Merge pull request #65 from RobLBaker/master

replace_blanks; update get_custom_flags

.github/workflows/test-coverage.yaml

@@ -0,0 +1,50 @@
+# 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

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: QCkit
 Type: Package
 Title: NPS Inventory and Monitoring Quality Control Toolkit
-Version: 0.1.3
+Version: 0.1.4
 Authors@R: c(
   person(given = "Robert",
            family = "Baker",
@@ -22,12 +22,12 @@ Authors@R: c(
            comment = c(ORCID = "0000-0003-0129-981X")),
   person(given = "Amy",
            family = "Sherman",
-           role = "aut",
+           role = "ctb",
            comment = c(ORCID = "0000-0002-9276-0087"))
            )
 Maintainer: Rob Baker <[email protected]>
 Description: This package contains a set of useful functions for data munging, quality control, and data flagging. Functions are contributed by multiple U.S. National Park Service staff, contractors, partners and others. These functions will likely be most useful for quality control of NPS data but may have utility beyond their intended functions.
-License: MIT + file LICENSE
+License: CC0
 Encoding: UTF-8
 LazyData: true
 Imports: 
@@ -47,15 +47,15 @@ Imports:
     data.table,
     jsonlite,
     here,
-    wk,
     tibble,
-    tidyselect,
-    rlang
+    tidyselect
 RoxygenNote: 7.2.3
 Suggests: 
     knitr,
     rmarkdown,
-    testthat (>= 3.0.0)
+    testthat (>= 3.0.0),
+    rlang,
+    wk
 VignetteBuilder: knitr
 URL: https://github.com/nationalparkservice/QCkit/
 BugReports: https://nationalparkservice.github.io/QCkit/

LICENSE.md

@@ -1,21 +1,43 @@
-# MIT License
-
-Copyright (c) 2022 QCkit authors
-
-Permission is hereby granted, free of charge, to any person obtaining a copy
-of this software and associated documentation files (the "Software"), to deal
-in the Software without restriction, including without limitation the rights
-to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-copies of the Software, and to permit persons to whom the Software is
-furnished to do so, subject to the following conditions:
-
-The above copyright notice and this permission notice shall be included in all
-copies or substantial portions of the Software.
-
-THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
-SOFTWARE.
+## creative commons
+
+# CC0 1.0 Universal
+
+CREATIVE COMMONS CORPORATION IS NOT A LAW FIRM AND DOES NOT PROVIDE LEGAL SERVICES. DISTRIBUTION OF THIS DOCUMENT DOES NOT CREATE AN ATTORNEY-CLIENT RELATIONSHIP. CREATIVE COMMONS PROVIDES THIS INFORMATION ON AN "AS-IS" BASIS. CREATIVE COMMONS MAKES NO WARRANTIES REGARDING THE USE OF THIS DOCUMENT OR THE INFORMATION OR WORKS PROVIDED HEREUNDER, AND DISCLAIMS LIABILITY FOR DAMAGES RESULTING FROM THE USE OF THIS DOCUMENT OR THE INFORMATION OR WORKS PROVIDED HEREUNDER.
+
+### Statement of Purpose
+
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+
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+
+3. __Public License Fallback.__ Should any part of the Waiver for any reason be judged legally invalid or ineffective under applicable law, then the Waiver shall be preserved to the maximum extent permitted taking into account Affirmer's express Statement of Purpose. In addition, to the extent the Waiver is so judged Affirmer hereby grants to each affected person a royalty-free, non transferable, non sublicensable, non exclusive, irrevocable and unconditional license to exercise Affirmer's Copyright and Related Rights in the Work (i) in all territories worldwide, (ii) for the maximum duration provided by applicable law or treaty (including future time extensions), (iii) in any current or future medium and for any number of copies, and (iv) for any purpose whatsoever, including without limitation commercial, advertising or promotional purposes (the "License"). The License shall be deemed effective as of the date CC0 was applied by Affirmer to the Work. Should any part of the License for any reason be judged legally invalid or ineffective under applicable law, such partial invalidity or ineffectiveness shall not invalidate the remainder of the License, and in such case Affirmer hereby affirms that he or she will not (i) exercise any of his or her remaining Copyright and Related Rights in the Work or (ii) assert any associated claims and causes of action with respect to the Work, in either case contrary to Affirmer's express Statement of Purpose.
+
+4. __Limitations and Disclaimers.__
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+
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+
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+
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NAMESPACE

