From 7ec22dd4750968e8b5f553f2dc56cb114d9edfe9 Mon Sep 17 00:00:00 2001 From: Rob Baker Date: Fri, 20 Sep 2024 16:32:28 -0600 Subject: [PATCH 1/4] private .* functions better hidden --- R/geography.R | 2 ++ R/utils.R | 2 ++ 2 files changed, 4 insertions(+) diff --git a/R/geography.R b/R/geography.R index 8f41d47..d043d1e 100644 --- a/R/geography.R +++ b/R/geography.R @@ -60,6 +60,8 @@ return(in_park) #' @param park_units String. Or list of strings. #' #' @return sf dataframe +#' @keywords internal +#' @noRd #' @examples #' \dontrun{ #' .get_unit_boundary("ROMO") diff --git a/R/utils.R b/R/utils.R index ef71488..b01a9f5 100644 --- a/R/utils.R +++ b/R/utils.R @@ -50,6 +50,8 @@ globalVariables(c("any_of", #' #' @return String. The user's email address. #' @export +#' @keywords internal +#' @noRd #' #' @examples #' \dontrun{ From 10d28ccb6e5e78a222a0d5ae21745306123ce43b Mon Sep 17 00:00:00 2001 From: Rob Baker Date: Fri, 20 Sep 2024 16:32:51 -0600 Subject: [PATCH 2/4] update via devtools::document and pkgdown::build_site_github_pages --- .github/workflows/pkgdown.yaml | 48 ------ .github/workflows/test-coverage.yaml | 50 ------ DESCRIPTION | 2 +- docs/404.html | 14 +- docs/LICENSE-text.html | 14 +- docs/LICENSE.html | 14 +- docs/articles/DRR_Purpose_and_Scope.html | 19 +-- docs/articles/Starting-a-DRR.html | 19 +-- docs/articles/Using-the-DRR-Template.html | 19 +-- docs/articles/index.html | 14 +- docs/authors.html | 20 +-- docs/index.html | 14 +- docs/news/index.html | 16 +- docs/pkgdown.yml | 11 +- docs/reference/DC_col_check.html | 23 +-- docs/reference/QCkit-package.html | 14 +- docs/reference/check_dc_cols.html | 23 +-- docs/reference/check_te.html | 32 ++-- docs/reference/convert_datetime_format.html | 24 +-- docs/reference/convert_long_to_utm.html | 22 +-- docs/reference/convert_utm_to_ll.html | 34 ++-- docs/reference/create_datastore_script.html | 30 ++-- docs/reference/document_missing_values.html | 34 ++-- docs/reference/dot-get_unit_boundary.html | 118 -------------- docs/reference/fix_utc_offset.html | 22 +-- docs/reference/fuzz_location.html | 28 ++-- docs/reference/generate_ll_from_utm.html | 36 ++--- docs/reference/get_custom_flags.html | 30 ++-- docs/reference/get_dc_flags.html | 26 +-- docs/reference/get_df_flags.html | 26 +-- docs/reference/get_dp_flags.html | 26 +-- docs/reference/get_elevation.html | 34 ++-- docs/reference/get_park_polygon.html | 22 +-- docs/reference/get_taxon_rank.html | 28 ++-- docs/reference/get_user_email.html | 117 -------------- docs/reference/get_utm_zone.html | 22 +-- docs/reference/index.html | 24 +-- docs/reference/long2UTM.html | 22 +-- docs/reference/order_cols.html | 23 +-- docs/reference/remove_empty_tables.html | 22 +-- docs/reference/replace_blanks.html | 28 ++-- docs/reference/te_check.html | 32 ++-- docs/reference/utm_to_ll.html | 34 ++-- docs/reference/validate_coord.html | 26 +-- docs/reference/validate_coord_list.html | 30 ++-- docs/sitemap.xml | 166 +++++--------------- man/dot-get_unit_boundary.Rd | 22 --- man/get_user_email.Rd | 24 --- 48 files changed, 514 insertions(+), 984 deletions(-) delete mode 100644 .github/workflows/pkgdown.yaml delete mode 100644 .github/workflows/test-coverage.yaml delete mode 100644 docs/reference/dot-get_unit_boundary.html delete mode 100644 docs/reference/get_user_email.html delete mode 100644 man/dot-get_unit_boundary.Rd delete mode 100644 man/get_user_email.Rd diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml deleted file mode 100644 index ed7650c..0000000 --- a/.github/workflows/pkgdown.yaml +++ /dev/null @@ -1,48 +0,0 @@ -# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples -# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help -on: - push: - branches: [main, master] - pull_request: - branches: [main, master] - release: - types: [published] - workflow_dispatch: - -name: pkgdown - -jobs: - pkgdown: - runs-on: ubuntu-latest - # Only restrict concurrency for non-PR jobs - concurrency: - group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }} - env: - GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} - permissions: - contents: write - steps: - - uses: actions/checkout@v3 - - - uses: r-lib/actions/setup-pandoc@v2 - - - uses: r-lib/actions/setup-r@v2 - with: - use-public-rspm: true - - - uses: r-lib/actions/setup-r-dependencies@v2 - with: - extra-packages: any::pkgdown, local::. - needs: website - - - name: Build site - run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE) - shell: Rscript {0} - - - name: Deploy to GitHub pages 🚀 - if: github.event_name != 'pull_request' - uses: JamesIves/github-pages-deploy-action@v4.4.1 - with: - clean: false - branch: gh-pages - folder: docs diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml deleted file mode 100644 index 960234c..0000000 --- a/.github/workflows/test-coverage.yaml +++ /dev/null @@ -1,50 +0,0 @@ -# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples -# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help -on: - push: - branches: [main, master] - pull_request: - branches: [main, master] - -name: test-coverage - -jobs: - test-coverage: - runs-on: ubuntu-latest - env: - GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} - - steps: - - uses: actions/checkout@v4 - - - uses: r-lib/actions/setup-r@v2 - with: - use-public-rspm: true - - - uses: r-lib/actions/setup-r-dependencies@v2 - with: - extra-packages: any::covr - needs: coverage - - - name: Test coverage - run: | - covr::codecov( - quiet = FALSE, - clean = FALSE, - install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package") - ) - shell: Rscript {0} - - - name: Show testthat output - if: always() - run: | - ## -------------------------------------------------------------------- - find ${{ runner.temp }}/package -name 'testthat.Rout*' -exec cat '{}' \; || true - shell: bash - - - name: Upload test results - if: failure() - uses: actions/upload-artifact@v4 - with: - name: coverage-test-failures - path: ${{ runner.temp }}/package diff --git a/DESCRIPTION b/DESCRIPTION index cc5a67c..01aa385 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -62,7 +62,7 @@ Imports: cli, purrr, lifecycle -RoxygenNote: 7.3.1 +RoxygenNote: 7.3.2 Suggests: knitr, rmarkdown, diff --git a/docs/404.html b/docs/404.html index c454bf5..1932044 100644 --- a/docs/404.html +++ b/docs/404.html @@ -18,7 +18,7 @@ - +
- +
@@ -106,16 +106,16 @@

Page not found (404)

-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.0.

- - + + diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html index daa2256..9642e7d 100644 --- a/docs/LICENSE-text.html +++ b/docs/LICENSE-text.html @@ -3,7 +3,7 @@ - +
- +
@@ -103,15 +103,15 @@

License

-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.0.

- - + + diff --git a/docs/LICENSE.html b/docs/LICENSE.html index eb36c9b..a0bdba0 100644 --- a/docs/LICENSE.html +++ b/docs/LICENSE.html @@ -3,7 +3,7 @@ - +
- +
@@ -112,15 +112,15 @@

Statement of Purpose -

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.0.

- - + + diff --git a/docs/articles/DRR_Purpose_and_Scope.html b/docs/articles/DRR_Purpose_and_Scope.html index 92ee143..10c5a8e 100644 --- a/docs/articles/DRR_Purpose_and_Scope.html +++ b/docs/articles/DRR_Purpose_and_Scope.html @@ -12,14 +12,13 @@ - - +
- +
@@ -416,9 +415,7 @@

References - -

+
@@ -431,16 +428,16 @@

References

-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.0.

- - + + diff --git a/docs/articles/Starting-a-DRR.html b/docs/articles/Starting-a-DRR.html index 0100707..8e8accf 100644 --- a/docs/articles/Starting-a-DRR.html +++ b/docs/articles/Starting-a-DRR.html @@ -12,14 +12,13 @@ - - +
- +
@@ -208,9 +207,7 @@

Examples - -

+
@@ -223,16 +220,16 @@

Examples

-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.0.

- - + + diff --git a/docs/articles/Using-the-DRR-Template.html b/docs/articles/Using-the-DRR-Template.html index 5aa0138..8fbd203 100644 --- a/docs/articles/Using-the-DRR-Template.html +++ b/docs/articles/Using-the-DRR-Template.html @@ -12,14 +12,13 @@ - - +
- +
@@ -647,9 +646,7 @@

Liability Statements - -

+
@@ -662,16 +659,16 @@

Liability Statements

-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.0.

- - + + diff --git a/docs/articles/index.html b/docs/articles/index.html index fa5d3a9..c836e50 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -3,7 +3,7 @@ - +
- +
@@ -82,15 +82,15 @@

All vignettes

-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.0.

- - + + diff --git a/docs/authors.html b/docs/authors.html index db3663a..d13740f 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -3,7 +3,7 @@ - +
- +
@@ -63,7 +63,7 @@

Authors and Citation

- +

  • Robert Baker. Author, maintainer.

    @@ -73,7 +73,7 @@

    Authors and Citation

  • -

    Joe DeVivo. Author. +

    Joe DeVivo. Author.

  • @@ -103,7 +103,7 @@

    Citation

    Baker R, Patterson J, DeVivo J, Quevedo I, Wright S (2024). QCkit: NPS Inventory and Monitoring Quality Control Toolkit. -R package version 0.1.7, https://github.com/nationalparkservice/QCkit/. +R package version 0.1.7, https://github.com/nationalparkservice/QCkit/. 

    @Manual{,
   title = {QCkit: NPS Inventory and Monitoring Quality Control Toolkit},
@@ -124,15 +124,15 @@ 
    Citation
-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.0.

- - + + diff --git a/docs/index.html b/docs/index.html index 2573281..472d49d 100644 --- a/docs/index.html +++ b/docs/index.html @@ -19,7 +19,7 @@ - +
- +
@@ -167,16 +167,16 @@

Dev status

-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.0.

- - + + diff --git a/docs/news/index.html b/docs/news/index.html index 9984134..09b9821 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -3,7 +3,7 @@ - +
- +
@@ -66,7 +66,7 @@

Changelog

QCkit v0.1.8 (not yet released)

2024-07-16 * Added experimental function document_missing_values(), which searches a file for multiple missing value codes, replaces them all with NA, and generates a new column with the missing value codes so that they can be properly documented in EML. This is a work-around for the fact that there is currently not a good way to get multiple missing value codes in a single column via EMLassemblyline. This function is still under development; expect substantial changes an improvements up to and including removing the function entirely.

-

2024-07-09 * Added function get_user_email(), which accesses NPS active directory via a powershell function to return the user’s email address. Probably won’t work for non-NPS users and probably won’t work for non-windows users. * Updated rest API from legacy v6 to current v7.

+

2024-07-09 * Added function get_user_email(), which accesses NPS active directory via a powershell function to return the user’s email address. Probably won’t work for non-NPS users and probably won’t work for non-windows users. * Updated rest API from legacy v6 to current v7.

2024-06-28 * Updated get_park_polygon() to use the new API (had been using a legacy API). Added documentation to specify that the function is getting the convexhull for the park, which may not work particularly well for some parks. 2024-06-27 * bug fixes for generate_ll_from_utm() * add function remove_empty_tables() (and associated unit tests) * update documentation for replace blanks() to indicate it can replace blanks with more than just NA

@@ -164,15 +164,15 @@

QCkit 0.1.0.0
-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.0.

- - + + diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index e07e1b3..dd166e1 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -1,9 +1,8 @@ pandoc: 3.1.11 -pkgdown: 2.0.9 +pkgdown: 2.1.0 pkgdown_sha: ~ articles: - DRR_Purpose_and_Scope: DRR_Purpose_and_Scope.html - Starting-a-DRR: Starting-a-DRR.html - Using-the-DRR-Template: Using-the-DRR-Template.html -last_built: 2024-07-16T15:01Z - + articles/DRR_Purpose_and_Scope: DRR_Purpose_and_Scope.html + articles/Starting-a-DRR: Starting-a-DRR.html + articles/Using-the-DRR-Template: Using-the-DRR-Template.html +last_built: 2024-09-20T20:54Z diff --git a/docs/reference/DC_col_check.html b/docs/reference/DC_col_check.html index be07306..bfbf28e 100644 --- a/docs/reference/DC_col_check.html +++ b/docs/reference/DC_col_check.html @@ -5,7 +5,7 @@ - +
- +
@@ -78,14 +78,15 @@

TDWG Darwin Core Column Name Check 08-23-2022

Arguments

-
working_df
+ + +
working_df

  • This is the dataframe you want to run against the function. To call, simply write working_df = "the name of your dataframe".

Value

-

  • The function returns a list of the column names you should fix (not fitting with simple Darwin Core terms, custom name formatting, data quality flagging formatting). Additionally, a small summary table is printed with the counts of the columns falling under each category (DarwinCore, Custom, DQ, Fix Me).

@@ -96,9 +97,9 @@

Details

Examples

- 
if (FALSE) {
+    
if (FALSE) { # \dontrun{
 DC_col_check(yourdataframe)
-}
+} # }
@@ -113,15 +114,15 @@

Examples

-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.0.

