Add boundaries argument to run_sdmtmb() and add new area to boundaries_data

R/calc_index_areas.R

@@ -14,15 +14,7 @@
 #'
 #' @inheritParams format_data
 #' @inheritParams diagnose
-#' @param boundaries A named list of northern and southern boundaries for a
-#'   set of areas. The list can contain as many areas as you would like but
-#'   it must contain at least one area and each area must be a vector of two
-#'   real numbers specified in decimal degrees. The order of the areas only
-#'   matters if you care what order they are plotted because the names will
-#'   be turned into factors. The default value uses a data object called
-#'   `boundaries_data`, which is a list of several areas along the U.S. West
-#'   Coast, including a coastwide area going from the northern Washington
-#'   border to the southern California border.
+#' @template boundaries
 #' @export
 #' @author Kelli F. Johnson
 #' @seealso

R/run_sdmtmb.R

@@ -8,6 +8,7 @@
 #'   mesh that is created by {INLA}. More knots is not always better. The
 #'   default is to use 500 knots. Future work will look at specifying a
 #'   threshold distance between points rather than number of knots.
+#' @template boundaries
 #' @param ... Optional arguments passed to [sdmTMB::sdmTMB()]. Note that users
 #'   cannot pass `anisotropy` or `sdmTMBcontrol` because both of these are set
 #'   internal to this function, where `anisotropy = TRUE` because the coastline
@@ -24,6 +25,7 @@ run_sdmtmb <- function(dir_main = getwd(),
                        family,
                        formula,
                        n_knots = 500,
+                       boundaries = boundaries_data["Coastwide"],
                        ...) {
   # Checks
   stopifnot(inherits(family, "family"))
@@ -141,7 +143,8 @@ run_sdmtmb <- function(dir_main = getwd(),
     data = data_truncated,
     fit = fit,
     prediction_grid = grid,
-    dir = dir_index
+    dir = dir_index,
+    boundaries = boundaries
   )
 
   # Add diagnostics

data-raw/boundaries_data.R

@@ -11,7 +11,10 @@ boundaries_data <- list(
   "South of Cape Mendocino" = c(40.166667, southern_CA),
   # For sablefish
   "North of Monterey Bay" = c(southern_BC, 36.00),
-  "South of Monterey Bay" = c(36.00, southern_CA)
+  "South of Monterey Bay" = c(36.00, southern_CA),
+  # Boundary used in some tribal U&A calculations
+  "North of 46deg 53.3min" = c(southern_BC, 46.888333),
+  "South of 46deg 53.3min" = c(46.888333, southern_CA)
 )
 
 usethis::use_data(

man-roxygen/boundaries.R

@@ -0,0 +1,9 @@
+#' @param boundaries A named list of northern and southern boundaries for a
+#'   set of areas. The list can contain as many areas as you would like but
+#'   it must contain at least one area and each area must be a vector of two
+#'   real numbers specified in decimal degrees. The order of the areas only
+#'   matters if you care what order they are plotted because the names will
+#'   be turned into factors. The default value uses a data object called
+#'   `boundaries_data`, which is a list of several areas along the U.S. West
+#'   Coast, including a coastwide area going from the northern Washington
+#'   border to the southern California border.