fix Barrier-Mesh

DESCRIPTION

@@ -1,55 +1,55 @@
-Package: VAST
-Type: Package
-Title: Vector-Autoregressive Spatio-Temporal (VAST) Model
-Version: 3.9.0
-Date: 2022-03-17
-Authors@R: 
-    c(person(given = "James",
-             family = "Thorson",
-             role = c("aut", "cre"),
-             email = "James.Thorson@noaa.gov",
-             comment = c(ORCID = "0000-0001-7415-1010")),
-	  person(given="Cole", 
-	         family="Monnahan",
-			 role="ctb",
-			 email="Cole.Monnahan@noaa.gov")
-    )
-Description: VAST is an R package for conducting spatio-temporal analysis
-    of data from multiple categories (species, sizes, etc.), and includes both
-    spatial and spatio-temporal variation in density for each category, with either
-    factor-analysis or autoregressive correlations among categories, with derived
-    calculation of abundance indices, center-of-gravity, and area-occupied.
-Imports:
-    deldir,
-    stats,
-    devtools,
-    abind,
-    MatrixModels,
-    ThorsonUtilities,
-    effects,
-    INLA,
-    SpatialDeltaGLMM
-Depends:
-    TMB,
-    R (>= 3.5.0),
-Suggests:
-    testthat,
-    knitr,
-    rmarkdown,
-    FishStatsUtils,
-    pscl,
-    tweedie,
-    mgcv,
-    lme4
-Remotes:
-    james-thorson-NOAA/FishStatsUtils,
-    james-thorson/utilities,
-    nwfsc-assess/geostatistical_delta-GLMM
-License: file LICENSE
-LazyData: true
-Encoding: UTF-8
-RoxygenNote: 7.1.1
-ByteCompile: true
-URL: http://github.com/James-Thorson-NOAA/VAST
-BugReports: http://github.com/James-Thorson-NOAA/VAST/issues
-VignetteBuilder: knitr
+Package: VAST
+Type: Package
+Title: Vector-Autoregressive Spatio-Temporal (VAST) Model
+Version: 3.9.1
+Date: 2022-07-07
+Authors@R: 
+    c(person(given = "James",
+             family = "Thorson",
+             role = c("aut", "cre"),
+             email = "James.Thorson@noaa.gov",
+             comment = c(ORCID = "0000-0001-7415-1010")),
+	  person(given="Cole", 
+	         family="Monnahan",
+			 role="ctb",
+			 email="Cole.Monnahan@noaa.gov")
+    )
+Description: VAST is an R package for conducting spatio-temporal analysis
+    of data from multiple categories (species, sizes, etc.), and includes both
+    spatial and spatio-temporal variation in density for each category, with either
+    factor-analysis or autoregressive correlations among categories, with derived
+    calculation of abundance indices, center-of-gravity, and area-occupied.
+Imports:
+    deldir,
+    stats,
+    devtools,
+    abind,
+    MatrixModels,
+    ThorsonUtilities,
+    effects,
+    INLA,
+    SpatialDeltaGLMM
+Depends:
+    TMB,
+    R (>= 3.5.0),
+Suggests:
+    testthat,
+    knitr,
+    rmarkdown,
+    FishStatsUtils,
+    pscl,
+    tweedie,
+    mgcv,
+    lme4
+Remotes:
+    james-thorson-NOAA/FishStatsUtils,
+    james-thorson/utilities,
+    nwfsc-assess/geostatistical_delta-GLMM
+License: file LICENSE
+LazyData: true
+Encoding: UTF-8
+RoxygenNote: 7.2.0
+ByteCompile: true
+URL: http://github.com/James-Thorson-NOAA/VAST
+BugReports: http://github.com/James-Thorson-NOAA/VAST/issues
+VignetteBuilder: knitr

R/make_data.R

@@ -189,6 +189,7 @@
 #'   \item{\code{Options["Calculate_proportion"]=TRUE}}{Turns on internal calculation and SE for proportion of response within each category (e.g., for calculating proportion-at-age or species turnover)}
 #'   \item{\code{Options["Calculate_Synchrony"]=TRUE}}{Turns on internal calculation and SE for Loreau metric of synchrony (a.k.a. portfolio effects)}
 #'   \item{\code{Options["report_additional_variables"]=TRUE}}{Export additional variables to \code{Report} object, to use for diagnostics or additional exploration}
+#'   \item{\code{Options["range_fraction"]}}{The decorrelation range when passing over land relative to over water; the default value \code{Options["range_fraction"]=0.2} indicates that the range is shorter over land, i.e., that correlations are strongest via water, while changing to \code{Options["range_fraction"]=5} would represent correlations transfer via land more than water}
 #' }
 #' @param yearbounds_zz matrix with two columns, giving first and last years for defining one or more periods (rows) used to
 #'        calculate changes in synchrony over time (only used if \code{Options['Calculate_Synchrony']=1})
@@ -288,7 +289,8 @@ function( b_i,
                    'zerosum_penalty' = 0,
                    'EOF_unity_trace' = 0,
                    'basin_method' = 0,
-                   'lagrange_multiplier' = 50 )
+                   'lagrange_multiplier' = 50,
+                   'range_fraction' = 0.2 )
 
   # Replace defaults for `Options` with provided values (if any)
   for( i in seq_along(Options) ){
@@ -1011,7 +1013,7 @@ function( b_i,
   if( "spde_aniso" %in% names(Return) ) Return[['spde_aniso']] = list("n_s"=MeshList$anisotropic_spde$n.spde, "n_tri"=nrow(MeshList$anisotropic_mesh$graph$tv), "Tri_Area"=MeshList$Tri_Area, "E0"=MeshList$E0, "E1"=MeshList$E1, "E2"=MeshList$E2, "TV"=MeshList$TV-1, "G0"=MeshList$anisotropic_spde$param.inla$M0, "G0_inv"=INLA::inla.as.dgTMatrix(solve(MeshList$anisotropic_spde$param.inla$M0)) )
   if( "spdeMatricesBarrier" %in% names(Return) ){
     Return[['spdeMatricesBarrier']] = MeshList$barrier_list
-    Return[['Barrier_scaling']] = c(0.2, 1)
+    Return[['Barrier_scaling']] = c(1, Options2use['range_fraction'])
   }
 
   #assign(x="X1_itp", value=X1_itp, envir=.GlobalEnv)