/ebird_species.html
-  
-  
-    /reference/ebird_states.html
-  
-  
-    /reference/ebird_taxonomy.html
-  
-  
-    /reference/filter_repeat_visits.html
-  
-  
-    /reference/format_unmarked_occu.html
-  
-  
-    /reference/get_ebird_taxonomy.html
-  
-  
-    /reference/index.html
-  
-  
-    /reference/process_barcharts.html
-  
-  
-    /reference/read_ebd.html
-  
-  
-    /reference/reexports.html
-  
-  
-    /reference/valid_protocols.html
-  
+
+https://cornelllabofornithology.github.io/auk/404.html
+https://cornelllabofornithology.github.io/auk/CONDUCT.html
+https://cornelllabofornithology.github.io/auk/CONTRIBUTING.html
+https://cornelllabofornithology.github.io/auk/LICENSE.html
+https://cornelllabofornithology.github.io/auk/articles/auk.html
+https://cornelllabofornithology.github.io/auk/articles/development.html
+https://cornelllabofornithology.github.io/auk/articles/index.html
+https://cornelllabofornithology.github.io/auk/authors.html
+https://cornelllabofornithology.github.io/auk/index.html
+https://cornelllabofornithology.github.io/auk/news/index.html
+https://cornelllabofornithology.github.io/auk/reference/auk-package.html
+https://cornelllabofornithology.github.io/auk/reference/auk_bbox.html
+https://cornelllabofornithology.github.io/auk/reference/auk_bcr.html
+https://cornelllabofornithology.github.io/auk/reference/auk_breeding.html
+https://cornelllabofornithology.github.io/auk/reference/auk_clean.html
+https://cornelllabofornithology.github.io/auk/reference/auk_complete.html
+https://cornelllabofornithology.github.io/auk/reference/auk_country.html
+https://cornelllabofornithology.github.io/auk/reference/auk_county.html
+https://cornelllabofornithology.github.io/auk/reference/auk_date.html
+https://cornelllabofornithology.github.io/auk/reference/auk_distance.html
+https://cornelllabofornithology.github.io/auk/reference/auk_duration.html
+https://cornelllabofornithology.github.io/auk/reference/auk_ebd.html
+https://cornelllabofornithology.github.io/auk/reference/auk_ebd_version.html
+https://cornelllabofornithology.github.io/auk/reference/auk_exotic.html
+https://cornelllabofornithology.github.io/auk/reference/auk_extent.html
+https://cornelllabofornithology.github.io/auk/reference/auk_filter.html
+https://cornelllabofornithology.github.io/auk/reference/auk_get_awk_path.html
+https://cornelllabofornithology.github.io/auk/reference/auk_get_ebd_path.html
+https://cornelllabofornithology.github.io/auk/reference/auk_last_edited.html
+https://cornelllabofornithology.github.io/auk/reference/auk_observer.html
+https://cornelllabofornithology.github.io/auk/reference/auk_project.html
+https://cornelllabofornithology.github.io/auk/reference/auk_protocol.html
+https://cornelllabofornithology.github.io/auk/reference/auk_rollup.html
+https://cornelllabofornithology.github.io/auk/reference/auk_sampling.html
+https://cornelllabofornithology.github.io/auk/reference/auk_select.html
+https://cornelllabofornithology.github.io/auk/reference/auk_set_awk_path.html
+https://cornelllabofornithology.github.io/auk/reference/auk_set_ebd_path.html
+https://cornelllabofornithology.github.io/auk/reference/auk_species.html
+https://cornelllabofornithology.github.io/auk/reference/auk_split.html
+https://cornelllabofornithology.github.io/auk/reference/auk_state.html
+https://cornelllabofornithology.github.io/auk/reference/auk_time.html
+https://cornelllabofornithology.github.io/auk/reference/auk_unique.html
+https://cornelllabofornithology.github.io/auk/reference/auk_version.html
+https://cornelllabofornithology.github.io/auk/reference/auk_year.html
+https://cornelllabofornithology.github.io/auk/reference/auk_zerofill.html
+https://cornelllabofornithology.github.io/auk/reference/bcr_codes.html
+https://cornelllabofornithology.github.io/auk/reference/ebird_species.html
+https://cornelllabofornithology.github.io/auk/reference/ebird_states.html
+https://cornelllabofornithology.github.io/auk/reference/ebird_taxonomy.html
+https://cornelllabofornithology.github.io/auk/reference/filter_repeat_visits.html
+https://cornelllabofornithology.github.io/auk/reference/format_unmarked_occu.html
+https://cornelllabofornithology.github.io/auk/reference/get_ebird_taxonomy.html
+https://cornelllabofornithology.github.io/auk/reference/index.html
+https://cornelllabofornithology.github.io/auk/reference/process_barcharts.html
+https://cornelllabofornithology.github.io/auk/reference/read_ebd.html
+https://cornelllabofornithology.github.io/auk/reference/reexports.html
+https://cornelllabofornithology.github.io/auk/reference/valid_protocols.html
 
+