- - + + diff --git a/docs/reference/QCkit-package.html b/docs/reference/QCkit-package.html index 8f9db73..86ecc16 100644 --- a/docs/reference/QCkit-package.html +++ b/docs/reference/QCkit-package.html @@ -3,7 +3,7 @@ - +
- +
@@ -98,15 +98,15 @@

Author

-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.0.

- - + + diff --git a/docs/reference/check_dc_cols.html b/docs/reference/check_dc_cols.html index 101d434..5b091ac 100644 --- a/docs/reference/check_dc_cols.html +++ b/docs/reference/check_dc_cols.html @@ -3,7 +3,7 @@ - +
- +
@@ -74,14 +74,15 @@

TDWG Darwin Core Column Name Check 08-23-2022

Arguments

-
working_df
+ + +
working_df

  • This is the dataframe you want to run against the function. To call, simply write working_df = "the name of your dataframe".

Value

-

  • The function returns a list of the column names you should fix (not fitting with simple Darwin Core terms, custom name formatting, data quality flagging formatting). Additionally, a small summary table is printed with the counts of the columns falling under each category (DarwinCore, Custom, DQ, Fix Me).

@@ -92,9 +93,9 @@

Details

Examples

- 
if (FALSE) {
+    
if (FALSE) { # \dontrun{
 check_dc_cols(yourdataframe)
-}
+} # }
@@ -109,15 +110,15 @@

Examples

-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.0.

- - + + diff --git a/docs/reference/check_te.html b/docs/reference/check_te.html index 8c49dab..3b6ada8 100644 --- a/docs/reference/check_te.html +++ b/docs/reference/check_te.html @@ -3,7 +3,7 @@ - +
- +
@@ -74,31 +74,31 @@

Threatened Or Endangered Species Checker Function

Arguments

-
x
+ + +
x

  • The name of your data frame containing species observations

-
species_col
+
species_col

  • The name of the column within your data frame containing the scientific names of the species (genus and specific epithet).

-
park_code
+
park_code

  • A four letter park code. Or a list of park codes.

-
expansion
+
expansion

  • Logical. Defaults to FALSE. The default setting will return only exact matches between your the scientific binomial (genera and specific epithet) in your data set and the federal match list. Setting expansion = TRUE will expand the list of matches to return all species (and subspecies) that from the match list that match any genera listed in your data set, regardless of whether a given species is actually in your data set. An additional column indicating whether the species returned is in your data set ("In your Data") or has been expanded to ("Expansion") is generated.

Value

- - -

The function returns a (modified) data frame with the names of all the species that fall under the federal conservation list. The resulting data frame may have multiple instances of a given species if it is listed in multiple parks (park codes for each listing are supplied). Technically it is a huxtable, but it should function identically to a data frame for downstream purposes.

+

The function returns a (modified) data frame with the names of all the species that fall under the federal conservation list. The resulting data frame may have multiple instances of a given species if it is listed in multiple parks (park codes for each listing are supplied). Technically it is a huxtable, but it should function identically to a data frame for downstream purposes.

Details

@@ -110,14 +110,14 @@

Details

Examples

- 
if (FALSE) {
+    
if (FALSE) { # \dontrun{
 #for individual parks:
 check_te(x = my_species_dataframe, species_col = "scientificName", park_code = "BICY")
 list<-check_te(data, "scientificName", "ROMO", expansion=TRUE)
 # for a list of parks:
 park_code<-c("ROMO", "YELL", "SAGU")
 list<-check_te(data, "scientificName", park_code, expansion=TRUE)
-}
+} # }
@@ -133,15 +133,15 @@

Examples

-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.0.

- - + + diff --git a/docs/reference/convert_datetime_format.html b/docs/reference/convert_datetime_format.html index 640a906..63f4e43 100644 --- a/docs/reference/convert_datetime_format.html +++ b/docs/reference/convert_datetime_format.html @@ -3,7 +3,7 @@ - +
- +
@@ -74,19 +74,19 @@

Convert EML date/time format string to one that R can parse

Arguments

-
eml_format_string
+ + +
eml_format_string

A character vector of EML date/time format strings. This function understands the following codes: YYYY = four digit year, YY = two digit year, MMM = three letter month abbrev., MM = two digit month, DD = two digit day, hh or HH = 24 hour time, mm = minutes, ss or SS = seconds, +/-hhmm, +/-hh:mm, or +/-hh = UTC offset.

-
convert_z
+
convert_z

Should a "Z" at the end of the format string (indicating UTC) be replaced by a "%z"? Only set to TRUE if you plan to use fix_utc_offset to change "Z" in datetime strings to "+0000".

Value

- - -

A character vector of date/time format strings that can be parsed by readr or strptime.

+

A character vector of date/time format strings that can be parsed by readr or strptime.

Details

@@ -114,15 +114,15 @@

Examples

-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.0.

- - + + diff --git a/docs/reference/convert_long_to_utm.html b/docs/reference/convert_long_to_utm.html index ecbf43d..f62c872 100644 --- a/docs/reference/convert_long_to_utm.html +++ b/docs/reference/convert_long_to_utm.html @@ -7,7 +7,7 @@ - +
- +
@@ -82,16 +82,16 @@

Return UTM Zone

Arguments

-
lon
+ + +
lon

  • Decimal degree longitude value

Value

- - -

The function returns a numeric UTM zone (between 1 and 60).

+

The function returns a numeric UTM zone (between 1 and 60).

Details

@@ -111,15 +111,15 @@

Details

-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.0.

- - + + diff --git a/docs/reference/convert_utm_to_ll.html b/docs/reference/convert_utm_to_ll.html index 452c7d2..f241fe9 100644 --- a/docs/reference/convert_utm_to_ll.html +++ b/docs/reference/convert_utm_to_ll.html @@ -13,7 +13,7 @@ - +
- +
@@ -94,30 +94,32 @@

Coordinate Conversion from UTM to Latitude and Longitude

Arguments

-
df
+ + +
df

  • The dataframe with UTM coordinates you would like to convert. Input the name of your dataframe.

-
EastingCol
+
EastingCol

  • The name of your Easting UTM column. Input the name in quotations, ie. "EastingCol".

-
NorthingCol
+
NorthingCol

  • The name of your Northing UTM column. Input the name in quotations, ie. "NorthingCol".

-
zone
+
zone

  • The UTM Zone. Input the zone number in quotations, ie. "17".

-
datum
+
datum

  • The datum used in the coordinate reference system of your coordinates. Input in quotations, ie. "WGS84"

@@ -125,9 +127,7 @@

Arguments

Value

- - -

The function returns your dataframe, mutated with an additional two +

The function returns your dataframe, mutated with an additional two columns of decimal Longitude and decimal Latitude.

@@ -144,7 +144,7 @@

Details

Examples

- 
if (FALSE) {
+    
if (FALSE) { # \dontrun{
 convert_utm_to_ll(
   df = mydataframe,
   EastingCol = "EastingCoords",
@@ -152,7 +152,7 @@ 
Examples

   zone = "17",
   datum = "WGS84"
 )
-}
+} # }
@@ -167,15 +167,15 @@

Examples

-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.0.

