Merge pull request #39 from USFWS/development

2024 AKaerial release

.gitignore

@@ -8,3 +8,4 @@ doc
 Meta
 /doc/
 /Meta/
+.Rproj.user2

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: AKaerial
 Type: Package
 Title: Analysis of Alaska Region Aerial Survey Data
-Version: 1.2.2023
+Version: 1.2.2024
 Imports: tidyverse, dplyr, ggplot2, ggspatial, kableExtra, leaflet, leafem, lwgeom, mapproj, outliers, plyr, raster, RColorBrewer, rmarkdown, smoothr, tidyr, tools, zoo
 Depends: tidyr, magrittr, dplyr, sf
 Author: Charles Frost

R/CompositeLong.R

@@ -28,12 +28,12 @@
 #' @return Long data frame of composite indices
 #'
 #' @export
-CompositeLong = function(tavs.year = c(1985:2023),
-                            pw.year = c(1985:2023),
-                            tusw.year = c(1985:2023),
-                            lesser.year = c(1964:2023),
-                            mcw.year = c(1964:2023),
-                            trsw.year = c(1964:2023),
+CompositeLong = function(tavs.year = c(1985:2024),
+                            pw.year = c(1985:2024),
+                            tusw.year = c(1985:2024),
+                            lesser.year = c(1964:2024),
+                            mcw.year = c(1964:2024),
+                            trsw.year = c(1964:2024),
                             versioning=FALSE){
 
 

R/NorthAmerican.R

@@ -722,45 +722,45 @@ CombineEstimatesByStrata=function(estimates){
 WBPHStidy = function(adj, flight){
 
   trans.f = flight %>%
-    group_by(Year, Stratum, Transect) %>%
-    summarise(SampledArea = sum(SampledArea))
+    dplyr::group_by(Year, Stratum, Transect) %>%
+    dplyr::summarise(SampledArea = sum(SampledArea))
 
   trans.adj = adj %>%
-    group_by(Year, Stratum, Transect, Species) %>%
-    filter(!(Species %in% c("START", "END", "NoBirdsSeen"))) %>%
-    summarise(total = sum(total), itotal = sum(itotal), ibb=sum(ibb), sing1pair2=sum(sing1pair2), flock=sum(flock))
+    dplyr::group_by(Year, Stratum, Transect, Species) %>%
+    dplyr::filter(!(Species %in% c("START", "END", "NoBirdsSeen"))) %>%
+    dplyr::summarise(total = sum(total), itotal = sum(itotal), ibb=sum(ibb), sing1pair2=sum(sing1pair2), flock=sum(flock))
 
   trans.merge = merge(trans.adj, trans.f) %>%
     complete(Year,  nesting(Stratum, Transect), Species, fill=list(total=0, itotal=0, ibb=0, sing1pair2=0, flock=0)) %>%
-    group_by(Stratum, Transect) %>%
+    dplyr::group_by(Stratum, Transect) %>%
     fill(SampledArea, .direction=c("updown"))
 
   eider = trans.merge %>%
     filter(Species %in% c("COEI", "STEI", "KIEI", "SPEI", "UNEI")) %>%
-    group_by(Year, Stratum, Transect, SampledArea) %>%
-    summarise(Species="Eider", total=sum(total), itotal=sum(itotal), ibb=sum(ibb), sing1pair2=sum(sing1pair2), flock=sum(flock))
+    dplyr::group_by(Year, Stratum, Transect, SampledArea) %>%
+    dplyr::summarise(Species="Eider", total=sum(total), itotal=sum(itotal), ibb=sum(ibb), sing1pair2=sum(sing1pair2), flock=sum(flock))
 
   merganser = trans.merge %>%
     filter(Species %in% c("COME", "RBME", "UNME")) %>%
-    group_by(Year, Stratum, Transect, SampledArea) %>%
-    summarise(Species="Merganser", total=sum(total), itotal=sum(itotal), ibb=sum(ibb), sing1pair2=sum(sing1pair2), flock=sum(flock))
+    dplyr::group_by(Year, Stratum, Transect, SampledArea) %>%
+    dplyr::summarise(Species="Merganser", total=sum(total), itotal=sum(itotal), ibb=sum(ibb), sing1pair2=sum(sing1pair2), flock=sum(flock))
 
