claude's roxygen build and test

.Rbuildignore

@@ -11,3 +11,4 @@
 ^.*\.Rproj$
 ^\.Rproj\.user$
 ^README\.Rmd$
+^LICENSE\.md$

DESCRIPTION

@@ -15,7 +15,7 @@ Description: Fits polygon spatial masks to XY point coordinates such as
 License: MIT + file LICENSE
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.3.2
+RoxygenNote: 7.3.3
 Depends:
     R (>= 4.1.0)
 Imports:

LICENSE

@@ -1,21 +1,2 @@
-MIT License
-
-Copyright (c) 2026 Raredon Lab
-
-Permission is hereby granted, free of charge, to any person obtaining a copy
-of this software and associated documentation files (the "Software"), to deal
-in the Software without restriction, including without limitation the rights
-to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-copies of the Software, and to permit persons to whom the Software is
-furnished to do so, subject to the following conditions:
-
-The above copyright notice and this permission notice shall be included in all
-copies or substantial portions of the Software.
-
-THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
-SOFTWARE.
+YEAR: 2026
+COPYRIGHT HOLDER: Raredon Laboratory

LICENSE.md

@@ -0,0 +1,21 @@
+# MIT License
+
+Copyright (c) 2026 Raredon Laboratory
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

NAMESPACE

@@ -2,13 +2,14 @@
 
 export(fit_spatial_mask)
 importFrom(parallel,mclapply)
+importFrom(sf,"st_crs<-")
 importFrom(sf,NA_crs_)
 importFrom(sf,st_area)
 importFrom(sf,st_as_sf)
 importFrom(sf,st_bbox)
 importFrom(sf,st_buffer)
 importFrom(sf,st_convex_hull)
-importFrom(sf,"st_crs<-")
+importFrom(sf,st_covered_by)
 importFrom(sf,st_difference)
 importFrom(sf,st_distance)
 importFrom(sf,st_geometry)
@@ -19,6 +20,4 @@ importFrom(sf,st_sfc)
 importFrom(sf,st_simplify)
 importFrom(sf,st_union)
 importFrom(sf,st_within)
-importFrom(stats,complete.cases)
 importFrom(stats,filter)
-importFrom(stats,quantile)

R/TissueMask-package.R

@@ -26,3 +26,7 @@
 #'
 #' @keywords internal
 "_PACKAGE"
+
+# Suppress R CMD check NOTE: "no visible binding for global variable 'x'/'y'"
+# These are ggplot2 aesthetic mappings in fit_spatial_mask(plot = TRUE).
+utils::globalVariables(c("x", "y"))