- - + + diff --git a/docs/reference/create_datastore_script.html b/docs/reference/create_datastore_script.html index dc35647..d7361fe 100644 --- a/docs/reference/create_datastore_script.html +++ b/docs/reference/create_datastore_script.html @@ -8,7 +8,7 @@ - +
- +
@@ -90,32 +90,34 @@

Turn a GitHub release into a DataStore Script Reference

Arguments

-
owner
+ + +
owner

String. The owner of the account where the GitHub repo resides. For example, "nationalparkservice"

-
repo
+
repo

String. The repo with a release that should be turned into a DataStore Script reference. For example, "EMLeditor"

-
path
+
path

String. The location where the release .zip from GitHub should be downloaded to (and uploaded from). Defaults to the working directory of the R Project (i.e. here::here()).

-
force
+
force

Logical. Defaults to FALSE. In the default status the function has a number of interactive components, such as searching DataStore for similarly titled References and asking if a new Reference is really what the user wants. When set to TRUE, all interactive components are turned off and the function will proceed unless it hits an error. Setting force = TRUE may be useful for scripting purposes.

-
dev
+
dev

Logical. Defaults to FALSE. In the default status, the function generates and populates a new draft Script reference on the DataStore production server. If set to TRUE, the draft Script reference will be generated and populated on the DataStore development server. Setting dev = TRUE may be useful for testing the function without generating excessive references on the DataStore production server.

Examples

- 
if (FALSE) {
+    
if (FALSE) { # \dontrun{
 create_datastore_script("nationalparkservice", "EMLeditor")
-}
+} # }
@@ -130,15 +132,15 @@

Examples

-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.0.

- - + + diff --git a/docs/reference/document_missing_values.html b/docs/reference/document_missing_values.html index c86f3d0..ca31267 100644 --- a/docs/reference/document_missing_values.html +++ b/docs/reference/document_missing_values.html @@ -16,7 +16,7 @@ - +
- +
@@ -106,31 +106,31 @@

Handles multiple missing values

Arguments

-
file_name
+ + +
file_name

String. The name of the file to inspect

-
directory
+
directory

String. Location of file to read/write. Defaults to the current working directory.

-
colname
+
colname

[Experimental] String. The columns to inspect. CURRENTLY ONLY WORKS AS SET TO DEFAULT "NA".

-
missing_val_codes
+
missing_val_codes

List. A list of strings containing the missing value code or codes to search for.

-
replace_value
+
replace_value

String. The value (singular) to replace multiple missing values with. Defaults to NA.

Value

- - -

writes a new dataframe to file. Return invisible.

+

writes a new dataframe to file. Return invisible.

Details

@@ -139,13 +139,13 @@

Details

Examples

- 
if (FALSE) {
+    
if (FALSE) { # \dontrun{
 document_missing_values(file_name = "mydata.csv",
                         directory = here::here(),
                         colname = NA, #do not change during function development
                         missing_val_codes = c("missing", "blank", "no data"),
                         replace_value = NA)
-                        }
+                        } # }
@@ -160,15 +160,15 @@

Examples

-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.0.

- - + + diff --git a/docs/reference/dot-get_unit_boundary.html b/docs/reference/dot-get_unit_boundary.html deleted file mode 100644 index a8da334..0000000 --- a/docs/reference/dot-get_unit_boundary.html +++ /dev/null @@ -1,118 +0,0 @@ - -Gets NPS unit boundaries from Arc GIS — .get_unit_boundary • QCkit - - -
-
- - - -
-
-
-

Gets NPS unit boundaries from Arc GIS

- Source: R/geography.R - -
- -
-

Gets NPS unit boundaries from Arc GIS

-
- -
- 
.get_unit_boundary(park_units)
-
- -
-

Arguments

-
park_units
-

String. Or list of strings.

- -
-
-

Value

- - -

sf dataframe

-
- -
-

Examples

- 
if (FALSE) {
-.get_unit_boundary("ROMO")
-}
-
-
-
- -
- - -
-

Developed by Robert Baker, Judd Patterson, Joe DeVivo, Issac Quevedo, Sarah Wright.

-
- -
-

Site built with pkgdown 2.0.9.

-
- -
- - - - - - - - diff --git a/docs/reference/fix_utc_offset.html b/docs/reference/fix_utc_offset.html index dd68880..dae698d 100644 --- a/docs/reference/fix_utc_offset.html +++ b/docs/reference/fix_utc_offset.html @@ -3,7 +3,7 @@ - +
- +
@@ -74,15 +74,15 @@

Fix UTC offset strings

Arguments

-
datetime_strings
+ + +
datetime_strings

Character vector of dates in ISO 8601 format

Value

- - -

datetime_strings with UTC offsets consistently formatted to four digits (e.g. "2023-11-16T03:32:49-0700").

+

datetime_strings with UTC offsets consistently formatted to four digits (e.g. "2023-11-16T03:32:49-0700").

@@ -108,15 +108,15 @@

Examples

-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.0.

- - + + diff --git a/docs/reference/fuzz_location.html b/docs/reference/fuzz_location.html index 6920e2a..6d7c048 100644 --- a/docs/reference/fuzz_location.html +++ b/docs/reference/fuzz_location.html @@ -9,7 +9,7 @@ - +
- +
@@ -86,17 +86,19 @@

Convert Coordinates Into a Polygon to Obscure Specific Location

Arguments

-
lat
+ + +
lat

  • The latitude in either UTMs or decimal degrees.

-
lon
+
lon

  • The longitude in either UTMs or decimal degrees

-
coord_ref_sys
+
coord_ref_sys

  • The EPSG coordinate system of the latitude and longitude coordinates. Either 4326 for decimal degrees/WGS84 datum, 4269 for decimal degrees/NAD83, or 326xx for UTM/WGS84 datum (where the xx is the @@ -104,7 +106,7 @@

    Arguments

-
fuzz_level
+
fuzz_level

  • Use "Fuzzed - 10km", "Fuzzed - 1km", or "Fuzzed - 100m"

@@ -116,10 +118,10 @@

Details

Examples

- 
if (FALSE) {
+    
if (FALSE) { # \dontrun{
 fuzz_location(703977, 4035059, 32616, "Fuzzed - 1km")
 fuzz_location(36.43909, -84.72429, 4326, "Fuzzed - 1km")
-}
+} # }
@@ -134,15 +136,15 @@

Examples

-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.0.

- - + + diff --git a/docs/reference/generate_ll_from_utm.html b/docs/reference/generate_ll_from_utm.html index 1fc0674..adb5881 100644 --- a/docs/reference/generate_ll_from_utm.html +++ b/docs/reference/generate_ll_from_utm.html @@ -11,7 +11,7 @@ - +
- +
@@ -97,45 +97,45 @@

Coordinate Conversion from UTM to Latitude and Longitude

Arguments

-
df
+ + +
df

  • The dataframe with UTM coordinates you would like to convert. Input the name of your dataframe.

