minor formatting differences in documentation and structure (e.g. F t…

…o FALSE, spaces added, etc)
bmaitner · Feb 22, 2022 · 7dd95e3 · 7dd95e3
1 parent 67ba4a8
commit 7dd95e3
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Showing 29 changed files with 603 additions and 378 deletions.
diff --git a/CRAN-SUBMISSION b/CRAN-SUBMISSION
@@ -0,0 +1,3 @@
+Version: 1.2.5
+Date: 2022-02-21 22:34:33 UTC
+SHA: 67ba4a8b5570bed36553e7d14e7e653413574267
diff --git a/R/BIEN.R b/R/BIEN.R
diff --git a/R/BIEN_info.R b/R/BIEN_info.R
@@ -14,14 +14,14 @@ NULL
 ###################
 
 
-.onAttach <- function(libname,pkgname) {
+.onAttach <- function(libname, pkgname) {
   packageStartupMessage('Type vignette("BIEN") or vignette("BIEN_tutorial") to get started')
 
 
-  suppressWarnings(x <- try(readLines("https://raw.githubusercontent.com/bmaitner/RBIEN/master/NOTES", warn = F), silent = T))
+  suppressWarnings(x <- try(readLines("https://raw.githubusercontent.com/bmaitner/RBIEN/master/NOTES", warn = FALSE), silent = TRUE))
   if(class(x)=="character"){
     if(length(x) != 0){
-      packageStartupMessage(x, appendLF = T)  
+      packageStartupMessage(x, appendLF = TRUE)  
 
     }  
 

diff --git a/R/BIEN_sql.R b/R/BIEN_sql.R
@@ -52,7 +52,7 @@
   if(print.query){
 
     query <- gsub(pattern = "\n",replacement = "",query)
-    query <- gsub("(?<=[\\s])\\s*|^\\s+|\\s+$", "", query, perl=TRUE)
+    query <- gsub("(?<=[\\s])\\s*|^\\s+|\\s+$", "", query, perl = TRUE)
     print(query)
 
   }
@@ -78,83 +78,114 @@
   if(!is.null(view_full_occurrence_individual)){
 
     #query<-gsub(pattern = "\\<view_full_occurrence_individual\\>",replacement = view_full_occurrence_individual,x = query)}
-    query <- gsub(pattern = "(?<!as |AS )(?<!\\S)view_full_occurrence_individual(?!\\S)",replacement = view_full_occurrence_individual,x = query,perl = T)
+    query <- gsub(pattern = "(?<!as |AS )(?<!\\S)view_full_occurrence_individual(?!\\S)",
+                  replacement = view_full_occurrence_individual,
+                  x = query,
+                  perl = TRUE)
 
     }
 
 
   if(!is.null(plot_metadata)){
 
     #query<-gsub(pattern = "\\<view_full_occurrence_individual\\>",replacement = view_full_occurrence_individual,x = query)}
-    query <- gsub(pattern = "(?<!as |AS )(?<!\\S)plot_metadata(?!\\S)",replacement = plot_metadata,x = query,perl = T)
+    query <- gsub(pattern = "(?<!as |AS )(?<!\\S)plot_metadata(?!\\S)",
+                  replacement = plot_metadata,
+                  x = query,
+                  perl = TRUE)
 
     }
 
   if(!is.null(analytical_stem)){
 
     #query<-gsub(pattern = "\\<view_full_occurrence_individual\\>",replacement = view_full_occurrence_individual,x = query)}
-    query <- gsub(pattern = "(?<!as |AS )(?<!\\S)analytical_stem(?!\\S)",replacement = analytical_stem,x = query,perl = T)
+    query <- gsub(pattern = "(?<!as |AS )(?<!\\S)analytical_stem(?!\\S)",
+                  replacement = analytical_stem,
+                  x = query,
+                  perl = TRUE)
 
     }
 
   if(!is.null(agg_traits)){
 
-    query <- gsub(pattern = "agg_traits",replacement = agg_traits,x = query)
+    query <- gsub(pattern = "agg_traits",
+                  replacement = agg_traits,
+                  x = query)
 
     }
 
   if(!is.null(species_by_political_division)){
 
-    query <- gsub(pattern = "species_by_political_division",replacement = species_by_political_division,x = query)
+    query <- gsub(pattern = "species_by_political_division",
+                  replacement = species_by_political_division,
+                  x = query)
 
     }
 
   if(!is.null(bien_species_all)){
 
-    query <- gsub(pattern = "bien_species_all",replacement = bien_species_all,x = query)
+    query <- gsub(pattern = "bien_species_all",
+                  replacement = bien_species_all,
+                  x = query)
     }
 
   if(!is.null(ranges)){
 
-    query <- gsub(pattern = "ranges",replacement = ranges,x = query)
+    query <- gsub(pattern = "ranges",
+                  replacement = ranges,
+                  x = query)
 
     }
 
   if(!is.null(bien_taxonomy)){
 
-    query <- gsub(pattern = "bien_taxonomy",replacement = bien_taxonomy,x = query)
+    query <- gsub(pattern = "bien_taxonomy",
+                  replacement = bien_taxonomy,
+                  x = query)
 
     }
 
   if(!is.null(phylogeny)){
 
-    query <- gsub(pattern = "\\<phylogeny\\>",replacement = phylogeny,x = query)
+    query <- gsub(pattern = "\\<phylogeny\\>",
+                  replacement = phylogeny,
+                  x = query)
 
     }
 
   if(!is.null(bien_metadata)){
 
-    query <- gsub(pattern = "\\<bien_metadata\\>",replacement = bien_metadata,x = query)
+    query <- gsub(pattern = "\\<bien_metadata\\>",
+                  replacement = bien_metadata,
+                  x = query)
 
     }
 
 
   if(!is.null(datasource)){
 
-    query <- gsub(pattern = "(?<=\\s)datasource(?=\\s)",replacement = datasource,x = query,perl = T)
+    query <- gsub(pattern = "(?<=\\s)datasource(?=\\s)",
+                  replacement = datasource,
+                  x = query,
+                  perl = TRUE)
 
     }  
 
   if(!is.null(centroid)){
 
-    query <- gsub(pattern = "(?<=\\s)centroid(?=\\s)",replacement = datasource,x = query,perl = T)
+    query <- gsub(pattern = "(?<=\\s)centroid(?=\\s)",
+                  replacement = datasource,
+                  x = query,
+                  perl = TRUE)
 
     }  
 
 
   if(!is.null(limit)){
 
-    query <- gsub(pattern = " ;",replacement = paste(" LIMIT ",limit,";"),x = query)
+    query <- gsub(pattern = " ;",
+                  replacement = paste(" LIMIT ",limit,";"),
+                  x = query)
 
     }