Merge pull request #373 from ncss-tech/vegtransect-groundsurface

Vegplot Transect: Add support for Transect Ground Surface Cover

Author: brownag

.github/workflows/R-CMD-check.yml

@@ -57,13 +57,13 @@ jobs:
       - uses: r-lib/actions/setup-r@v2
         with:
           r-version: ${{ matrix.config.r }}
-          extra-repositories: "https://rspatial.r-universe.dev/"
+          extra-repositories: "https://ncss-tech.r-universe.dev/"
 
       - uses: r-lib/actions/setup-pandoc@v2
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages: any::rcmdcheck, any::remotes, RSQLite=?ignore-before-r=4.0.0, testthat=?ignore-before-r=4.0.0, local::.
+          extra-packages: any::rcmdcheck, any::remotes, any::soilDBdata, RSQLite=?ignore-before-r=4.0.0, testthat=?ignore-before-r=4.0.0, local::.
           # upgrade: 'TRUE' ## NB: required to force building of source packages
           cache: always
           cache-version: 1
@@ -75,11 +75,6 @@ jobs:
           remotes::install_github("ncss-tech/aqp", dependencies = NA, build = FALSE)
         shell: Rscript {0}
 
-      - name: Install soilDBdata off GitHub
-        run: |
-          remotes::install_github("brownag/soilDBdata", dependencies = NA, build = FALSE)
-        shell: Rscript {0}
-        
       - uses: r-lib/actions/check-r-package@v2
         with:
           upload-snapshots: true

NAMESPACE

@@ -134,6 +134,7 @@ export(get_veg_from_NPS_PLOTS_db)
 export(get_veg_other_from_MT_veg_db)
 export(get_veg_species_from_MT_veg_db)
 export(get_vegplot_from_NASIS_db)
+export(get_vegplot_groundsurface_from_NASIS_db)
 export(get_vegplot_location_from_NASIS_db)
 export(get_vegplot_prodquadrats_from_NASIS_db)
 export(get_vegplot_species_from_NASIS_db)

R/fetchVegdata.R

@@ -12,7 +12,7 @@
 #' @param dsn Optional: path to local SQLite database containing NASIS table structure; default:
 #'   `NULL`
 #'
-#' @return A named list containing: "vegplot", "vegplotlocation", "vegplotrhi", "vegplotspecies",
+#' @return `fetchVegdata()`: A named list containing: "vegplot", "vegplotlocation", "vegplotrhi", "vegplotspecies",
 #'   "vegtransect", "vegtransplantsum", 'vegsiteindexsum', "vegsiteindexdet", "vegbasalarea", and
 #'   "vegplottext" tables
 #'
@@ -29,26 +29,31 @@ fetchVegdata <- function(SS = TRUE, include_pedon = TRUE, stringsAsFactors = NUL
     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, include_pedon = ifelse(include_pedon == "assocuserpedonid", TRUE, include_pedon), dsn = dsn)
+  site <- get_site_data_from_NASIS_db(
+    SS = SS,
+    include_pedon = ifelse(include_pedon == "assocuserpedonid", TRUE, include_pedon),
+    dsn = dsn
+  )
   vegplot <- get_vegplot_from_NASIS_db(SS = SS, dsn =  dsn)
-  vegplotlocation <- get_vegplot_location_from_NASIS_db(SS = SS,  dsn =  dsn)
+  vegplotlocation <- get_vegplot_location_from_NASIS_db(SS = SS, dsn =  dsn)
   vegplotrhi <-  get_vegplot_trhi_from_NASIS_db(SS = SS, dsn =  dsn)
   vegplotspecies <- get_vegplot_species_from_NASIS_db(SS = SS, dsn =  dsn)
   vegtransect <- get_vegplot_transect_from_NASIS_db(SS = SS, dsn =  dsn)
   vegtransplantsum <- get_vegplot_transpecies_from_NASIS_db(SS = SS, dsn =  dsn)
   vegtranspoint <- get_vegplot_transpoints_from_NASIS_db(SS = SS, dsn = dsn)
+  veggroundsurface <- get_vegplot_groundsurface_from_NASIS_db(SS = SS, dsn = dsn)
   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)
+  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)
-
-
+  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 :)')
@@ -78,6 +83,7 @@ fetchVegdata <- function(SS = TRUE, include_pedon = TRUE, stringsAsFactors = NUL
       vegtransect = vegtransect,
       vegtransplantsum = vegtransplantsum,
       vegtranspoint = vegtranspoint,
+      veggroundsurface = veggroundsurface,
       vegprodquadrat = vegprodquadrat,
       vegsiteindexsum = vegsiteindexsum,
       vegsiteindexdet = vegsiteindexdet,