-
EastingCol
+
EastingCol

  • The name of your Easting UTM column. You may input the name with or without quotations, ie. EastingCol and "EastingCol" are both valid.

-
NorthingCol
+
NorthingCol

  • The name of your Northing UTM column. You may input the name with or without quotations, ie. NorthingCol and "NorthingCol" are both valid.

-
ZoneCol
+
ZoneCol

  • The column containing the UTM zone, with or without quotations.

-
DatumCol
+
DatumCol

  • The column containing the datum for your UTM coordinates, with or without quotations.

-
latlong_datum
+
latlong_datum

  • The datum to use for lat/long coordinates. Defaults to NAD83.

Value

- - -

The function returns your dataframe, mutated with an additional two +

The function returns your dataframe, mutated with an additional two columns of decimalLongitude and decimalLatitude plus a column LatLong_CRS containing a PROJ string that specifies the coordinate reference system for these data.

@@ -157,7 +157,7 @@

Details

Examples

- 
if (FALSE) {
+    
if (FALSE) { # \dontrun{
 
 # Using magrittr pipe (%>%) and unquoted column names
 my_dataframe %>%
@@ -194,7 +194,7 @@ 
Examples

   latlong_datum = latlong_dat  # this isn't a column name so it doesn't need {{}}
 )
 
-}
+} # }
@@ -209,15 +209,15 @@

Examples

-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.0.

- - + + diff --git a/docs/reference/get_custom_flags.html b/docs/reference/get_custom_flags.html index 5abf6eb..0679de9 100644 --- a/docs/reference/get_custom_flags.html +++ b/docs/reference/get_custom_flags.html @@ -18,7 +18,7 @@ - +
- +
@@ -108,17 +108,19 @@

Creates dataframe(s) summarizing data quality

Arguments

-
directory
+ + +
directory

is the path to the data package .csv files (defaults to the current working directory).

-
cols
+
cols

A comma delimited list of column names. If left unspecified, defaults to just flagged columns.

-
output
+
output

A string indicating what output should be provided. "columns" returns a summary table of QC flags and RRU values in each specified column for every data file. "files" returns a summary table of total QC flags and @@ -128,9 +130,7 @@

Arguments

Value

- - -

a dataframe with quality control summary information summarized at +

a dataframe with quality control summary information summarized at the specified level(s).

@@ -147,14 +147,14 @@

Details

Examples

- 
if (FALSE) {
+    
if (FALSE) { # \dontrun{
 
 get_custom_flags("~/my_data_package_directory", cols = c("scientificName",
                                                          "locality"),
                                                          output="all")
 cols <- colnames(read.csv("mydata.csv"))[c(1:4, 7, 10)]
 get_custom_flags(cols = cols, output="files")
-}
+} # }
@@ -169,15 +169,15 @@

Examples

-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.0.

- - + + diff --git a/docs/reference/get_dc_flags.html b/docs/reference/get_dc_flags.html index 6614c76..42afc2f 100644 --- a/docs/reference/get_dc_flags.html +++ b/docs/reference/get_dc_flags.html @@ -9,7 +9,7 @@ - +
- +
@@ -86,16 +86,16 @@

Create Table of Data Quality Flags in Flagging Columns within individual dat

Arguments

-
directory
+ + +
directory

is the path to the data package .csv files (defaults to the current working directory).

Value

- - -

a dataframe named dc_flag that contains a row for each .csv file in +

a dataframe named dc_flag that contains a row for each .csv file in the directory with the file name, the count of each flag and total number of data points in each .csv (including data flagging columns).

@@ -111,13 +111,13 @@

Details

Examples

- 
if (FALSE) {
+    
if (FALSE) { # \dontrun{
 get_df_flags("~/my_data_package_directory")
 get_df_flags() # if your current working directory IS the data package
 directory.
 # ->
 get_custom_flags(output="columns")
-}
+} # }
@@ -133,15 +133,15 @@

Examples

-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.0.

- - + + diff --git a/docs/reference/get_df_flags.html b/docs/reference/get_df_flags.html index 7fb2983..2099a37 100644 --- a/docs/reference/get_df_flags.html +++ b/docs/reference/get_df_flags.html @@ -9,7 +9,7 @@ - +
- +
@@ -86,16 +86,16 @@

Create Table of Data Quality Flags Found in Data Files within a Data Package

Arguments

-
directory
+ + +
directory

is the path to the data package .csv files (defaults to the current working directory).

Value

- - -

a dataframe named df_flag that contains a row for each .csv file in +

a dataframe named df_flag that contains a row for each .csv file in the directory with the file name, the count of each flag and total number of data points in each .csv (including data flagging columns).

@@ -111,13 +111,13 @@

Details

Examples

- 
if (FALSE) {
+    
if (FALSE) { # \dontrun{
 get_df_flags("~/my_data_package_directory")
 get_df_flags() # if your current working directory IS the data package
 directory.
 # ->
 get_custom_flags(output="files")
-}
+} # }
@@ -133,15 +133,15 @@

Examples

-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.0.

- - + + diff --git a/docs/reference/get_dp_flags.html b/docs/reference/get_dp_flags.html index 526f185..f2f92d8 100644 --- a/docs/reference/get_dp_flags.html +++ b/docs/reference/get_dp_flags.html @@ -9,7 +9,7 @@ - +
- +
@@ -86,16 +86,16 @@

Create Table of Data Quality Flags Found in a Data Package

Arguments

-
directory
+ + +
directory

is the path to the data package .csv files (defaults to the current working directory).

Value

- - -

a dataframe named dp_flag that contains the four flags, the count of +

a dataframe named dp_flag that contains the four flags, the count of each flag and total number of data points in the entire data package.

@@ -111,13 +111,13 @@

Details

Examples

- 
if (FALSE) {
+    
if (FALSE) { # \dontrun{
 get_dp_flags("~/my_data_package_directory")
 get_dp_flags() # if your current working directory IS the data package
 directory.
 # ->
 get_custom_flags(output="package")
-}
+} # }
@@ -133,15 +133,15 @@

Examples

-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.0.

- - + + diff --git a/docs/reference/get_elevation.html b/docs/reference/get_elevation.html index cd8a710..b9054e4 100644 --- a/docs/reference/get_elevation.html +++ b/docs/reference/get_elevation.html @@ -3,7 +3,7 @@ - +
- +
@@ -80,31 +80,31 @@

Add elevation to a dataset

Arguments

-
df
+ + +
df

a data frame containing GPS decimal coordinates for individual points with latitude and longitude in separate columns.

-
decimal_lat
+
decimal_lat

String. The name of the column containing longitudes

-
decimal_long
+
decimal_long

String. The name of the column containing latitudes

-
spatial_ref
+
spatial_ref

Categorical. Defaults to 4326. Can also be set to 102100.

