From 94927aa1f5ba199e92002a1c32188c3d72910dc4 Mon Sep 17 00:00:00 2001 From: Matt Strimas-Mackey Date: Mon, 21 Aug 2023 09:04:15 -0700 Subject: [PATCH] fixing roxygen2 package-level documentation weirdness --- NEWS.md | 1 + R/auk-package.r | 10 ++- README.md | 2 +- cran-comments.md | 1 + docs/articles/auk.html | 12 +-- docs/index.html | 2 +- docs/news/index.html | 1 + docs/pkgdown.yml | 2 +- docs/reference/auk-package.html | 99 ++++++++++++++++++++++++ docs/reference/auk.html | 85 -------------------- docs/reference/auk_bbox.html | 4 +- docs/reference/auk_bcr.html | 4 +- docs/reference/auk_breeding.html | 2 +- docs/reference/auk_complete.html | 2 +- docs/reference/auk_country.html | 4 +- docs/reference/auk_county.html | 4 +- docs/reference/auk_date.html | 8 +- docs/reference/auk_distance.html | 4 +- docs/reference/auk_duration.html | 4 +- docs/reference/auk_ebd.html | 6 +- docs/reference/auk_extent.html | 4 +- docs/reference/auk_last_edited.html | 2 +- docs/reference/auk_observer.html | 4 +- docs/reference/auk_project.html | 4 +- docs/reference/auk_protocol.html | 4 +- docs/reference/auk_sampling.html | 2 +- docs/reference/auk_species.html | 4 +- docs/reference/auk_state.html | 4 +- docs/reference/auk_time.html | 4 +- docs/reference/auk_year.html | 6 +- docs/reference/filter_repeat_visits.html | 2 +- docs/reference/format_unmarked_occu.html | 24 +++--- docs/sitemap.xml | 2 +- man/auk-package.Rd | 36 +++++++++ man/auk.Rd | 11 --- 35 files changed, 207 insertions(+), 163 deletions(-) create mode 100644 docs/reference/auk-package.html delete mode 100644 docs/reference/auk.html create mode 100644 man/auk-package.Rd delete mode 100644 man/auk.Rd diff --git a/NEWS.md b/NEWS.md index 85ad652..3d75169 100644 --- a/NEWS.md +++ b/NEWS.md @@ -2,6 +2,7 @@ - retain breeding codes in `auk_zerofill()` - changes to conform with deprecation of `.data$` in tidyselect expressions +- changes to package-level documentation in roxygen2 # auk 0.6.0 diff --git a/R/auk-package.r b/R/auk-package.r index 425bea6..71041be 100644 --- a/R/auk-package.r +++ b/R/auk-package.r @@ -3,9 +3,11 @@ #' Tools for extracting and processing eBird data from the eBird Basic Dataset #' (EBD). #' -#' @name auk -#' @docType package -#' @importFrom stringr str_interp -#' @importFrom rlang .data #' @keywords internal +"_PACKAGE" + +## usethis namespace: start +#' @importFrom rlang .data +#' @importFrom stringr str_interp +## usethis namespace: end NULL diff --git a/README.md b/README.md index d384e42..3ddd0bc 100644 --- a/README.md +++ b/README.md @@ -294,7 +294,7 @@ eBird Basic Dataset files can be read with `read_ebd()`: #> $ locality_type : chr [1:494] "P" "P" "P" "P" ... #> $ latitude : num [1:494] 20.7 15.8 15.8 15.8 15.7 ... #> $ longitude : num [1:494] -88.6 -93 -93 -92.9 -92.9 ... - #> $ observation_date : Date[1:494], format: "2010-09-05" "2011-08-18" ... + #> $ observation_date : Date[1:494], format: "2010-09-05" "2011-08-18" "2012-02-02" ... #> $ time_observations_started: chr [1:494] "06:30:00" "08:00:00" "09:13:00" "06:40:00" ... #> $ observer_id : chr [1:494] "obsr55719" "obsr313215" "obsr313215" "obsr313215" ... #> $ sampling_event_identifier: chr [1:494] "S6852862" "S14432467" "S39033556" "S38303088" ... diff --git a/cran-comments.md b/cran-comments.md index 0a2f09e..b1d6659 100644 --- a/cran-comments.md +++ b/cran-comments.md @@ -2,6 +2,7 @@ - retain breeding codes in `auk_zerofill()` - changes to conform with deprecation of `.data$` in tidyselect expressions +- changes to package-level documentation in roxygen2 # Test environments diff --git a/docs/articles/auk.html b/docs/articles/auk.html index 65c50a3..2617d98 100644 --- a/docs/articles/auk.html +++ b/docs/articles/auk.html @@ -329,7 +329,7 @@

The auk_ebd object auk_ebd() ebd #> Input -#> EBD: /private/var/folders/mg/qh40qmqd7376xn8qxd6hm5lwjyy0h2/T/Rtmp7o8rJG/temp_libpathc44a3830802e/auk/extdata/ebd-sample.txt +#> EBD: /private/var/folders/mg/qh40qmqd7376xn8qxd6hm5lwjyy0h2/T/RtmpiRmICh/temp_libpath35e33c916c85/auk/extdata/ebd-sample.txt #> #> Output #> Filters not executed @@ -434,7 +434,7 @@

