Fix bug...

... triggered when fine_scale=TRUE and observations are only available in a subset of the extrapolation-grid
James-Thorson-NOAA · Nov 9, 2019 · 3ab2411 · 3ab2411
2 parents 7537c71 + 736f670
commit 3ab2411
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Showing 5 changed files with 8 additions and 13 deletions.
diff --git a/R/Calc_Anisotropic_Mesh.R b/R/Calc_Anisotropic_Mesh.R
@@ -26,7 +26,7 @@ function(loc_x, loc_g, loc_i, Method, Extrapolation_List, anisotropic_mesh=NULL,
     }
   }else{
     loc_z = rbind( loc_x, loc_g, loc_i )
-    outer_hull = INLA::inla.nonconvex.hull(loc_i, convex = -0.05, concave = -0.05)
+    outer_hull = INLA::inla.nonconvex.hull( as.matrix(loc_z), convex = -0.05, concave = -0.05)
     anisotropic_mesh = INLA::inla.mesh.create( loc_x, plot.delay=NULL, refine=refine, boundary=outer_hull, ...)
   }
 

diff --git a/R/Convert_LL_to_UTM_Fn.R b/R/Convert_LL_to_UTM_Fn.R
@@ -21,7 +21,7 @@ function( Lon, Lat, zone=NA, flip_around_dateline=FALSE ){
   # Convert
   # if zone=NA or NULL, then it automatically detects appropriate zone
   Tmp = cbind('PID'=1,'POS'=1:length(Lon),'X'=Lon,'Y'=Lat)
-  if( flip_around_dateline==TRUE ) Tmp[,'X'] = 180 + ifelse( Tmp[,'X']>0, Tmp[,'X']-360, Tmp[,'X'])
+  if( flip_around_dateline==TRUE ) Tmp[,'X'] = ifelse( Tmp[,'X']>0, Tmp[,'X']-180, Tmp[,'X']+180)
   attr(Tmp,"projection") = "LL"
   attr(Tmp,"zone") = zone
   tmpUTM = PBSmapping::convUL(Tmp)                                                         #$

diff --git a/R/Prepare_AI_Extrapolation_Data_Fn.R b/R/Prepare_AI_Extrapolation_Data_Fn.R
@@ -12,7 +12,6 @@ function( strata.limits=NULL, zone=NA, flip_around_dateline=TRUE, ... ){
   Data_Extrap <- aleutian_islands_grid
 
   # Survey areas
-  #Area_km2_x = 4 * 1.852^2 * ifelse( Data_Extrap[,'EBS_STRATUM']!=0, 1, 0 )
   Area_km2_x = Data_Extrap[,'Area_km2']
 
   # Augment with strata for each extrapolation cell

diff --git a/R/Prepare_NZ_Extrapolation_Data_Fn.R b/R/Prepare_NZ_Extrapolation_Data_Fn.R
@@ -8,13 +8,8 @@ function( strata.limits=NULL, zone=NA, survey="Chatham_rise", flip_around_dateli
   message("Using strata ", strata.limits)
 
   # Read extrapolation data
-  if( is.null(Data) ){
-    utils::data( chatham_rise_grid, package="FishStatsUtils" )
-    Data_Extrap <- chatham_rise_grid
-  }else{
-    #stop( "Survey doesn't match New Zealand grid options" )
-    Data_Extrap <- Data
-  }
+  utils::data( chatham_rise_grid, package="FishStatsUtils" )
+  Data_Extrap <- chatham_rise_grid
 
   # Survey areas
   #Area_km2_x = 4 * 1.852^2 * ifelse( Data_Extrap[,'EBS_STRATUM']!=0, 1, 0 )
@@ -29,9 +24,9 @@ function( strata.limits=NULL, zone=NA, survey="Chatham_rise", flip_around_dateli
   }
 
   # Convert extrapolation-data to an Eastings-Northings coordinate system
-  if( is.numeric(zone) ){
-    tmpUTM = Convert_LL_to_UTM_Fn( Lon=Data_Extrap[,'Lon'], Lat=Data_Extrap[,'Lat'], zone=zone, flip_around_dateline=flip_around_dateline)                                                         #$
-    colnames(tmpUTM) = c('E_km','N_km')
+  if( is.na(zone) || is.numeric(zone) ){
+    tmpUTM = Convert_LL_to_UTM_Fn( Lon=Data_Extrap[,'Lon'], Lat=Data_Extrap[,'Lat'], zone=zone, flip_around_dateline=flip_around_dateline)
+    colnames(tmpUTM)[3:4] = c('E_km','N_km')
   }else{
     tmpUTM = Convert_LL_to_EastNorth_Fn( Lon=Data_Extrap[,'Lon'], Lat=Data_Extrap[,'Lat'], crs=zone )
   }

diff --git a/R/make_spatial_info.R b/R/make_spatial_info.R
@@ -58,6 +58,7 @@ make_spatial_info = function( n_x, Lon_i, Lat_i, Extrapolation_List, knot_method
       LON_intensity = Extrapolation_List$Data_Extrap[ which_rows, 'Lon']
       LAT_intensity = Extrapolation_List$Data_Extrap[ which_rows, 'Lat']
     }
+    if( !(knot_method %in% c("samples","grid")) ) stop("`knot_method` must be either `samples` or `grid`")
   }
 
   # Convert to an Eastings-Northings coordinate system