-
force
+
force

Logical. Defaults to FALSE. Returns verbose comments, interactions, and information. Set to TRUE to remove all interactive components and reduce/remove all comments and informative print statements.

Value

- - -

a data frame with two new columns, minimumElevationInMeters and maximumElevationInMeters

+

a data frame with two new columns, minimumElevationInMeters and maximumElevationInMeters

Details

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

Details

Examples

- 
 if (FALSE) {
+    
 if (FALSE) { # \dontrun{
 new_dataframe <- get_elevation(df,
                               "decimalLatitude",
                               "decimalLongitude",
@@ -125,7 +125,7 @@ 
Examples

                               "decimalLongitude",
                               spatial_ref="102100",
                               force=TRUE)
- }
+ } # }
@@ -140,15 +140,15 @@

Examples

-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.0.

- - + + diff --git a/docs/reference/get_park_polygon.html b/docs/reference/get_park_polygon.html index 346f7ed..17cf265 100644 --- a/docs/reference/get_park_polygon.html +++ b/docs/reference/get_park_polygon.html @@ -5,7 +5,7 @@ - +
- +
@@ -78,16 +78,18 @@

Retrieve the polygon information for the park unit from NPS REST services

Arguments

-
unit_code
+ + +
unit_code

is the four-character unit code as designated by NPS.

Examples

- 
if (FALSE) {
+    
if (FALSE) { # \dontrun{
 qc_getParkPolygon("OBRI")
-}
+} # }
@@ -102,15 +104,15 @@

Examples

-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.0.

- - + + diff --git a/docs/reference/get_taxon_rank.html b/docs/reference/get_taxon_rank.html index 146c3eb..36f0caa 100644 --- a/docs/reference/get_taxon_rank.html +++ b/docs/reference/get_taxon_rank.html @@ -3,7 +3,7 @@ - +
- +
@@ -74,21 +74,21 @@

Taxonomic Rank Determination Function

Arguments

-
df
+ + +
df

  • The name of your data frame containing species observations

-
sciName_col
+
sciName_col

  • The name of the column within your data frame containing the scientific names of the species.

Value

- - -

The function returns a new column in the given data frame named taxonRank with the taxonomic rank of the corresponding scientific name in each column. If there is no name in a row, then it returns as NA for that row.

+

The function returns a new column in the given data frame named taxonRank with the taxonomic rank of the corresponding scientific name in each column. If there is no name in a row, then it returns as NA for that row.

Details

@@ -98,9 +98,9 @@

Details

Examples

- 
if (FALSE) {
+    
if (FALSE) { # \dontrun{
 mydf <- get_taxon_rank(df = mydf, sciName_col = "scientificName")
-}
+} # }
@@ -116,15 +116,15 @@

Examples

-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.0.

- - + + diff --git a/docs/reference/get_user_email.html b/docs/reference/get_user_email.html deleted file mode 100644 index b8bbd47..0000000 --- a/docs/reference/get_user_email.html +++ /dev/null @@ -1,117 +0,0 @@ - -Retrieves an NPS user's email address — get_user_email • QCkit - - -
-
- - - -
-
-
-

Retrieves an NPS user's email address

- Source: R/utils.R - -
- -
-

Retrieves an NPS user's email address

-
- -
- 
get_user_email()
-
- -
-

Value

- - -

String. The user's email address.

-
-
-

Details

-

The function accesses the system username and then uses a powershell wrapper to access NPS active directory and supply information about the user. That information is then parsed down to the user's email address.

-

This function probaby won't work for anyone outside of NPS and likely won't work for anyone who is not using a Windows machine. So build those prerequisites (NPS = FALSE) in when calling it from within other function.

-
- -
-

Examples

- 
if (FALSE) {
-email <- get_user_email()
-}
-
-
-
- -
- - -
-

Developed by Robert Baker, Judd Patterson, Joe DeVivo, Issac Quevedo, Sarah Wright.

-
- -
-

Site built with pkgdown 2.0.9.

-
- -
- - - - - - - - diff --git a/docs/reference/get_utm_zone.html b/docs/reference/get_utm_zone.html index dd93d6f..004111e 100644 --- a/docs/reference/get_utm_zone.html +++ b/docs/reference/get_utm_zone.html @@ -5,7 +5,7 @@ - +
- +
@@ -78,16 +78,16 @@

Return UTM Zone

Arguments

-
lon
+ + +
lon

  • Decimal degree longitude value

Value

- - -

The function returns a numeric UTM zone (between 1 and 60).

+

The function returns a numeric UTM zone (between 1 and 60).

Details

@@ -107,15 +107,15 @@

Details

-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.0.

- - + + diff --git a/docs/reference/index.html b/docs/reference/index.html index b7d29f1..5d08aba 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -1,9 +1,9 @@ -Function reference • QCkitPackage index • QCkit - +
- +
@@ -94,10 +94,6 @@

All functions document_missing_values()

Handles multiple missing values

- -

.get_unit_boundary()

- -

Gets NPS unit boundaries from Arc GIS

fix_utc_offset()

@@ -126,10 +122,6 @@

All functions get_taxon_rank()

Taxonomic Rank Determination Function

- -

get_user_email()

- -

Retrieves an NPS user's email address

get_utm_zone()

@@ -167,15 +159,15 @@

All functions
-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.0.

- - + + diff --git a/docs/reference/long2UTM.html b/docs/reference/long2UTM.html index d778541..9647400 100644 --- a/docs/reference/long2UTM.html +++ b/docs/reference/long2UTM.html @@ -8,7 +8,7 @@ - +
- +
@@ -84,16 +84,16 @@

Return UTM Zone

Arguments

-
lon
+ + +
lon

  • Decimal degree longitude value

Value

- - -

The function returns a numeric UTM zone (between 1 and 60).

+

The function returns a numeric UTM zone (between 1 and 60).

Details

@@ -113,15 +113,15 @@

Details

-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.0.

- - + + diff --git a/docs/reference/order_cols.html b/docs/reference/order_cols.html index 707fee6..a4355e7 100644 --- a/docs/reference/order_cols.html +++ b/docs/reference/order_cols.html @@ -3,7 +3,7 @@ - +
- +
@@ -74,14 +74,15 @@

Ordering Columns Function 03-21-2023

Arguments

-
df
+ + +
df

  • This is the dataframe you want to run against the function. To call, simply type df = "the name of your dataframe".

Value

-

  • The function returns a list of required and suggested columns to include in your dataset. When assigning to an object, the object contains your new dataset with all columns ordered properly.

@@ -96,9 +97,9 @@

Details

Examples

- 
if (FALSE) {
+    
if (FALSE) { # \dontrun{
 order_cols(df)
-}
+} # }
@@ -113,15 +114,15 @@

Examples

-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.0.