Defining filters auk_complete() ebd_filters #> Input -#> EBD: /private/var/folders/mg/qh40qmqd7376xn8qxd6hm5lwjyy0h2/T/Rtmp7o8rJG/temp_libpathc44a3830802e/auk/extdata/ebd-sample.txt +#> EBD: /private/var/folders/mg/qh40qmqd7376xn8qxd6hm5lwjyy0h2/T/RtmpiRmICh/temp_libpath35e33c916c85/auk/extdata/ebd-sample.txt #> #> Output #> Filters not executed @@ -728,8 +728,8 @@

Filteringauk_complete() filters #> Input -#> EBD: /private/var/folders/mg/qh40qmqd7376xn8qxd6hm5lwjyy0h2/T/Rtmp7o8rJG/temp_libpathc44a3830802e/auk/extdata/zerofill-ex_ebd.txt -#> Sampling events: /private/var/folders/mg/qh40qmqd7376xn8qxd6hm5lwjyy0h2/T/Rtmp7o8rJG/temp_libpathc44a3830802e/auk/extdata/zerofill-ex_sampling.txt +#> EBD: /private/var/folders/mg/qh40qmqd7376xn8qxd6hm5lwjyy0h2/T/RtmpiRmICh/temp_libpath35e33c916c85/auk/extdata/zerofill-ex_ebd.txt +#> Sampling events: /private/var/folders/mg/qh40qmqd7376xn8qxd6hm5lwjyy0h2/T/RtmpiRmICh/temp_libpath35e33c916c85/auk/extdata/zerofill-ex_sampling.txt #> #> Output #> Filters not executed @@ -760,8 +760,8 @@

Filtering## file_sampling = "sampling-filtered.txt") ebd_sed_filtered #> Input -#> EBD: /private/var/folders/mg/qh40qmqd7376xn8qxd6hm5lwjyy0h2/T/Rtmp7o8rJG/temp_libpathc44a3830802e/auk/extdata/zerofill-ex_ebd.txt -#> Sampling events: /private/var/folders/mg/qh40qmqd7376xn8qxd6hm5lwjyy0h2/T/Rtmp7o8rJG/temp_libpathc44a3830802e/auk/extdata/zerofill-ex_sampling.txt +#> EBD: /private/var/folders/mg/qh40qmqd7376xn8qxd6hm5lwjyy0h2/T/RtmpiRmICh/temp_libpath35e33c916c85/auk/extdata/zerofill-ex_ebd.txt +#> Sampling events: /private/var/folders/mg/qh40qmqd7376xn8qxd6hm5lwjyy0h2/T/RtmpiRmICh/temp_libpath35e33c916c85/auk/extdata/zerofill-ex_sampling.txt #> #> Output #> EBD: ebd-filtered.txt diff --git a/docs/index.html b/docs/index.html index 65c50b8..163f20f 100644 --- a/docs/index.html +++ b/docs/index.html @@ -289,7 +289,7 @@

Reading#> $ locality_type : chr [1:494] "P" "P" "P" "P" ... #> $ latitude : num [1:494] 20.7 15.8 15.8 15.8 15.7 ... #> $ longitude : num [1:494] -88.6 -93 -93 -92.9 -92.9 ... -#> $ observation_date : Date[1:494], format: "2010-09-05" "2011-08-18" ... +#> $ observation_date : Date[1:494], format: "2010-09-05" "2011-08-18" "2012-02-02" ... #> $ time_observations_started: chr [1:494] "06:30:00" "08:00:00" "09:13:00" "06:40:00" ... #> $ observer_id : chr [1:494] "obsr55719" "obsr313215" "obsr313215" "obsr313215" ... #> $ sampling_event_identifier: chr [1:494] "S6852862" "S14432467" "S39033556" "S38303088" ... diff --git a/docs/news/index.html b/docs/news/index.html index 8139a32..014a964 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -55,6 +55,7 @@

auk 0.6.1auk_zerofill()
  • changes to conform with deprecation of .data$ in tidyselect expressions
    • +
  • changes to package-level documentation in roxygen2

    • auk 0.6.02022-10-29

    diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index d7de124..3615562 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -4,5 +4,5 @@ pkgdown_sha: ~ articles: auk: auk.html development: development.html -last_built: 2023-07-07T17:31Z +last_built: 2023-08-21T16:01Z diff --git a/docs/reference/auk-package.html b/docs/reference/auk-package.html new file mode 100644 index 0000000..1566c31 --- /dev/null +++ b/docs/reference/auk-package.html @@ -0,0 +1,99 @@ + +auk: eBird Data Extraction and Processing in R — auk-package • auk + + +
    +
    + + + +
    +
    +
    +

    auk: eBird Data Extraction and Processing in R

    + Source: R/auk-package.R + +
    + +
    +

    Tools for extracting and processing eBird data from the eBird Basic Dataset +(EBD).

    +
    + + + +
    +

    Author

    +

    Maintainer: Matthew Strimas-Mackey mes335@cornell.edu (ORCID)

    +

    Authors:

    • Eliot Miller

      • +

    • Wesley Hochachka

      • +

    Other contributors:

    • Cornell Lab of Ornithology [copyright holder]

      • +
    + +
    + +
    + + +
    + + + + + + + + diff --git a/docs/reference/auk.html b/docs/reference/auk.html deleted file mode 100644 index 22b3b7c..0000000 --- a/docs/reference/auk.html +++ /dev/null @@ -1,85 +0,0 @@ - -auk: eBird Data Extraction and Processing in R — auk • auk - - -
    -
    - - - -
    -
    -
    -

    auk: eBird Data Extraction and Processing in R

    - Source: R/auk-package.R - -
    - -
    -

    Tools for extracting and processing eBird data from the eBird Basic Dataset -(EBD).

