remove standardization

nickmckay · Mar 19, 2024 · 7e777a2 · 7e777a2
1 parent 3826365
commit 7e777a2
Show file tree

Hide file tree

Showing 19 changed files with 45 additions and 904 deletions.
diff --git a/.DS_Store b/.DS_Store
diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml
@@ -19,8 +19,10 @@ jobs:
       group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }}
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    permissions:
+      contents: write
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-pandoc@v2
 
@@ -39,7 +41,7 @@ jobs:
 
       - name: Deploy to GitHub pages 🚀
         if: github.event_name != 'pull_request'
-        uses: JamesIves/github-pages-deploy-action@4.1.4
+        uses: JamesIves/github-pages-deploy-action@v4.5.0
         with:
           clean: false
           branch: gh-pages

diff --git a/DESCRIPTION b/DESCRIPTION
@@ -18,7 +18,7 @@ Maintainer: Nicholas McKay <nick@nau.edu>
 Description: Functions to open, modify, analyze, and save LiPD data. 
 Depends: R (>= 3.5.0)
 License: MIT + file LICENSE
-RoxygenNote: 7.2.1
+RoxygenNote: 7.3.1
 URL: www.lipd.net
 Encoding: UTF-8
 Imports: 

diff --git a/NAMESPACE b/NAMESPACE
@@ -1,5 +1,6 @@
 # Generated by roxygen2: do not edit by hand
 
+S3method(cbind,"NA")
 S3method(print,lipd)
 S3method(print,lipd_ts)
 S3method(print,lipd_ts_tibble)
@@ -82,8 +83,6 @@ export(is.multiLipd)
 export(is.url)
 export(isDirectory)
 export(isNullOb)
-export(isValidAll)
-export(isValidValue)
 export(lipdSummary)
 export(lipdTSSummary)
 export(lipd_read)
@@ -115,7 +114,6 @@ export(rm_empty_fields)
 export(rm_existing_tables)
 export(splitInterpretationByScope)
 export(standardizeQCsheetValues)
-export(standardizeValue)
 export(stripExtension)
 export(swapGeoCoordinates)
 export(tabulateTs)
@@ -126,7 +124,6 @@ export(unindex_geo)
 export(untidyTs)
 export(unzipper)
 export(updateChangelog)
-export(updateMetaDataFromStandardTables)
 export(updateQueryTable)
 export(update_lipd_v1_1)
 export(update_lipd_v1_2)

diff --git a/R/cbind_NA.R b/R/cbind_NA.R
@@ -1,3 +1,10 @@
+#' handle NAs in cbind
+#'
+#' @param ... whatever you're binding
+#' @param fill unused parameter
+#'
+#' @return bound columns
+#' @export
 cbind.NA <- function (..., fill = NA)
 {
   DFx <- list(...)
@@ -10,7 +17,7 @@ cbind.NA <- function (..., fill = NA)
       DFx[[i]] <- data.frame(rep(NA, 1))
     }
   }
-  
+
   vertLen <-  function(dfIn){
     if(is.null(dim(dfIn))){
       vertical <- length(dfIn)
@@ -19,7 +26,7 @@ cbind.NA <- function (..., fill = NA)
     }
     return(vertical)
   }
-  
+
   lengthsDF <- as.numeric(lapply(DFx, vertLen))
   maxLen <- max(lengthsDF)
   newDF <- rep(NA, maxLen)