   scoter = trans.merge %>%
     filter(Species %in% c("SCOT", "WWSC", "SUSC", "BLSC")) %>%
-    group_by(Year, Stratum, Transect, SampledArea) %>%
-    summarise(Species="Scoter", total=sum(total), itotal=sum(itotal), ibb=sum(ibb), sing1pair2=sum(sing1pair2), flock=sum(flock))
+    dplyr::group_by(Year, Stratum, Transect, SampledArea) %>%
+    dplyr::summarise(Species="Scoter", total=sum(total), itotal=sum(itotal), ibb=sum(ibb), sing1pair2=sum(sing1pair2), flock=sum(flock))
 
   grebe = trans.merge %>%
     filter(Species %in% c("HOGR", "RNGR", "UNGR")) %>%
-    group_by(Year, Stratum, Transect, SampledArea) %>%
-    summarise(Species="Grebe", total=sum(total), itotal=sum(itotal), ibb=sum(ibb), sing1pair2=sum(sing1pair2), flock=sum(flock))
+    dplyr::group_by(Year, Stratum, Transect, SampledArea) %>%
+    dplyr::summarise(Species="Grebe", total=sum(total), itotal=sum(itotal), ibb=sum(ibb), sing1pair2=sum(sing1pair2), flock=sum(flock))
 
 
   trans.merge = rbind(trans.merge, eider, merganser, scoter, grebe)
 
   by.stratum = trans.merge %>%
-    group_by(Year, Stratum, Species) %>%
-    summarise(total.density = sum(total)/sum(SampledArea),
+    dplyr::group_by(Year, Stratum, Species) %>%
+    dplyr::summarise(total.density = sum(total)/sum(SampledArea),
               itotal.density = sum(itotal)/sum(SampledArea),
               ibb.density = sum(ibb)/sum(SampledArea),
               sing1pair2.density = sum(sing1pair2)/sum(SampledArea),
@@ -798,7 +798,7 @@ WBPHStidy = function(adj, flight){
   vcf = WBPHS_VCF %>%
     select(SPECIES, STRATUM, VCF, VCF_SE) %>%
     mutate(VCF.var = VCF_SE^2) %>%
-    rename(Species=SPECIES, Stratum = STRATUM)
+    dplyr::rename(Species=SPECIES, Stratum = STRATUM)
 
   estimates = merge(estimates, vcf, all.x=TRUE)
 

R/TransectSample.R

@@ -56,32 +56,24 @@ TransectSample <- function(data.select, sample, n, plot="on", seed=0){
 
     plot.data=sf::st_as_sf(data.select$design)
 
-    data.select$design@data$sort.by = data.select$design@data$mid.Lat
-
-    for (i in 1:length(data.select$design@data$STRATNAME)){
-    if(data.select$design@data$STRATNAME[i] %in% c("Egg Island", "Egg", "egg")){
-
-      data.select$design@data$sort.by[i] = data.select$design@data$mid.Lon[i]
-    }
-    }
+    resample=data.frame("keep"=unique(data.select$design$OBJECTID)) %>%
+      dplyr::arrange(keep) %>%
+      dplyr::filter(dplyr::row_number() %% n == seed)
 
+    trans = data.select$design %>%
+      dplyr::filter(OBJECTID %in% resample$keep) %>%
+      dplyr::filter(units::drop_units(LENGTH) > 0.01)
 
-    trans = data.select$design@data %>%
-      dplyr::filter(len > 0.01) %>%
-      dplyr::distinct(., SPLIT, STRATNAME, .keep_all=TRUE) %>%
-      dplyr::filter(len > 0.01) %>%
-      dplyr::group_by(STRATNAME) %>%
-      dplyr::arrange(sort.by, .by_group = TRUE) %>%
-      dplyr::filter(dplyr::row_number() %% n == seed)
 
+    #data.select$design = data.select$design[data.select$design$SPLIT %in% trans$SPLIT,]
 