    -
    - - - -
    - -
    - - -
    - - - - - - - - diff --git a/docs/reference/auk_bbox.html b/docs/reference/auk_bbox.html index 6e245f2..91cfcde 100644 --- a/docs/reference/auk_bbox.html +++ b/docs/reference/auk_bbox.html @@ -121,7 +121,7 @@

    Examples

    auk_ebd() %>% auk_bbox(bbox = c(-125, 37, -120, 52)) #> Input -#> EBD: /private/var/folders/mg/qh40qmqd7376xn8qxd6hm5lwjyy0h2/T/Rtmp7o8rJG/temp_libpathc44a3830802e/auk/extdata/ebd-sample.txt +#> EBD: /private/var/folders/mg/qh40qmqd7376xn8qxd6hm5lwjyy0h2/T/RtmpiRmICh/temp_libpath35e33c916c85/auk/extdata/ebd-sample.txt #> #> Output #> Filters not executed @@ -148,7 +148,7 @@

    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/Rtmp7o8rJG/temp_libpathc44a3830802e/auk/extdata/ebd-sample.txt +#> EBD: /private/var/folders/mg/qh40qmqd7376xn8qxd6hm5lwjyy0h2/T/RtmpiRmICh/temp_libpath35e33c916c85/auk/extdata/ebd-sample.txt #> #> Output #> Filters not executed diff --git a/docs/reference/auk_bcr.html b/docs/reference/auk_bcr.html index 7f9c94f..8960994 100644 --- a/docs/reference/auk_bcr.html +++ b/docs/reference/auk_bcr.html @@ -133,7 +133,7 @@

    Examples

    auk_ebd() %>% auk_bcr(bcr = 24) #> Input -#> EBD: /private/var/folders/mg/qh40qmqd7376xn8qxd6hm5lwjyy0h2/T/Rtmp7o8rJG/temp_libpathc44a3830802e/auk/extdata/ebd-sample.txt +#> EBD: /private/var/folders/mg/qh40qmqd7376xn8qxd6hm5lwjyy0h2/T/RtmpiRmICh/temp_libpath35e33c916c85/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_bcr(ebd, bcr = 24) #> Input -#> EBD: /private/var/folders/mg/qh40qmqd7376xn8qxd6hm5lwjyy0h2/T/Rtmp7o8rJG/temp_libpathc44a3830802e/auk/extdata/ebd-sample.txt +#> EBD: /private/var/folders/mg/qh40qmqd7376xn8qxd6hm5lwjyy0h2/T/RtmpiRmICh/temp_libpath35e33c916c85/auk/extdata/ebd-sample.txt #> #> Output #> Filters not executed diff --git a/docs/reference/auk_breeding.html b/docs/reference/auk_breeding.html index 685c341..42e2cdc 100644 --- a/docs/reference/auk_breeding.html +++ b/docs/reference/auk_breeding.html @@ -109,7 +109,7 @@

    Examples

    auk_ebd() %>% auk_breeding() #> Input -#> EBD: /private/var/folders/mg/qh40qmqd7376xn8qxd6hm5lwjyy0h2/T/Rtmp7o8rJG/temp_libpathc44a3830802e/auk/extdata/ebd-sample.txt +#> EBD: /private/var/folders/mg/qh40qmqd7376xn8qxd6hm5lwjyy0h2/T/RtmpiRmICh/temp_libpath35e33c916c85/auk/extdata/ebd-sample.txt #> #> Output #> Filters not executed diff --git a/docs/reference/auk_complete.html b/docs/reference/auk_complete.html index 7075218..412e4f2 100644 --- a/docs/reference/auk_complete.html +++ b/docs/reference/auk_complete.html @@ -116,7 +116,7 @@

    Examples

    auk_ebd() %>% auk_complete() #> Input -#> EBD: /private/var/folders/mg/qh40qmqd7376xn8qxd6hm5lwjyy0h2/T/Rtmp7o8rJG/temp_libpathc44a3830802e/auk/extdata/ebd-sample.txt +#> EBD: /private/var/folders/mg/qh40qmqd7376xn8qxd6hm5lwjyy0h2/T/RtmpiRmICh/temp_libpath35e33c916c85/auk/extdata/ebd-sample.txt #> #> Output #> Filters not executed diff --git a/docs/reference/auk_country.html b/docs/reference/auk_country.html index caccb40..d4f3cd2 100644 --- a/docs/reference/auk_country.html +++ b/docs/reference/auk_country.html @@ -129,7 +129,7 @@

    Examples

    auk_ebd() %>% auk_country(country) #> Input -#> EBD: /private/var/folders/mg/qh40qmqd7376xn8qxd6hm5lwjyy0h2/T/Rtmp7o8rJG/temp_libpathc44a3830802e/auk/extdata/ebd-sample.txt +#> EBD: /private/var/folders/mg/qh40qmqd7376xn8qxd6hm5lwjyy0h2/T/RtmpiRmICh/temp_libpath35e33c916c85/auk/extdata/ebd-sample.txt #> #> Output #> Filters not executed @@ -156,7 +156,7 @@

