Merge pull request #366 from natearoe/roe

fetchVegdata: add siteobsiid to vegplot tables; activate vegbasalarea table

Author: brownag

R/fetchVegdata.R

@@ -8,27 +8,27 @@
 #' get_vegplot_transpecies_from_NASIS_db
 #' get_vegplot_tree_si_details_from_NASIS_db
 #' get_vegplot_tree_si_summary_from_NASIS_db get_vegplot_trhi_from_NASIS_db
-#' 
+#'
 #' @param SS fetch data from the currently loaded selected set in NASIS or from the entire local database (default: `TRUE`)
 #' @param stringsAsFactors deprecated
 #' @param dsn Optional: path to local SQLite database containing NASIS
 #' table structure; default: `NULL`
 #'
-#' @return A named list containing: "vegplot", "vegplotlocation", "vegplotrhi", "vegplotspecies", "vegtransect", "vegtransplantsum", 'vegsiteindexsum', "vegsiteindexdet", and  "vegplottext" tables
-#' 
+#' @return A named list containing: "vegplot", "vegplotlocation", "vegplotrhi", "vegplotspecies", "vegtransect", "vegtransplantsum", 'vegsiteindexsum', "vegsiteindexdet", "vegbasalarea", and  "vegplottext" tables
+#'
 #' @export
 #'
 fetchVegdata <- function(SS=TRUE, stringsAsFactors = NULL, dsn = NULL) {
-	
+
   if (!missing(stringsAsFactors) && is.logical(stringsAsFactors)) {
     .Deprecated(msg = sprintf("stringsAsFactors argument is deprecated.\nSetting package option with `NASISDomainsAsFactor(%s)`", stringsAsFactors))
     NASISDomainsAsFactor(stringsAsFactors)
   }
-  
-  
+
+
   # check if NASIS local DB instance/ODBC data source is available
   .soilDB_test_NASIS_connection(dsn = dsn)
-  
+
 	# 1. load data in pieces
 	site <- get_site_data_from_NASIS_db(SS = SS, dsn = dsn)
   vegplot <- get_vegplot_from_NASIS_db(SS = SS, dsn =  dsn)
@@ -41,18 +41,19 @@ fetchVegdata <- function(SS=TRUE, stringsAsFactors = NULL, dsn = NULL) {
   vegprodquadrat <- get_vegplot_prodquadrats_from_NASIS_db(SS = SS, dsn =  dsn)
   vegsiteindexsum <- get_vegplot_tree_si_summary_from_NASIS_db(SS = SS, dsn =  dsn)
   vegsiteindexdet <- get_vegplot_tree_si_details_from_NASIS_db(SS = SS, dsn =  dsn)
+  vegbasalarea <- get_vegplot_speciesbasalarea_from_NASIS(SS = SS, dsn =  dsn)
   vegplottext <-  get_vegplot_textnote_from_NASIS_db(SS = SS, fixLineEndings = TRUE, dsn =  dsn)
 
 
 	# test to see if the selected set is loaded
 	if (nrow(site) == 0 || nrow(vegplot) == 0) {
 	  message('Selected set is missing either the vegplot, pedon or site table, please load and try again :)')
 	}
-	
+
   # add ecosite id, corrdate, selection method to vegplot
   vegplot <- merge(site[,c("siteiid", "ecositeid",  "ecositecorrdate", "siteecositehistory.classifier", "es_selection_method")],
                    vegplot, by = "siteiid", all.x = TRUE, sort = FALSE)
-  
+
 	# done
 	return(list(
 	    vegplot = vegplot,
@@ -65,8 +66,9 @@ fetchVegdata <- function(SS=TRUE, stringsAsFactors = NULL, dsn = NULL) {
 	    vegprodquadrat = vegprodquadrat,
 	    vegsiteindexsum = vegsiteindexsum,
 	    vegsiteindexdet = vegsiteindexdet,
+	    vegbasalarea = vegbasalarea,
 	    vegplottext = vegplottext,
 	    site = site
 	  ))
-}	
+}