Updating AFSC grids for EBS / NBS and adding Chukchi ... (#79)

... h/t Jason Conner for these improvements!

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: FishStatsUtils
 Type: Package
 Title: Utilities (shared code and data) for FishStats spatio-temporal modeling toolbox
-Version: 2.10.2
-Date: 2021-11-08
+Version: 2.11.0
+Date: 2022-03-17
 Authors@R: 
     c(person(given = "James",
              family = "Thorson",
@@ -57,6 +57,6 @@ License: GPL-3
 LazyData: yes
 BuildVignettes: yes
 Encoding: UTF-8
-RoxygenNote: 7.1.1
+RoxygenNote: 7.1.2
 URL: http://github.com/james-thorson-NOAA/FishStatsUtils
 BugReports: http://github.com/james-thorson-NOAA/FishStatsUtils/issues

NAMESPACE

@@ -18,6 +18,7 @@ export(Prepare_AI_Extrapolation_Data_Fn)
 export(Prepare_BC_Coast_Extrapolation_Data_Fn)
 export(Prepare_BFISH_MHI_Extrapolation_Data_Fn)
 export(Prepare_BSslope_Extrapolation_Data_Fn)
+export(Prepare_Chukchi_Extrapolation_Data_Fn)
 export(Prepare_EBS_Extrapolation_Data_Fn)
 export(Prepare_GOA_Extrapolation_Data_Fn)
 export(Prepare_GOM_Extrapolation_Data_Fn)

R/Prepare_XXXX_Extrapolation_Data_Fn.R

@@ -145,7 +145,7 @@ function( strata.limits=NULL, projargs=NA, zone=NA, flip_around_dateline=TRUE, .
 
   # Extra junk
   Data_Extrap = cbind( Data_Extrap, 'Include'=1)
-  Data_Extrap[,c('E_km','N_km')] = tmpUTM[,c('X','Y')]
+  Data_Extrap = cbind( Data_Extrap, "E_km"=tmpUTM[,'X'], "N_km"=tmpUTM[,'Y'] )
 
   # Return
   Return = list( "a_el"=a_el, "Data_Extrap"=Data_Extrap, "zone"=attr(tmpUTM,"zone"), "projargs"=attr(tmpUTM,"projargs"),
@@ -325,7 +325,7 @@ function( strata.limits=NULL, projargs=NA, zone=NA, flip_around_dateline=FALSE,
   Area_km2_x = Data_Extrap[,'Area_in_survey_km2']
 
   # Augment with strata for each extrapolation cell
-  Tmp = cbind("BEST_DEPTH_M"=0, "BEST_LAT_DD"=Data_Extrap[,'Lat'], "propInSurvey"=1)
+  Tmp = cbind("BEST_DEPTH_M"=0, "BEST_LAT_DD"=Data_Extrap[,'Lat'], "BEST_LON_DD"=Data_Extrap[,'Lon'], "propInSurvey"=1)
   a_el = as.data.frame(matrix(NA, nrow=nrow(Data_Extrap), ncol=nrow(strata.limits), dimnames=list(NULL,strata.limits[,'STRATA'])))
   for(l in 1:ncol(a_el)){
     a_el[,l] = apply(Tmp, MARGIN=1, FUN=match_strata_fn, strata_dataframe=strata.limits[l,,drop=FALSE])
@@ -338,7 +338,45 @@ function( strata.limits=NULL, projargs=NA, zone=NA, flip_around_dateline=FALSE,
 
   # Extra junk
   Data_Extrap = cbind( Data_Extrap, 'Include'=1)
-  Data_Extrap[,c('E_km','N_km')] = tmpUTM[,c('X','Y')]
+  Data_Extrap = cbind( Data_Extrap, "E_km"=tmpUTM[,'X'], "N_km"=tmpUTM[,'Y'] )
+
+  # Return
+  Return = list( "a_el"=a_el, "Data_Extrap"=Data_Extrap, "zone"=attr(tmpUTM,"zone"), "projargs"=attr(tmpUTM,"projargs"),
+    "flip_around_dateline"=flip_around_dateline, "Area_km2_x"=Area_km2_x)
+  return( Return )
+}
+
+#' @export
+Prepare_Chukchi_Extrapolation_Data_Fn <-
+function( strata.limits=NULL, projargs=NA, zone=NA, flip_around_dateline=FALSE, ... ){
+  # Infer strata
+  if( is.null(strata.limits)){
+    strata.limits = data.frame('STRATA'="All_areas")
+  }
+  message("Using strata ", strata.limits)
+
+  # Read extrapolation data
+  utils::data( chukchi_sea_grid, package="FishStatsUtils" )
+  Data_Extrap <- chukchi_sea_grid
+
+  # Survey areas
+  Area_km2_x = Data_Extrap[,'Area_in_survey_km2']
+
+  # Augment with strata for each extrapolation cell
+  Tmp = cbind("BEST_DEPTH_M"=0, "BEST_LAT_DD"=Data_Extrap[,'Lat'], "BEST_LON_DD"=Data_Extrap[,'Lon'], "propInSurvey"=1)
+  a_el = as.data.frame(matrix(NA, nrow=nrow(Data_Extrap), ncol=nrow(strata.limits), dimnames=list(NULL,strata.limits[,'STRATA'])))
+  for(l in 1:ncol(a_el)){
+    a_el[,l] = apply(Tmp, MARGIN=1, FUN=match_strata_fn, strata_dataframe=strata.limits[l,,drop=FALSE])
+    a_el[,l] = ifelse( is.na(a_el[,l]), 0, Area_km2_x)
+  }
+             #
+  # Convert extrapolation-data to an Eastings-Northings coordinate system
+  #tmpUTM = Convert_LL_to_UTM_Fn( Lon=Data_Extrap[,'Lon'], Lat=Data_Extrap[,'Lat'], zone=zone, flip_around_dateline=flip_around_dateline)                                                         #$
+  tmpUTM = project_coordinates( X=Data_Extrap[,'Lon'], Y=Data_Extrap[,'Lat'], projargs=projargs, zone=zone, flip_around_dateline=flip_around_dateline)                                                         #$
+
+  # Extra junk
+  Data_Extrap = cbind( Data_Extrap, 'Include'=1)
+  Data_Extrap = cbind( Data_Extrap, "E_km"=tmpUTM[,'X'], "N_km"=tmpUTM[,'Y'] )
 