R/get_NASIS_table_name_by_purpose.R

@@ -170,7 +170,8 @@ get_NASIS_table_name_by_purpose <- function(purpose = c("metadata", "lookup", "n
       "pointplantcoverdetails",
       "plantprodquadratdetails",
       "plotspeciesbasalarea",
-      "basalareatreescounted"
+      "basalareatreescounted",
+      "transectgroundsurfcover"
     ),
     project = c(
       "project",

R/get_vegplot_data_from_NASIS_db.R

@@ -80,8 +80,8 @@ get_vegplot_from_NASIS_db <- function(SS = TRUE,
 }
 
 
-# get location data from the corresponding record in the site table
 #' @export
+#' @return `get_vegplot_location_from_NASIS_db()`: a data.frame containing location data from the corresponding record in the site table
 #' @rdname fetchVegdata
 get_vegplot_location_from_NASIS_db <- function(SS = TRUE,
                                                stringsAsFactors = NULL,
@@ -149,7 +149,7 @@ get_vegplot_location_from_NASIS_db <- function(SS = TRUE,
 
 
 
-# get Rangeland Health Indicator(RHI) associated fields in the vegplot table
+#' @return `get_vegplot_trhi_from_NASIS_db()`: a data.frame containing Rangeland Health Indicator (RHI) data from the `vegplot` table
 #' @export
 #' @rdname fetchVegdata
 get_vegplot_trhi_from_NASIS_db <- function(SS = TRUE,
@@ -195,8 +195,7 @@ get_vegplot_trhi_from_NASIS_db <- function(SS = TRUE,
   return(d)
 }
 
-
-# get vegplot species - this is a reconstruction of a site existing species list
+#' @return `get_vegplot_species_from_NASIS_db()`: a data.frame containing Plot Plant Inventory data
 #' @export
 #' @rdname fetchVegdata
 get_vegplot_species_from_NASIS_db <-  function(SS = TRUE,
@@ -251,7 +250,7 @@ get_vegplot_species_from_NASIS_db <-  function(SS = TRUE,
 }
 
 
-# get vegplot transect data
+#' @return `get_vegplot_transect_from_NASIS_db()`: a data.frame containing Vegetation Transect data
 #' @export
 #' @rdname fetchVegdata
 get_vegplot_transect_from_NASIS_db <-  function(SS = TRUE,
@@ -318,7 +317,7 @@ get_vegplot_transect_from_NASIS_db <-  function(SS = TRUE,
 }
 
 
-# get vegplot transect species data
+#' @return `get_vegplot_transect_from_NASIS_db()`: a data.frame containing Vegetation Transect Plant Summary data
 #' @export
 #' @rdname fetchVegdata
 get_vegplot_transpecies_from_NASIS_db <-  function(SS = TRUE,
@@ -390,7 +389,7 @@ get_vegplot_transpecies_from_NASIS_db <-  function(SS = TRUE,
   return(d)
 }
 
-# get point plant cover details for vegtransect plant summary
+#' @return `get_vegplot_transpoints_from_NASIS_db()`: a data.frame containing Vegetation Transect Point Plant Cover Details
 #' @export
 #' @rdname fetchVegdata
 get_vegplot_transpoints_from_NASIS_db <- function(SS = TRUE, dsn = NULL) {
@@ -418,8 +417,7 @@ get_vegplot_transpoints_from_NASIS_db <- function(SS = TRUE, dsn = NULL) {
   uncode(res)
 }
 