- - + + diff --git a/docs/reference/remove_empty_tables.html b/docs/reference/remove_empty_tables.html index 02a245c..4d6add1 100644 --- a/docs/reference/remove_empty_tables.html +++ b/docs/reference/remove_empty_tables.html @@ -3,7 +3,7 @@ - +
- +
@@ -74,15 +74,15 @@

Remove empty tables from a list

Arguments

-
df_list
+ + +
df_list

A list of tibbles or dataframes.

Value

- - -

The same list but with empty tables removed.

+

The same list but with empty tables removed.

@@ -108,15 +108,15 @@

Examples

-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.0.

- - + + diff --git a/docs/reference/replace_blanks.html b/docs/reference/replace_blanks.html index 364491f..156f2ea 100644 --- a/docs/reference/replace_blanks.html +++ b/docs/reference/replace_blanks.html @@ -23,7 +23,7 @@ - +
- +
@@ -114,20 +114,20 @@

Replaces all blank cells a missing value code of your choice

Arguments

-
directory
+ + +
directory

String. Path to the file(s) to have blanks replaced with NAs. Defaults to the working directory of the project (here::here())

-
missing_val_code
+
missing_val_code

String, integer, double, or float. Defaults to NA.

Value

- - -

list of data frames (invisibly)

+

list of data frames (invisibly)

Details

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

Details

Examples

- 
 if (FALSE) {
+    
 if (FALSE) { # \dontrun{
 #replaces all blank cells in .csvs in the current directory with NA:
  replace_blanks()
 
@@ -148,7 +148,7 @@ 
Examples

 
 #replace all blank cells in .csvs in the current directory with -99999
 replace_blanks(missing_val_code = -99999)
-}
+} # }
@@ -163,15 +163,15 @@

Examples

-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.0.

- - + + diff --git a/docs/reference/te_check.html b/docs/reference/te_check.html index 792489a..ff101bd 100644 --- a/docs/reference/te_check.html +++ b/docs/reference/te_check.html @@ -5,7 +5,7 @@ - +
- +
@@ -78,31 +78,31 @@

Threatened Or Endangered Species Checker Function

Arguments

-
x
+ + +
x

  • The name of your data frame containing species observations

-
species_col
+
species_col

  • The name of the column within your data frame containing the scientific names of the species (genus and specific epithet).

-
park_code
+
park_code

  • A four letter park code. Or a list of park codes.

-
expansion
+
expansion

  • Logical. Defaults to FALSE. The default setting will return only exact matches between your the scientific binomial (genera and specific epithet) in your data set and the federal match list. Setting expansion = TRUE will expand the list of matches to return all species (and subspecies) that from the match list that match any genera listed in your data set, regardless of whether a given species is actually in your data set. An additional column indicating whether the species returned is in your data set ("In your Data") or has been expanded to ("Expansion") is generated.

Value

- - -

The function returns a (modified) data frame with the names of all the species that fall under the federal conservation list. The resulting data frame may have multiple instances of a given species if it is listed in multiple parks (park codes for each listing are supplied). Technically it is a huxtable, but it should function identically to a data frame for downstream purposes.

+

The function returns a (modified) data frame with the names of all the species that fall under the federal conservation list. The resulting data frame may have multiple instances of a given species if it is listed in multiple parks (park codes for each listing are supplied). Technically it is a huxtable, but it should function identically to a data frame for downstream purposes.

Details

@@ -114,14 +114,14 @@

Details

Examples

- 
if (FALSE) {
+    
if (FALSE) { # \dontrun{
 #for individual parks:
 te_check(x = my_species_dataframe, species_col = "scientificName", park_code = "BICY")
 list<-te_check(data, "scientificName", "ROMO", expansion=TRUE)
 # for a list of parks:
 park_code<-c("ROMO", "YELL", "SAGU")
 list<-te_check(data, "scientificName", park_code, expansion=TRUE)
-}
+} # }
@@ -137,15 +137,15 @@

Examples

-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.0.

- - + + diff --git a/docs/reference/utm_to_ll.html b/docs/reference/utm_to_ll.html index d080346..9c20563 100644 --- a/docs/reference/utm_to_ll.html +++ b/docs/reference/utm_to_ll.html @@ -5,7 +5,7 @@ - +
- +
@@ -78,36 +78,36 @@

Coordinate Conversion from UTM to Latitude and Longitude

Arguments

-
df
+ + +
df

  • The dataframe with UTM coordinates you would like to convert. Input the name of your dataframe.

-
EastingCol
+
EastingCol

  • The name of your Easting UTM column. Input the name in quotations, ie. "EastingCol".

-
NorthingCol
+
NorthingCol

  • The name of your Northing UTM column. Input the name in quotations, ie. "NorthingCol".

-
zone
+
zone

  • The UTM Zone. Input the zone number in quotations, ie. "17".

-
datum
+
datum

  • The datum used in the coordinate reference system of your coordinates. Input in quotations, ie. "WGS84"

Value

- - -

The function returns your dataframe, mutated with an additional two columns of decimal Longitude and decimal Latitude.

+

The function returns your dataframe, mutated with an additional two columns of decimal Longitude and decimal Latitude.

Details

@@ -116,7 +116,7 @@

Details

Examples

- 
if (FALSE) {
+    
if (FALSE) { # \dontrun{
 utm_to_ll(
   df = mydataframe,
   EastingCol = "EastingCoords",
@@ -124,7 +124,7 @@ 
Examples

   zone = "17",
   datum = "WGS84"
 )
-}
+} # }
@@ -139,15 +139,15 @@

Examples

-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.0.

- - + + diff --git a/docs/reference/validate_coord.html b/docs/reference/validate_coord.html index 9a14605..e740aaa 100644 --- a/docs/reference/validate_coord.html +++ b/docs/reference/validate_coord.html @@ -5,7 +5,7 @@ - +
- +
@@ -78,24 +78,26 @@

Check whether a coordinate pair is within the polygon of a park unit

Arguments

-
unit_code
+ + +
unit_code

is the four-character unit code as designated by NPS.

-
lat
+
lat

latitude, in decimal degrees.

-
lon
+
lon

longitude, in decimal degrees.

Examples

- 
if (FALSE) {
+    
if (FALSE) { # \dontrun{
 validate_coord("OBRI", 36.07951, -84.65610)
-}
+} # }
@@ -110,15 +112,15 @@

Examples

-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.0.

- - + + diff --git a/docs/reference/validate_coord_list.html b/docs/reference/validate_coord_list.html index 645c94a..47edd15 100644 --- a/docs/reference/validate_coord_list.html +++ b/docs/reference/validate_coord_list.html @@ -5,7 +5,7 @@ - +
- +
@@ -78,31 +78,31 @@

Test whether decimal GPS coordinates are inside a park unit

Arguments

-
lat
+ + +
lat

numeric. An individual or vector of numeric values representing the decimal degree latitude of a coordinate

-
lon
+
lon

numeric. An individual or vector of numeric values representing the decimal degree longitude of a coordinate

-
park_units
+
park_units

String. Or list of strings each containing the four letter park unit designation

Value

- - -

logical

+

logical

Examples

- 
if (FALSE) {
+    
if (FALSE) { # \dontrun{
 x <- validate_coord_list(lat = 105.555, long = -47.4332, park_units = "DRTO")
 
 # or a dataframe with many coordinates and potentially many park units:
@@ -111,7 +111,7 @@ 
Examples

                 park_units = df$park_units)
 # you can then merge it back in to the original dataframe:
 df$test_GPS_coord <- x
-}
+} # }
@@ -126,15 +126,15 @@

Examples

-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.0.