    Examples

    ebd <- auk_ebd(system.file("extdata/ebd-sample.txt", package = "auk")) auk_country(ebd, country) #> Input -#> EBD: /private/var/folders/mg/qh40qmqd7376xn8qxd6hm5lwjyy0h2/T/Rtmp7o8rJG/temp_libpathc44a3830802e/auk/extdata/ebd-sample.txt +#> EBD: /private/var/folders/mg/qh40qmqd7376xn8qxd6hm5lwjyy0h2/T/RtmpiRmICh/temp_libpath35e33c916c85/auk/extdata/ebd-sample.txt #> #> Output #> Filters not executed diff --git a/docs/reference/auk_county.html b/docs/reference/auk_county.html index ab90f9f..f7f6f80 100644 --- a/docs/reference/auk_county.html +++ b/docs/reference/auk_county.html @@ -130,7 +130,7 @@

    Examples

    auk_ebd() %>% auk_county("US-NY-109") #> Input -#> EBD: /private/var/folders/mg/qh40qmqd7376xn8qxd6hm5lwjyy0h2/T/Rtmp7o8rJG/temp_libpathc44a3830802e/auk/extdata/ebd-sample.txt +#> EBD: /private/var/folders/mg/qh40qmqd7376xn8qxd6hm5lwjyy0h2/T/RtmpiRmICh/temp_libpath35e33c916c85/auk/extdata/ebd-sample.txt #> #> Output #> Filters not executed @@ -157,7 +157,7 @@

    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/Rtmp7o8rJG/temp_libpathc44a3830802e/auk/extdata/ebd-sample.txt +#> EBD: /private/var/folders/mg/qh40qmqd7376xn8qxd6hm5lwjyy0h2/T/RtmpiRmICh/temp_libpath35e33c916c85/auk/extdata/ebd-sample.txt #> #> Output #> Filters not executed diff --git a/docs/reference/auk_date.html b/docs/reference/auk_date.html index c910878..3cbee5a 100644 --- a/docs/reference/auk_date.html +++ b/docs/reference/auk_date.html @@ -123,7 +123,7 @@

    Examples

    auk_ebd() %>% auk_date(date = c("2010-01-01", "2010-12-31")) #> Input -#> EBD: /private/var/folders/mg/qh40qmqd7376xn8qxd6hm5lwjyy0h2/T/Rtmp7o8rJG/temp_libpathc44a3830802e/auk/extdata/ebd-sample.txt +#> EBD: /private/var/folders/mg/qh40qmqd7376xn8qxd6hm5lwjyy0h2/T/RtmpiRmICh/temp_libpath35e33c916c85/auk/extdata/ebd-sample.txt #> #> Output #> Filters not executed @@ -150,7 +150,7 @@

    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/Rtmp7o8rJG/temp_libpathc44a3830802e/auk/extdata/ebd-sample.txt +#> EBD: /private/var/folders/mg/qh40qmqd7376xn8qxd6hm5lwjyy0h2/T/RtmpiRmICh/temp_libpath35e33c916c85/auk/extdata/ebd-sample.txt #> #> Output #> Filters not executed @@ -179,7 +179,7 @@

    Examples

    # may-june records from all years auk_date(date = c("*-05-01", "*-06-30")) #> Input -#> EBD: /private/var/folders/mg/qh40qmqd7376xn8qxd6hm5lwjyy0h2/T/Rtmp7o8rJG/temp_libpathc44a3830802e/auk/extdata/ebd-sample.txt +#> EBD: /private/var/folders/mg/qh40qmqd7376xn8qxd6hm5lwjyy0h2/T/RtmpiRmICh/temp_libpath35e33c916c85/auk/extdata/ebd-sample.txt #> #> Output #> Filters not executed @@ -208,7 +208,7 @@

    Examples

    # dec-jan records from all years auk_date(date = c("*-12-01", "*-01-31")) #> Input -#> EBD: /private/var/folders/mg/qh40qmqd7376xn8qxd6hm5lwjyy0h2/T/Rtmp7o8rJG/temp_libpathc44a3830802e/auk/extdata/ebd-sample.txt +#> EBD: /private/var/folders/mg/qh40qmqd7376xn8qxd6hm5lwjyy0h2/T/RtmpiRmICh/temp_libpath35e33c916c85/auk/extdata/ebd-sample.txt #> #> Output #> Filters not executed diff --git a/docs/reference/auk_distance.html b/docs/reference/auk_distance.html index b91d016..1b6f9f8 100644 --- a/docs/reference/auk_distance.html +++ b/docs/reference/auk_distance.html @@ -130,7 +130,7 @@

    Examples

    auk_ebd() %>% auk_distance(distance = c(0, 10)) #> Input -#> EBD: /private/var/folders/mg/qh40qmqd7376xn8qxd6hm5lwjyy0h2/T/Rtmp7o8rJG/temp_libpathc44a3830802e/auk/extdata/ebd-sample.txt +#> EBD: /private/var/folders/mg/qh40qmqd7376xn8qxd6hm5lwjyy0h2/T/RtmpiRmICh/temp_libpath35e33c916c85/auk/extdata/ebd-sample.txt #> #> Output #> Filters not executed @@ -157,7 +157,7 @@