   # Return
   Return = list( "a_el"=a_el, "Data_Extrap"=Data_Extrap, "zone"=attr(tmpUTM,"zone"), "projargs"=attr(tmpUTM,"projargs"),

R/make_extrapolation_info.R

@@ -34,9 +34,10 @@
 #'   \item{\code{"california_current"}}{The spatial fooprint of the bottom trawl surveys operated by AFSC/NWFSC, including the AFSC triennial from 1977-2004 and the NWFSC combined shelf-slope survey from 2003 onward (as identified by B. Feist and C. Whitmire); specify subsets via \code{surveyname}}
 #'   \item{\code{"west_coast_hook_and_line"}}{The spatial fooprint of the fixed-station hook-and-line survey in the California Bight operated by NWFSC (as identified by J. Harms)}
 #'   \item{\code{"british_columbia"}}{The spatial fooprint of the various stratified-random bottom trawl surveys operated by PBS (as identified by N. Olsen); see \code{strata_to_use} for further specification}
-#'   \item{\code{"eastern_bering_sea"}}{The spatial fooprint of the fixed station bottom trawl survey operated by AFSC in the eastern Bering Sea (as identified by A. Greig)}
-#'   \item{\code{"northern_bering_sea"}}{The spatial fooprint of the fixed station bottom trawl survey operated by AFSC in the northern Bering Sea (as identified by J. Conner)}
+#'   \item{\code{"eastern_bering_sea"}}{The spatial fooprint of the fixed station bottom trawl survey operated by AFSC in the eastern Bering Sea (as identified by J. Conner)}
+#'   \item{\code{"northern_bering_sea"}}{The spatial fooprint of the systematic bottom trawl survey operated by AFSC in the northern Bering Sea (as identified by J. Conner)}
 #'   \item{\code{"bering_sea_slope"}}{The spatial fooprint of the stratified random bottom trawl survey operated by AFSC in the Bering Sea slope (as identified by A. Greig)}
+#'   \item{\code{"chukchi_sea"}}{The spatial fooprint of the systematic bottom trawl survey operated by AFSC in the Bering Sea slope (as identified by J. Conner)}
 #'   \item{\code{"st_matthews_island"}}{The spatial fooprint of the survey area defined around St. Matthews Island, representing regular and corner stations from the eastern Bering Sea bottom trawl survey}
 #'   \item{\code{"aleutian_islands"}}{The spatial fooprint of the stratified random bottom trawl survey operated by AFSC in the Aleutian Islands (as identified by A. Greig)}
 #'   \item{\code{"gulf_of_alaska"}}{The spatial fooprint of the stratified random bottom trawl survey operated by AFSC in the Gulf of Alaska and containing shallow and deep stations, where the latter are not consistently sampled in later years (as identified by A. Greig)}
@@ -145,6 +146,10 @@ make_extrapolation_info = function( Region,
       if(missing(flip_around_dateline)) flip_around_dateline = FALSE
       Extrapolation_List = Prepare_BSslope_Extrapolation_Data_Fn( strata.limits=strata.limits, projargs=projargs, zone=zone, flip_around_dateline=flip_around_dateline, ... )
     }
+    if( tolower(Region[rI]) == "chukchi_sea" ){ #
+      if(missing(flip_around_dateline)) flip_around_dateline = FALSE
+      Extrapolation_List = Prepare_Chukchi_Extrapolation_Data_Fn( strata.limits=strata.limits, projargs=projargs, zone=zone, flip_around_dateline=flip_around_dateline, ... )
+    }
     if( tolower(Region[rI]) %in% c("st_matthews_island","smi") ){ #
       if(missing(flip_around_dateline)) flip_around_dateline = TRUE
       Extrapolation_List = Prepare_SMI_Extrapolation_Data_Fn( strata.limits=strata.limits, projargs=projargs, zone=zone, flip_around_dateline=flip_around_dateline, ... )