-    data.select$design = data.select$design[data.select$design$SPLIT %in% trans$SPLIT,]
+    data.select$design = trans
 
-    data.select$obs = data.select$obs %>% dplyr::filter(ctran %in% trans$SPLIT)
+    data.select$obs = data.select$obs %>% dplyr::filter(ctran %in% data.select$design$ctran)
 
-    data.select$flight = data.select$flight %>% dplyr::filter(PartOf %in% trans$SPLIT)
+    data.select$flight = data.select$flight %>% dplyr::filter(ctran %in% data.select$design$ctran)
 
-    data.select$transect = data.select$transect %>% dplyr::filter(ctran %in% trans$SPLIT)
+    data.select$transect = data.select$transect %>% dplyr::filter(ctran %in% data.select$design$ctran)
 
 
 

R/greenlightscribe.R

@@ -615,10 +615,17 @@ ScribeMerge=function(folder, string, addWBPHS=FALSE){
     files$Wind_Vel=NA
   }
 
+  if(!("Sky" %in% colnames(files))){
+    files$Sky=NA
+    files$Wind_Dir=NA
+    files$Wind_Vel=NA
+  }
+
   files$Observer=toupper(files$Observer)
   files$Seat=toupper(files$Seat)
 
 
+
   readr::write_csv(files, file=paste(area, "_", year, "_RawObs_", string, ".csv", sep=""))
 
   setwd(current.dir)

R/main.R

@@ -540,8 +540,8 @@ if(strata=="all"){
 #' \item itotal - Indicated total.  Singles doubled, pairs doubled, opens added, flkdrake 1-4 doubled, flkdrake 5+ added.
 #' \item ibb - Indicated breeding birds.  Singles doubled, pairs doubled, opens removed, flkdrake 1-4 doubled, flkdrake 5+ removed.
 #' \item total - Total birds.  Singles added, pairs doubled, opens added, flkdrake added.
-#' \item sing1pair2 - Singles and pairs.  Singles added, pairs doubled, opens removed, flkdrake removed.
-#' \item flock - Flocks.  Singles removed, pairs removed, opens added, flkdrake added.
+#' \item sing1pair2 - Singles and pairs.  Singles added, pairs doubled, opens removed, flkdrake 1-4 added.
+#' \item flock - Flocks.  Singles removed, pairs removed, opens added, flkdrake 5+ added.
 #' }
 #'
 #'
@@ -596,12 +596,14 @@ AdjustCounts <- function(full.data){
     }
 
     #Flocked drakes are doubled for 1-4 seen for indicated bb/totals.  Reference would be useful.
+    #Added 1-4 flkdrake to sing1pair2 in 2024, removed them from flock index.
+
     else if(full.data$Obs_Type[i]=="flkdrake" & full.data$Num[i]<5){
       full.data$itotal[i]=2*full.data$Num[i]
       full.data$total[i]=full.data$Num[i]
       full.data$ibb[i]=2*full.data$Num[i]
-      full.data$sing1pair2[i]=0
-      full.data$flock[i]=full.data$Num[i]
+      full.data$sing1pair2[i]=full.data$Num[i]
+      full.data$flock[i]=0
 
     }
 
@@ -2084,6 +2086,10 @@ EstimatesTable=function(area, year, sample="full", n=0, seed=0, method="process"
   combined=CombineEstimates(output.table)
   combined$area=area
 
+  output.table = output.table %>% filter(!(Species %in% c("START", "END")))
+  expanded.table = expanded.table %>% filter(!(Species %in% c("START", "END")))
+  combined = combined %>% filter(!(Species %in% c("START", "END")))
+
   return(list(output.table=output.table, expanded.table=expanded.table, combined=combined))
 
 
@@ -2893,6 +2899,8 @@ UpdateAllObjects=function(input.path, output.path){
 AppendYear = function(area, year){
 
   update=EstimatesTable(area=area, year=year)
+  update$expanded.table$sha=system("git rev-parse HEAD", intern=TRUE)
+
 
   if(area=="ACP"){
     ACPHistoric$output.table=rbind(ACPHistoric$output.table, update$output.table)