    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/Rtmp7o8rJG/temp_libpathc44a3830802e/auk/extdata/ebd-sample.txt +#> EBD: /private/var/folders/mg/qh40qmqd7376xn8qxd6hm5lwjyy0h2/T/RtmpiRmICh/temp_libpath35e33c916c85/auk/extdata/ebd-sample.txt #> #> Output #> Filters not executed diff --git a/docs/reference/auk_duration.html b/docs/reference/auk_duration.html index ab9eaa1..d3829f1 100644 --- a/docs/reference/auk_duration.html +++ b/docs/reference/auk_duration.html @@ -122,7 +122,7 @@

    Examples

    auk_ebd() %>% auk_duration(duration = c(0, 60)) #> Input -#> EBD: /private/var/folders/mg/qh40qmqd7376xn8qxd6hm5lwjyy0h2/T/Rtmp7o8rJG/temp_libpathc44a3830802e/auk/extdata/ebd-sample.txt +#> EBD: /private/var/folders/mg/qh40qmqd7376xn8qxd6hm5lwjyy0h2/T/RtmpiRmICh/temp_libpath35e33c916c85/auk/extdata/ebd-sample.txt #> #> Output #> Filters not executed @@ -149,7 +149,7 @@

    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/Rtmp7o8rJG/temp_libpathc44a3830802e/auk/extdata/ebd-sample.txt +#> EBD: /private/var/folders/mg/qh40qmqd7376xn8qxd6hm5lwjyy0h2/T/RtmpiRmICh/temp_libpath35e33c916c85/auk/extdata/ebd-sample.txt #> #> Output #> Filters not executed diff --git a/docs/reference/auk_ebd.html b/docs/reference/auk_ebd.html index bd8a92a..a5eda2b 100644 --- a/docs/reference/auk_ebd.html +++ b/docs/reference/auk_ebd.html @@ -125,7 +125,7 @@

    Examples

    f <- system.file("extdata/ebd-sample.txt", package = "auk") auk_ebd(f) #> Input -#> EBD: /private/var/folders/mg/qh40qmqd7376xn8qxd6hm5lwjyy0h2/T/Rtmp7o8rJG/temp_libpathc44a3830802e/auk/extdata/ebd-sample.txt +#> EBD: /private/var/folders/mg/qh40qmqd7376xn8qxd6hm5lwjyy0h2/T/RtmpiRmICh/temp_libpath35e33c916c85/auk/extdata/ebd-sample.txt #> #> Output #> Filters not executed @@ -152,8 +152,8 @@

    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/Rtmp7o8rJG/temp_libpathc44a3830802e/auk/extdata/zerofill-ex_ebd.txt -#> Sampling events: /private/var/folders/mg/qh40qmqd7376xn8qxd6hm5lwjyy0h2/T/Rtmp7o8rJG/temp_libpathc44a3830802e/auk/extdata/zerofill-ex_sampling.txt +#> EBD: /private/var/folders/mg/qh40qmqd7376xn8qxd6hm5lwjyy0h2/T/RtmpiRmICh/temp_libpath35e33c916c85/auk/extdata/zerofill-ex_ebd.txt +#> Sampling events: /private/var/folders/mg/qh40qmqd7376xn8qxd6hm5lwjyy0h2/T/RtmpiRmICh/temp_libpath35e33c916c85/auk/extdata/zerofill-ex_sampling.txt #> #> Output #> Filters not executed diff --git a/docs/reference/auk_extent.html b/docs/reference/auk_extent.html index 699cd6f..1564ab5 100644 --- a/docs/reference/auk_extent.html +++ b/docs/reference/auk_extent.html @@ -109,7 +109,7 @@

    Examples

    auk_ebd() %>% auk_bbox(bbox = c(-125, 37, -120, 52)) #> Input -#> EBD: /private/var/folders/mg/qh40qmqd7376xn8qxd6hm5lwjyy0h2/T/Rtmp7o8rJG/temp_libpathc44a3830802e/auk/extdata/ebd-sample.txt +#> EBD: /private/var/folders/mg/qh40qmqd7376xn8qxd6hm5lwjyy0h2/T/RtmpiRmICh/temp_libpath35e33c916c85/auk/extdata/ebd-sample.txt #> #> Output #> Filters not executed @@ -136,7 +136,7 @@

    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/Rtmp7o8rJG/temp_libpathc44a3830802e/auk/extdata/ebd-sample.txt +#> EBD: /private/var/folders/mg/qh40qmqd7376xn8qxd6hm5lwjyy0h2/T/RtmpiRmICh/temp_libpath35e33c916c85/auk/extdata/ebd-sample.txt #> #> Output #> Filters not executed diff --git a/docs/reference/auk_last_edited.html b/docs/reference/auk_last_edited.html index 31307e6..b453a24 100644 --- a/docs/reference/auk_last_edited.html +++ b/docs/reference/auk_last_edited.html @@ -119,7 +119,7 @@

    Examples

    auk_ebd() %>% auk_last_edited(date = c("2010-01-01", "2010-12-31")) #> Input -#> EBD: /private/var/folders/mg/qh40qmqd7376xn8qxd6hm5lwjyy0h2/T/Rtmp7o8rJG/temp_libpathc44a3830802e/auk/extdata/ebd-sample.txt +#> EBD: /private/var/folders/mg/qh40qmqd7376xn8qxd6hm5lwjyy0h2/T/RtmpiRmICh/temp_libpath35e33c916c85/auk/extdata/ebd-sample.txt #> #> Output #> Filters not executed diff --git a/docs/reference/auk_observer.html b/docs/reference/auk_observer.html index 32d752a..6d1acbf 100644 --- a/docs/reference/auk_observer.html +++ b/docs/reference/auk_observer.html @@ -113,7 +113,7 @@

