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biodiversitydata-se · May 12, 2021 · b5a7910 · b5a7910
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diff --git a/docs/articles/SBDI4R.html b/docs/articles/SBDI4R.html
diff --git a/docs/articles/SBDI4R_files/figure-html/Datahangling-2.png b/docs/articles/SBDI4R_files/figure-html/Datahangling-2.png
diff --git a/docs/articles/SBDI4R_files/figure-html/plotBIRDSspatial-1.png b/docs/articles/SBDI4R_files/figure-html/plotBIRDSspatial-1.png
diff --git a/docs/articles/SBDI4R_files/figure-html/unnamed-chunk-39-1.png b/docs/articles/SBDI4R_files/figure-html/unnamed-chunk-39-1.png
diff --git a/docs/articles/SBDI4R_files/figure-html/unnamed-chunk-40-1.png b/docs/articles/SBDI4R_files/figure-html/unnamed-chunk-40-1.png
diff --git a/docs/articles/SBDI4R_files/figure-html/unnamed-chunk-41-1.png b/docs/articles/SBDI4R_files/figure-html/unnamed-chunk-41-1.png
diff --git a/docs/articles/SBDI4R_files/figure-html/unnamed-chunk-41-2.png b/docs/articles/SBDI4R_files/figure-html/unnamed-chunk-41-2.png
diff --git a/docs/articles/SBDI4R_files/figure-html/unnamed-chunk-41-3.png b/docs/articles/SBDI4R_files/figure-html/unnamed-chunk-41-3.png
diff --git a/docs/articles/SBDI4R_files/figure-html/unnamed-chunk-7-1.png b/docs/articles/SBDI4R_files/figure-html/unnamed-chunk-7-1.png
diff --git a/docs/articles/SBDI4R_files/header-attrs-2.8/header-attrs.js b/docs/articles/SBDI4R_files/header-attrs-2.8/header-attrs.js
@@ -0,0 +1,12 @@
+// Pandoc 2.9 adds attributes on both header and div. We remove the former (to
+// be compatible with the behavior of Pandoc < 2.8).
+document.addEventListener('DOMContentLoaded', function(e) {
+  var hs = document.querySelectorAll("div.section[class*='level'] > :first-child");
+  var i, h, a;
+  for (i = 0; i < hs.length; i++) {
+    h = hs[i];
+    if (!/^h[1-6]$/i.test(h.tagName)) continue;  // it should be a header h1-h6
+    a = h.attributes;
+    while (a.length > 0) h.removeAttribute(a[0].name);
+  }
+});
diff --git a/docs/index.html b/docs/index.html
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
@@ -3,5 +3,5 @@ pkgdown: 1.6.1
 pkgdown_sha: ~
 articles:
   SBDI4R: SBDI4R.html
-last_built: 2021-04-21T14:00Z
+last_built: 2021-05-12T13:44Z
 
diff --git a/docs/reference/figures/sbdi-logo-orginal-large.png b/docs/reference/figures/sbdi-logo-orginal-large.png
diff --git a/docs/reference/occurrences.html b/docs/reference/occurrences.html
diff --git a/docs/reference/pick_filter.html b/docs/reference/pick_filter.html
diff --git a/docs/reference/sbdi_fields.html b/docs/reference/sbdi_fields.html
diff --git a/docs/reference/sbdi_list.html b/docs/reference/sbdi_list.html
diff --git a/docs/reference/species_list.html b/docs/reference/species_list.html
diff --git a/vignettes/SBDI4R.R b/vignettes/SBDI4R.R
@@ -258,6 +258,7 @@ nCells <- length(ObsInGridList)
 
 res <- data.frame("nObs"=as.numeric(rep(NA,nCells)),
                   "nYears"=as.numeric(rep(NA,nCells)),
+                  row.names = row.names(grid),
                   stringsAsFactors = FALSE)
 
 cols2use <- c("scientificName", "year")
@@ -271,16 +272,9 @@ dataRes <- lapply(ObsInGridList[wNonEmpty], function(x){
   ))
 })
 
-dataRes <- data.frame(matrix(unlist(dataRes),
-                             nrow=length(dataRes), 
-                             byrow=TRUE),
-                    stringsAsFactors = FALSE)
+dataRes <- as.data.frame(dplyr::bind_rows(dataRes, .id = "gridID"))
 
-dataRes$X1 <- as.numeric(dataRes$X1)
-dataRes$X2 <- as.numeric(dataRes$X2)
-
-res[wNonEmpty,] <- dataRes
-rownames(res) <- row.names(grid)
+res[wNonEmpty,] <- dataRes[,-1]
 
 resSp <- sp::SpatialPolygonsDataFrame(grid, res)
 

diff --git a/vignettes/SBDI4R.Rmd b/vignettes/SBDI4R.Rmd
@@ -4,7 +4,6 @@ author: "Alejandro Ruete and Debora Arlt"
 date: "`r Sys.Date()`"
 output: 
   rmarkdown::html_vignette:
-    highlight: tango
     fig_caption: TRUE
 vignette: >
   %\VignetteIndexEntry{Introduction to SBDI4R}
@@ -391,7 +390,7 @@ dataRes <- lapply(ObsInGridList[wNonEmpty], function(x){
 
 dataRes <- as.data.frame(dplyr::bind_rows(dataRes, .id = "gridID"))
 
-res[wNonEmpty,] <- dataRes
+res[wNonEmpty,] <- dataRes[,-1]
 
 resSp <- sp::SpatialPolygonsDataFrame(grid, res)
 ```  

diff --git a/vignettes/SBDI4R.html b/vignettes/SBDI4R.html