@@ -19,8 +19,10 @@ export(get_taxon_rank)
 export(get_utm_zone)
 export(long2UTM)
 export(order_cols)
+export(replace_blanks)
 export(te_check)
 export(utm_to_ll)
+export(validate_coord)
 importFrom(lifecycle,deprecated)
 importFrom(magrittr,"%>%")
 importFrom(stats,sd)

NEWS.md

@@ -1,11 +1,16 @@
+# QCkit v0.1.4
+2024-01-23
+* Maintenance on `get_custom_flag()` to align with updated DRR requirements
+* Added function `replace_blanks()` to ingest a directory of .csvs and write them back out to .csv (overwriting the original files) with blanks converted to NA (except if a file has NO data - then it remains blank and needs to be dealt with manually)
+
 # QC kit v0.1.3
 2023-12-18
 * Bugfix for `create_datastore_script()`
 * Added automated build check and pkgdown github pages builds via github actions
 * Code cleanup via linter suggests 
 * Added warning about turning off VPN for the `covert_utm_to_ll()` documentation
 * Moved `convert_datetime_format()` from DPchecker to QCkit
-* Added funtion `fix_utc_offset()`
+* Added function `fix_utc_offset()`
 
 # QCkit 0.1.2 "Automated Shuttle Pilot"
 2023-11-20

R/dates_and_times.R

@@ -1,15 +1,16 @@
 #' Fix UTC offset strings
 #'
-#' UTC offsets can be formatted in multiple ways (e.g. -07, -07:00, -0700) and R often struggles to parse these offsets. This function takes date/time strings with valid UTC offsets, and formats them so that they are consistent and readable by R.
+#' UTC offsets can be formatted in multiple ways (e.g. -07, -07:00, -0700) and R often struggles to parse these offsets. This function takes date/time strings with valid UTC offsets, and formats them so that they are consistent and readable by R. Here, you can supply a vector of dates in ISO 8601 format and they will be returned in a consistent format compatible with R. Date strings with missing or invalid UTC offsets will result in a warning.
 #'
 #' @param datetime_strings Character vector of dates in ISO 8601 format
 #'
 #' @return datetime_strings with UTC offsets consistently formatted to four digits (e.g. "2023-11-16T03:32:49-0700").
 #' @export
 #'
 #' @examples
-#' datetimes <- c("2023-11-16T03:32:49+07:00","2023-11-16T03:32:49-07","2023-11-16T03:32:49","2023-11-16T03:32:49Z")
-#' fix_utc_offset(datetimes)  # returns c("2023-11-16T03:32:49+0700", "2023-11-16T03:32:49-0700", "2023-11-16T03:32:49", "2023-11-16T03:32:49+0000") and warns about missing offset (see third element)
+#' datetimes <- c("2023-11-16T03:32:49+07:00", "2023-11-16T03:32:49-07",
+#' "2023-11-16T03:32:49","2023-11-16T03:32:49Z")
+#' fix_utc_offset(datetimes)
 #'
 fix_utc_offset <- function(datetime_strings) {
   datetime_strings <- stringr::str_replace_all(datetime_strings, "[\u2212\u2010\u2011\u2012\u2013\u2014\u2015\ufe58\ufe63\uff0d]", "-") # replace every possible type of dash with a regular minus sign
@@ -19,8 +20,11 @@ fix_utc_offset <- function(datetime_strings) {
     stringr::str_extract("[Zz]|((?<=[+-])[0-9]{1,2}:?[0-9]{0,2})$") %>%
     stringr::str_remove(":") %>%
     stringr::str_replace("[Zz]", "0000")
-  new_offsets <- dplyr::case_when(nchar(new_offsets) == 1 ~ paste0("0", new_offsets, "00"),
-                                  nchar(new_offsets) == 2 ~ paste0(new_offsets, "00"),
+  new_offsets <- dplyr::case_when(nchar(new_offsets) == 1 ~ paste0("0",
+                                                                   new_offsets,
+                                                                   "00"),
+                                  nchar(new_offsets) == 2 ~ paste0(new_offsets,
+                                                                   "00"),
                                   nchar(new_offsets) == 4 ~ new_offsets,
                                   .default = "")
   if (any(new_offsets == "")) {