    Examples

    auk_ebd() %>% auk_observer("obsr313215") #> Input -#> EBD: /private/var/folders/mg/qh40qmqd7376xn8qxd6hm5lwjyy0h2/T/Rtmp7o8rJG/temp_libpathc44a3830802e/auk/extdata/ebd-sample.txt +#> EBD: /private/var/folders/mg/qh40qmqd7376xn8qxd6hm5lwjyy0h2/T/RtmpiRmICh/temp_libpath35e33c916c85/auk/extdata/ebd-sample.txt #> #> Output #> Filters not executed @@ -140,7 +140,7 @@

    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/Rtmp7o8rJG/temp_libpathc44a3830802e/auk/extdata/ebd-sample.txt +#> EBD: /private/var/folders/mg/qh40qmqd7376xn8qxd6hm5lwjyy0h2/T/RtmpiRmICh/temp_libpath35e33c916c85/auk/extdata/ebd-sample.txt #> #> Output #> Filters not executed diff --git a/docs/reference/auk_project.html b/docs/reference/auk_project.html index 4ea4bec..26217d5 100644 --- a/docs/reference/auk_project.html +++ b/docs/reference/auk_project.html @@ -119,7 +119,7 @@

    Examples

    auk_ebd() %>% auk_project("EBIRD_MEX") #> Input -#> EBD: /private/var/folders/mg/qh40qmqd7376xn8qxd6hm5lwjyy0h2/T/Rtmp7o8rJG/temp_libpathc44a3830802e/auk/extdata/ebd-sample.txt +#> EBD: /private/var/folders/mg/qh40qmqd7376xn8qxd6hm5lwjyy0h2/T/RtmpiRmICh/temp_libpath35e33c916c85/auk/extdata/ebd-sample.txt #> #> Output #> Filters not executed @@ -146,7 +146,7 @@

    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/Rtmp7o8rJG/temp_libpathc44a3830802e/auk/extdata/ebd-sample.txt +#> EBD: /private/var/folders/mg/qh40qmqd7376xn8qxd6hm5lwjyy0h2/T/RtmpiRmICh/temp_libpath35e33c916c85/auk/extdata/ebd-sample.txt #> #> Output #> Filters not executed diff --git a/docs/reference/auk_protocol.html b/docs/reference/auk_protocol.html index 6dda119..2af8aec 100644 --- a/docs/reference/auk_protocol.html +++ b/docs/reference/auk_protocol.html @@ -123,7 +123,7 @@

    Examples

    auk_ebd() %>% auk_protocol("Stationary") #> Input -#> EBD: /private/var/folders/mg/qh40qmqd7376xn8qxd6hm5lwjyy0h2/T/Rtmp7o8rJG/temp_libpathc44a3830802e/auk/extdata/ebd-sample.txt +#> EBD: /private/var/folders/mg/qh40qmqd7376xn8qxd6hm5lwjyy0h2/T/RtmpiRmICh/temp_libpath35e33c916c85/auk/extdata/ebd-sample.txt #> #> Output #> Filters not executed @@ -150,7 +150,7 @@

    Examples

    ebd <- auk_ebd(system.file("extdata/ebd-sample.txt", package = "auk")) auk_protocol(ebd, "Stationary") #> Input -#> EBD: /private/var/folders/mg/qh40qmqd7376xn8qxd6hm5lwjyy0h2/T/Rtmp7o8rJG/temp_libpathc44a3830802e/auk/extdata/ebd-sample.txt +#> EBD: /private/var/folders/mg/qh40qmqd7376xn8qxd6hm5lwjyy0h2/T/RtmpiRmICh/temp_libpath35e33c916c85/auk/extdata/ebd-sample.txt #> #> Output #> Filters not executed diff --git a/docs/reference/auk_sampling.html b/docs/reference/auk_sampling.html index 3e91277..d65fc28 100644 --- a/docs/reference/auk_sampling.html +++ b/docs/reference/auk_sampling.html @@ -109,7 +109,7 @@

    Examples

    f <- system.file("extdata/zerofill-ex_sampling.txt", package = "auk") auk_sampling(f) #> Input -#> Sampling events: /private/var/folders/mg/qh40qmqd7376xn8qxd6hm5lwjyy0h2/T/Rtmp7o8rJG/temp_libpathc44a3830802e/auk/extdata/zerofill-ex_sampling.txt +#> Sampling events: /private/var/folders/mg/qh40qmqd7376xn8qxd6hm5lwjyy0h2/T/RtmpiRmICh/temp_libpath35e33c916c85/auk/extdata/zerofill-ex_sampling.txt #> #> Output #> Filters not executed diff --git a/docs/reference/auk_species.html b/docs/reference/auk_species.html index 197379b..01afe40 100644 --- a/docs/reference/auk_species.html +++ b/docs/reference/auk_species.html @@ -133,7 +133,7 @@