- - + + diff --git a/docs/sitemap.xml b/docs/sitemap.xml index ec11d5b..4c43436 100644 --- a/docs/sitemap.xml +++ b/docs/sitemap.xml @@ -1,126 +1,42 @@ - - - - /404.html - - - /articles/DRR_Purpose_and_Scope.html - - - /articles/index.html - - - /articles/Starting-a-DRR.html - - - /articles/Using-the-DRR-Template.html - - - /authors.html - - - /index.html - - - /LICENSE-text.html - - - /LICENSE.html - - - /news/index.html - - - /reference/check_dc_cols.html - - - /reference/check_te.html - - - /reference/convert_datetime_format.html - - - /reference/convert_long_to_utm.html - - - /reference/convert_utm_to_ll.html - - - /reference/create_datastore_script.html - - - /reference/DC_col_check.html - - - /reference/document_missing_values.html - - - /reference/dot-get_unit_boundary.html - - - /reference/fix_utc_offset.html - - - /reference/fuzz_location.html - - - /reference/generate_ll_from_utm.html - - - /reference/get_custom_flags.html - - - /reference/get_dc_flags.html - - - /reference/get_df_flags.html - - - /reference/get_dp_flags.html - - - /reference/get_elevation.html - - - /reference/get_park_polygon.html - - - /reference/get_taxon_rank.html - - - /reference/get_user_email.html - - - /reference/get_utm_zone.html - - - /reference/index.html - - - /reference/long2UTM.html - - - /reference/order_cols.html - - - /reference/QCkit-package.html - - - /reference/remove_empty_tables.html - - - /reference/replace_blanks.html - - - /reference/te_check.html - - - /reference/utm_to_ll.html - - - /reference/validate_coord.html - - - /reference/validate_coord_list.html - + +/404.html +/articles/DRR_Purpose_and_Scope.html +/articles/index.html +/articles/Starting-a-DRR.html +/articles/Using-the-DRR-Template.html +/authors.html +/index.html +/LICENSE-text.html +/LICENSE.html +/news/index.html +/reference/check_dc_cols.html +/reference/check_te.html +/reference/convert_datetime_format.html +/reference/convert_long_to_utm.html +/reference/convert_utm_to_ll.html +/reference/create_datastore_script.html +/reference/DC_col_check.html +/reference/document_missing_values.html +/reference/fix_utc_offset.html +/reference/fuzz_location.html +/reference/generate_ll_from_utm.html +/reference/get_custom_flags.html +/reference/get_dc_flags.html +/reference/get_df_flags.html +/reference/get_dp_flags.html +/reference/get_elevation.html +/reference/get_park_polygon.html +/reference/get_taxon_rank.html +/reference/get_utm_zone.html +/reference/index.html +/reference/long2UTM.html +/reference/order_cols.html +/reference/QCkit-package.html +/reference/remove_empty_tables.html +/reference/replace_blanks.html +/reference/te_check.html +/reference/utm_to_ll.html +/reference/validate_coord.html +/reference/validate_coord_list.html + diff --git a/man/dot-get_unit_boundary.Rd b/man/dot-get_unit_boundary.Rd deleted file mode 100644 index efa9f80..0000000 --- a/man/dot-get_unit_boundary.Rd +++ /dev/null @@ -1,22 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/geography.R -\name{.get_unit_boundary} -\alias{.get_unit_boundary} -\title{Gets NPS unit boundaries from Arc GIS} -\usage{ -.get_unit_boundary(park_units) -} -\arguments{ -\item{park_units}{String. Or list of strings.} -} -\value{ -sf dataframe -} -\description{ -Gets NPS unit boundaries from Arc GIS -} -\examples{ -\dontrun{ -.get_unit_boundary("ROMO") -} -} diff --git a/man/get_user_email.Rd b/man/get_user_email.Rd deleted file mode 100644 index 6a1840f..0000000 --- a/man/get_user_email.Rd +++ /dev/null @@ -1,24 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/utils.R -\name{get_user_email} -\alias{get_user_email} -\title{Retrieves an NPS user's email address} -\usage{ -get_user_email() -} -\value{ -String. The user's email address. -} -\description{ -Retrieves an NPS user's email address -} -\details{ -The function accesses the system username and then uses a powershell wrapper to access NPS active directory and supply information about the user. That information is then parsed down to the user's email address. - -This function probaby won't work for anyone outside of NPS and likely won't work for anyone who is not using a Windows machine. So build those prerequisites (NPS = FALSE) in when calling it from within other function. -} -\examples{ -\dontrun{ -email <- get_user_email() -} -} From b7fa21e9520bf948ca308f649ddefc0dafc12231 Mon Sep 17 00:00:00 2001 From: Rob Baker Date: Fri, 20 Sep 2024 16:40:44 -0600 Subject: [PATCH 3/4] remove @export from .get_user_email documentation --- R/utils.R | 1 - 1 file changed, 1 deletion(-) diff --git a/R/utils.R b/R/utils.R index b01a9f5..225a72c 100644 --- a/R/utils.R +++ b/R/utils.R @@ -49,7 +49,6 @@ globalVariables(c("any_of", #' This function probaby won't work for anyone outside of NPS and likely won't work for anyone who is not using a Windows machine. So build those prerequisites (NPS = FALSE) in when calling it from within other function. #' #' @return String. The user's email address. -#' @export #' @keywords internal #' @noRd #' From be64c6ae136dd5337fc2a52e9f7838fbdc56b204 Mon Sep 17 00:00:00 2001 From: Rob Baker Date: Fri, 20 Sep 2024 16:41:00 -0600 Subject: [PATCH 4/4] devtools::document and pkgdown::build_site_github_pages --- NAMESPACE | 1 - docs/pkgdown.yml | 2 +- 2 files changed, 1 insertion(+), 2 deletions(-) diff --git a/NAMESPACE b/NAMESPACE index 07bc09a..1d6c0b5 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -18,7 +18,6 @@ export(get_dp_flags) export(get_elevation) export(get_park_polygon) export(get_taxon_rank) -export(get_user_email) export(get_utm_zone) export(long2UTM) export(order_cols) diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index dd166e1..e38c9ef 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -5,4 +5,4 @@ articles: articles/DRR_Purpose_and_Scope: DRR_Purpose_and_Scope.html articles/Starting-a-DRR: Starting-a-DRR.html articles/Using-the-DRR-Template: Using-the-DRR-Template.html -last_built: 2024-09-20T20:54Z +last_built: 2024-09-20T22:35Z