From 70d096abb81a15ecdef5620af5a7ae972945a55b Mon Sep 17 00:00:00 2001
From: Brandon Edwards <brandon.edwards144@gmail.com>
Date: Tue, 8 Nov 2022 12:45:55 -0700
Subject: [PATCH] calculate number of projects per BCR in  spatial analysis

---
 src/6-napops-spatial-summary.R | 39 +++++++++++++++++++++++++++++++++-
 1 file changed, 38 insertions(+), 1 deletion(-)

diff --git a/src/6-napops-spatial-summary.R b/src/6-napops-spatial-summary.R
index 9aa2459..45ff517 100755
--- a/src/6-napops-spatial-summary.R
+++ b/src/6-napops-spatial-summary.R
@@ -3,7 +3,7 @@
 # NA-POPS: analysis
 # 6-napops-spatial-summary.R
 # Created February 2021
-# Last Updated January 2022
+# Last Updated November 2022
 
 ####### Import Libraries and External Files #######
 
@@ -48,6 +48,42 @@ bcr_coverage <- data.frame(BCR = bcr$ST_12,
                            stringsAsFactors = FALSE)
 bcr_coverage$nc_cat <- cut(bcr_coverage$ncounts, breaks = c(-1,0,(c(100,200,500,1000,15000))))
 
+####### Projects by BCR ###########################
+
+coords <- project_samples[, c("Latitude", "Longitude")]
+
+coords <- coords[!is.na(coords$Latitude), ]
+coords <- coords[!is.na(coords$Longitude), ]
+
+coords <- st_as_sf(coords,coords = c("Longitude","Latitude"), crs = laea)
+bcr <- bcr %>% st_transform(st_crs(coords))
+
+bcr_list <- apply(st_intersects(bcr, coords, sparse = FALSE), 2, 
+                     function(col) { 
+                       bcr[which(col), ]$ST_12
+                     })
+bcr_list[which(lengths(bcr_list) == 0)] <- NA
+
+ps_red <- project_samples[!is.na(project_samples$Latitude), ]
+ps_red$BCR <- unlist(bcr_list)
+ps_red <- ps_red[-which(is.na(ps_red$BCR)), ]
+
+# Create unique indicator for project x BCR, then get rid of duplicates
+ps_red$proj_bcr <- paste0(ps_red$Project, "-", ps_red$BCR)
+ps_red_unique <- ps_red[!duplicated(ps_red$proj_bcr), ]
+
+coords <- ps_red_unique[, c("Latitude", "Longitude")]
+
+coords <- st_as_sf(coords,coords = c("Longitude","Latitude"), crs = laea)
+bcr <- bcr %>% st_transform(st_crs(coords))
+
+counts_bcr_proj <- st_intersects(bcr, coords)
+bcr_coverage_project <- data.frame(BCR = bcr$ST_12,
+                           ncounts = lengths(counts_bcr_proj),
+                           sqrt_ncounts = sqrt(lengths(counts_bcr_proj)),
+                           stringsAsFactors = FALSE)
+bcr_coverage_project$nc_cat <- cut(bcr_coverage_project$ncounts, breaks = c(-1,0,(c(10,20,30, 40,50,60,70,80,90,100))))
+
 ####### Analysis by Species (BCR, Distance) #######
 
 bcr_dis_coverage <- vector(mode = "list", length = length(names(dis_species_summary)))
@@ -109,5 +145,6 @@ for (sp in names(rem_species_summary))
 ####### Output Summary Statistics and Tables ######
 
 save(bcr_coverage, file = "../results/spatial-summary/project_coverage_bcr.rda")
+save(bcr_coverage_project, file = "../results/spatial-summary/nproj_coverage_bcr.rda")
 save(bcr_dis_coverage, file = "../results/spatial-summary/dis_coverage_bcr.rda")
 save(bcr_rem_coverage, file = "../results/spatial-summary/rem_coverage_bcr.rda")