    Examples

    auk_ebd() %>% auk_species(species) #> Input -#> EBD: /private/var/folders/mg/qh40qmqd7376xn8qxd6hm5lwjyy0h2/T/Rtmp7o8rJG/temp_libpathc44a3830802e/auk/extdata/ebd-sample.txt +#> EBD: /private/var/folders/mg/qh40qmqd7376xn8qxd6hm5lwjyy0h2/T/RtmpiRmICh/temp_libpath35e33c916c85/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_species(ebd, species) #> Input -#> EBD: /private/var/folders/mg/qh40qmqd7376xn8qxd6hm5lwjyy0h2/T/Rtmp7o8rJG/temp_libpathc44a3830802e/auk/extdata/ebd-sample.txt +#> EBD: /private/var/folders/mg/qh40qmqd7376xn8qxd6hm5lwjyy0h2/T/RtmpiRmICh/temp_libpath35e33c916c85/auk/extdata/ebd-sample.txt #> #> Output #> Filters not executed diff --git a/docs/reference/auk_state.html b/docs/reference/auk_state.html index 77cca79..21b22bc 100644 --- a/docs/reference/auk_state.html +++ b/docs/reference/auk_state.html @@ -142,7 +142,7 @@

    Examples

    auk_ebd() %>% auk_state(states) #> Input -#> EBD: /private/var/folders/mg/qh40qmqd7376xn8qxd6hm5lwjyy0h2/T/Rtmp7o8rJG/temp_libpathc44a3830802e/auk/extdata/ebd-sample.txt +#> EBD: /private/var/folders/mg/qh40qmqd7376xn8qxd6hm5lwjyy0h2/T/RtmpiRmICh/temp_libpath35e33c916c85/auk/extdata/ebd-sample.txt #> #> Output #> Filters not executed @@ -169,7 +169,7 @@

    Examples

    ebd <- auk_ebd(system.file("extdata/ebd-sample.txt", package = "auk")) auk_state(ebd, states) #> Input -#> EBD: /private/var/folders/mg/qh40qmqd7376xn8qxd6hm5lwjyy0h2/T/Rtmp7o8rJG/temp_libpathc44a3830802e/auk/extdata/ebd-sample.txt +#> EBD: /private/var/folders/mg/qh40qmqd7376xn8qxd6hm5lwjyy0h2/T/RtmpiRmICh/temp_libpath35e33c916c85/auk/extdata/ebd-sample.txt #> #> Output #> Filters not executed diff --git a/docs/reference/auk_time.html b/docs/reference/auk_time.html index 8fef220..0d0b5f9 100644 --- a/docs/reference/auk_time.html +++ b/docs/reference/auk_time.html @@ -118,7 +118,7 @@

    Examples

    auk_ebd() %>% auk_time(start_time = c("06:00", "08:00")) #> Input -#> EBD: /private/var/folders/mg/qh40qmqd7376xn8qxd6hm5lwjyy0h2/T/Rtmp7o8rJG/temp_libpathc44a3830802e/auk/extdata/ebd-sample.txt +#> EBD: /private/var/folders/mg/qh40qmqd7376xn8qxd6hm5lwjyy0h2/T/RtmpiRmICh/temp_libpath35e33c916c85/auk/extdata/ebd-sample.txt #> #> Output #> Filters not executed @@ -145,7 +145,7 @@

    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/Rtmp7o8rJG/temp_libpathc44a3830802e/auk/extdata/ebd-sample.txt +#> EBD: /private/var/folders/mg/qh40qmqd7376xn8qxd6hm5lwjyy0h2/T/RtmpiRmICh/temp_libpath35e33c916c85/auk/extdata/ebd-sample.txt #> #> Output #> Filters not executed diff --git a/docs/reference/auk_year.html b/docs/reference/auk_year.html index 1f6e4cb..f9fc8fc 100644 --- a/docs/reference/auk_year.html +++ b/docs/reference/auk_year.html @@ -132,7 +132,7 @@

    Examples

    auk_ebd() %>% auk_year(year = years) #> Input -#> EBD: /private/var/folders/mg/qh40qmqd7376xn8qxd6hm5lwjyy0h2/T/Rtmp7o8rJG/temp_libpathc44a3830802e/auk/extdata/ebd-sample.txt +#> EBD: /private/var/folders/mg/qh40qmqd7376xn8qxd6hm5lwjyy0h2/T/RtmpiRmICh/temp_libpath35e33c916c85/auk/extdata/ebd-sample.txt #> #> Output #> Filters not executed @@ -159,7 +159,7 @@

    Examples

    ebd <- auk_ebd(system.file("extdata/ebd-sample.txt", package = "auk")) auk_year(ebd, years) #> Input -#> EBD: /private/var/folders/mg/qh40qmqd7376xn8qxd6hm5lwjyy0h2/T/Rtmp7o8rJG/temp_libpathc44a3830802e/auk/extdata/ebd-sample.txt +#> EBD: /private/var/folders/mg/qh40qmqd7376xn8qxd6hm5lwjyy0h2/T/RtmpiRmICh/temp_libpath35e33c916c85/auk/extdata/ebd-sample.txt #> #> Output #> Filters not executed @@ -188,7 +188,7 @@

    Examples

    auk_year(year = c(2010, 2012)) %>% auk_date(date = c("*-05-01", "*-06-30")) #> Input -#> EBD: /private/var/folders/mg/qh40qmqd7376xn8qxd6hm5lwjyy0h2/T/Rtmp7o8rJG/temp_libpathc44a3830802e/auk/extdata/ebd-sample.txt +#> EBD: /private/var/folders/mg/qh40qmqd7376xn8qxd6hm5lwjyy0h2/T/RtmpiRmICh/temp_libpath35e33c916c85/auk/extdata/ebd-sample.txt #> #> Output #> Filters not executed diff --git a/docs/reference/filter_repeat_visits.html b/docs/reference/filter_repeat_visits.html index 9f2aa67..0cf9d9d 100644 --- a/docs/reference/filter_repeat_visits.html +++ b/docs/reference/filter_repeat_visits.html @@ -189,7 +189,7 @@