-
-# get vegplot transect production quadrats
+#' @return `get_vegplot_prodquadrats_from_NASIS_db()`: a data.frame containing Vegetation Transect Production Quadrat data
 #' @export
 #' @rdname fetchVegdata
 get_vegplot_prodquadrats_from_NASIS_db <- function(SS = TRUE, dsn = NULL) {
@@ -448,7 +446,35 @@ get_vegplot_prodquadrats_from_NASIS_db <- function(SS = TRUE, dsn = NULL) {
   uncode(res)
 }
 
-# get vegplot tree site index summary data
+
+#' @return `get_vegplot_groundsurface_from_NASIS_db()`: a data.frame containing summary data for line point intercept ground surface cover hits by cover type.
+#' @export
+#' @rdname fetchVegdata
+#' @examplesIf local_NASIS_defined()
+#' \donttest{
+#' vsurf <- get_vegplot_groundsurface_from_NASIS_db()
+#' }
+get_vegplot_groundsurface_from_NASIS_db <- function(SS = TRUE, dsn = NULL) {
+  q <- "SELECT siteiid, siteobsiid, vegplotid, vegplotname, vegtransectid, vt.totalpointssampledcount, vt.transectlength, groundsurfcovtype, groundcoverptcount, groundcoverptpct, quadratsize, quadratshape, groundcoverquadpctave
+              FROM site_View_1 AS s
+              INNER JOIN siteobs_View_1 AS so ON so.siteiidref=s.siteiid
+              INNER JOIN vegplot_View_1 AS v ON v.siteobsiidref=so.siteobsiid
+              INNER JOIN vegtransect_View_1 AS vt
+                     ON vt.vegplotiidref = v.vegplotiid
+              LEFT JOIN transectgroundsurfcover_View_1 AS vtps
+                     ON vtps.vegtransectiidref = vt.vegtransectiid"
+  # LEFT JOIN groundsurfcovdetails_View_1 AS vtpsd
+  #        ON vtpsd.transectgrsurfcoviidref = vtps.transectgroundsurfcoveriid
+  
+  if (!SS) {
+    q <- gsub("_View_1", "", q)
+  }
+  
+  res <- dbQueryNASIS(NASIS(dsn = dsn), q)
+  uncode(res)
+}
+
+#' @return `get_vegplot_tree_si_summary_from_NASIS_db()`: a data.frame containing Vegetation Plot Tree Site Index Summary data
 #' @export
 #' @rdname fetchVegdata
 get_vegplot_tree_si_summary_from_NASIS_db <-  function(SS = TRUE,
@@ -495,7 +521,7 @@ get_vegplot_tree_si_summary_from_NASIS_db <-  function(SS = TRUE,
   return(d)
 }
 
-# get vegplot species basal area
+#' @return `get_vegplot_speciesbasalarea_from_NASIS()`: a data.frame containing Vegetation Plot Species Basal Area and Trees Counted data
 #' @export
 #' @rdname fetchVegdata
 get_vegplot_speciesbasalarea_from_NASIS <- function(SS = TRUE, dsn = NULL) {
@@ -524,7 +550,7 @@ get_vegplot_speciesbasalarea_from_NASIS <- function(SS = TRUE, dsn = NULL) {
   uncode(dbQueryNASIS(channel, q), dsn = dsn)
 }
 
-# get vegplot tree site index details data
+#' @return `get_vegplot_tree_si_details_from_NASIS_db()`: a data.frame containing Vegetation Plot Tree Site Index Details data
 #' @export
 #' @rdname fetchVegdata
 get_vegplot_tree_si_details_from_NASIS_db <- function(SS = TRUE,
@@ -573,7 +599,7 @@ get_vegplot_tree_si_details_from_NASIS_db <- function(SS = TRUE,
 }
 
 
-# get vegplot textnotes
+#' @return `get_vegplot_textnote_from_NASIS_db()`: a data.frame containing Vegetation Plot text notes
 #' @param fixLineEndings Replace `'\r\n'` with `'\n'`; Default: `TRUE`
 #' @export
 #' @rdname fetchVegdata