    Examples

    #> 5 L1277940_obs… 2012-8 3 S11668164 2017-05-27 10:2… Singap… #> 6 L1361109_obs… 2012-0 10 S9513531 2017-05-27 10:3… Singap… #> 7 L1361109_obs… 2012-0 10 S9598863 2017-05-27 10:3… Singap… -#> 8 L1361109_obs… 2012-0 10 S9612576 2017-05-27 10:3… Singap… +#> 8 L1361109_obs… 2012-0 10 S9640246 2012-03-20 03:2… Singap… #> 9 L1361109_obs… 2012-0 10 S9652466 2012-03-20 03:2… Singap… #> 10 L1361109_obs… 2012-0 10 S9663623 2013-09-11 12:2… Singap… #> # ℹ 171 more rows diff --git a/docs/reference/format_unmarked_occu.html b/docs/reference/format_unmarked_occu.html index 1a3f89d..5c34532 100644 --- a/docs/reference/format_unmarked_occu.html +++ b/docs/reference/format_unmarked_occu.html @@ -177,7 +177,7 @@

    Examples

    #> #> Tabulation of y observations: #> FALSE TRUE <NA> -#> 132 49 289 +#> 131 50 289 #> #> Site-level covariates: #> latitude longitude @@ -190,13 +190,13 @@

    Examples

    #> #> Observation-level covariates: #> effort_distance_km duration_minutes -#> Min. : 0.100 Min. : 1.0 -#> 1st Qu.: 0.200 1st Qu.: 15.0 -#> Median : 1.000 Median : 30.0 -#> Mean : 1.574 Mean : 68.3 -#> 3rd Qu.: 2.000 3rd Qu.: 90.0 -#> Max. :10.000 Max. :480.0 -#> NA's :392 NA's :391 +#> Min. : 0.100 Min. : 1.00 +#> 1st Qu.: 0.200 1st Qu.: 15.00 +#> Median : 1.000 Median : 30.00 +#> Mean : 1.592 Mean : 67.97 +#> 3rd Qu.: 2.000 3rd Qu.: 90.00 +#> Max. :10.000 Max. :480.00 +#> NA's :395 NA's :394 # this function can also be used for abundance modeling abd <- ebd_zf %>% @@ -229,7 +229,7 @@

    Examples

    #> #> Tabulation of y observations: #> 0 1 2 3 5 10 <NA> -#> 132 18 9 3 7 2 269 +#> 130 20 9 3 7 2 269 #> #> Site-level covariates: #> latitude longitude @@ -245,10 +245,10 @@

    Examples

    #> Min. : 0.100 Min. : 1.00 #> 1st Qu.: 0.200 1st Qu.: 15.00 #> Median : 1.000 Median : 30.00 -#> Mean : 1.595 Mean : 68.24 -#> 3rd Qu.: 2.000 3rd Qu.: 90.00 +#> Mean : 1.563 Mean : 65.75 +#> 3rd Qu.: 2.000 3rd Qu.: 75.00 #> Max. :10.000 Max. :480.00 -#> NA's :362 NA's :361 +#> NA's :360 NA's :359
    diff --git a/docs/sitemap.xml b/docs/sitemap.xml index 3470e14..7e8349b 100644 --- a/docs/sitemap.xml +++ b/docs/sitemap.xml @@ -31,7 +31,7 @@ /news/index.html - /reference/auk.html + /reference/auk-package.html /reference/auk_bbox.html diff --git a/man/auk-package.Rd b/man/auk-package.Rd new file mode 100644 index 0000000..b72d0c0 --- /dev/null +++ b/man/auk-package.Rd @@ -0,0 +1,36 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/auk-package.R +\docType{package} +\name{auk-package} +\alias{auk} +\alias{auk-package} +\title{\code{auk}: eBird Data Extraction and Processing in R} +\description{ +Tools for extracting and processing eBird data from the eBird Basic Dataset +(EBD). +} +\seealso{ +Useful links: +\itemize{ + \item \url{https://github.com/CornellLabofOrnithology/auk} + \item \url{https://cornelllabofornithology.github.io/auk/} + \item Report bugs at \url{https://github.com/CornellLabofOrnithology/auk/issues} +} + +} +\author{ +\strong{Maintainer}: Matthew Strimas-Mackey \email{mes335@cornell.edu} (\href{https://orcid.org/0000-0001-8929-7776}{ORCID}) + +Authors: +\itemize{ + \item Eliot Miller + \item Wesley Hochachka +} + +Other contributors: +\itemize{ + \item Cornell Lab of Ornithology [copyright holder] +} + +} +\keyword{internal} diff --git a/man/auk.Rd b/man/auk.Rd deleted file mode 100644 index 1a673ba..0000000 --- a/man/auk.Rd +++ /dev/null @@ -1,11 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/auk-package.R -\docType{package} -\name{auk} -\alias{auk} -\title{\code{auk}: eBird Data Extraction and Processing in R} -\description{ -Tools for extracting and processing eBird data from the eBird Basic Dataset -(EBD). -} -\keyword{internal}