R/fit_spatial_mask.R

@@ -1,8 +1,8 @@
 #' Fit a Spatial Boundary Mask to Point Coordinate Data
 #'
 #' @description
-#' Fits a polygon (or multi-polygon) spatial mask — an [sf::sfc] geometry
-#' object — to a set of XY point coordinates. Suitable for cell centroids,
+#' Fits a polygon (or multi-polygon) spatial mask (an [sf::sfc] geometry
+#' object) to a set of XY point coordinates. Suitable for cell centroids,
 #' single-molecule transcript locations, or any spatial point process data.
 #' The mask faithfully captures tissue shape including internal voids (vessel
 #' lumens, necrotic cores, tissue tears) and disconnected fragments.
@@ -20,9 +20,9 @@
 #' 1. Bin point coordinates onto a regular grid.
 #' 2. Convolve the occupancy grid with a 2-D Gaussian of width `raster_sigma`
 #'    (in coordinate units).
-#' 3. Threshold at `raster_threshold × max`. Cells above threshold are "inside".
+#' 3. Threshold at `raster_threshold * max`. Cells above threshold are "inside".
 #' 4. Convert each "inside" cell to an axis-aligned rectangle and dissolve via
-#'    GEOS union. Holes and islands emerge from the geometry naturally — no
+#'    GEOS union. Holes and islands emerge from the geometry naturally -- no
 #'    ring-winding logic required.
 #' 5. Apply a morphological close (buffer out then in) to smooth staircase
 #'    boundaries.
@@ -31,15 +31,15 @@
 #'   names differ, the first two columns are used and renamed. Rows containing
 #'   `NA` in `x` or `y` are silently dropped.
 #' @param method Character scalar. Masking algorithm. One of:
-#'   * `"raster"` *(default)* — Gaussian smoothing on a rasterised grid,
+#'   * `"raster"` *(default)* -- Gaussian smoothing on a rasterised grid,
 #'     binary threshold, then GEOS union of "on" cells. Supports holes and
 #'     islands. Recommended for most datasets.
-#'   * `"kde"` — 2-D kernel density estimate via [MASS::kde2d()] contoured
+#'   * `"kde"` -- 2-D kernel density estimate via [MASS::kde2d()] contoured
 #'     with [isoband::isobands()]. Supports holes and islands. Requires
 #'     packages **MASS** and **isoband**.
-#'   * `"concave"` — Concave hull via [concaveman::concaveman()]. No holes or
+#'   * `"concave"` -- Concave hull via [concaveman::concaveman()]. No holes or
 #'     islands. Requires package **concaveman**.
-#'   * `"convex"` — Convex hull via [sf::st_convex_hull()]. No holes or
+#'   * `"convex"` -- Convex hull via [sf::st_convex_hull()]. No holes or
 #'     islands. No additional packages required.
 #' @param concavity Numeric. Relative concavity for `method = "concave"`.
 #'   Lower values produce tighter, more concave boundaries; higher values
@@ -62,11 +62,11 @@
 #' @param raster_sigma Numeric. Standard deviation of the Gaussian kernel in
 #'   **coordinate units** (the same units as `x` and `y`). This is the key
 #'   tuning parameter:
-#'   * Larger `raster_sigma` → holes fill in, islands merge, boundary smooths.
-#'   * Smaller `raster_sigma` → holes and fine structure are preserved.
-#'   * `NULL` (default) → auto-set to 3% of the domain width.
+#'   * Larger `raster_sigma` -> holes fill in, islands merge, boundary smooths.
+#'   * Smaller `raster_sigma` -> holes and fine structure are preserved.
+#'   * `NULL` (default) -> auto-set to 3% of the domain width.
 #' @param raster_threshold Numeric in `(0, 1)`. A grid cell is "inside" when
-#'   its smoothed value exceeds `raster_threshold × max(smoothed_grid)`.
+#'   its smoothed value exceeds `raster_threshold * max(smoothed_grid)`.
 #'   Higher values shrink the mask; lower values grow it. Default `0.15`.
 #' @param raster_min_pts Integer. Minimum number of points that must fall in
 #'   a grid cell before it is eligible for the convolution. Cells with fewer
@@ -75,8 +75,8 @@
 #'   [sf::st_buffer()]. Zero means no expansion. Default `0`.
 #' @param smooth_mask Logical. If `TRUE`, the mask boundary is simplified with
 #'   [sf::st_simplify()] after fitting. Default `FALSE`.
-#' @param smooth_tolerance Numeric. Douglas–Peucker tolerance passed to
-#'   [sf::st_simplify()]. `NULL` → auto-set to 1% of the bounding-box
+#' @param smooth_tolerance Numeric. Douglas-Peucker tolerance passed to
+#'   [sf::st_simplify()]. `NULL` -> auto-set to 1% of the bounding-box
 #'   diagonal. Default `NULL`.
 #' @param n_cores Integer. Number of cores for parallel row-smoothing in
 #'   [parallel::mclapply()] (Unix/macOS only; ignored on Windows). Default
@@ -105,27 +105,27 @@
 #' # Raster method (recommended default)
 #' mask <- fit_spatial_mask(coords, verbose = FALSE)
 #'
-#' # Convex hull — instant, no additional packages
+#' # Convex hull -- instant, no additional packages
 #' mask_cv <- fit_spatial_mask(coords, method = "convex", verbose = FALSE)
 #'
-#' # Concave hull — requires 'concaveman'
+#' # Concave hull -- requires 'concaveman'
 #' \donttest{
 #' mask_cc <- fit_spatial_mask(coords, method = "concave",
 #'                             concavity = 1.5, verbose = FALSE)
 #' }
 #'
-#' # Verify all points are inside the mask
+#' # Verify all points are covered by the mask (boundary counts as covered)
 #' library(sf)
 #' pts <- sf::st_as_sf(coords, coords = c("x", "y"), crs = sf::NA_crs_)
-#' all(sf::st_within(pts, sf::st_union(mask), sparse = FALSE)[, 1])
+#' all(sf::st_covered_by(pts, sf::st_union(mask), sparse = FALSE)[, 1])
 #'
 #' @seealso [sf::st_sfc()], [sf::st_union()], [sf::st_buffer()]
 #'
 #' @export
 #' @importFrom sf st_as_sf st_convex_hull st_union st_sfc st_polygon
 #' @importFrom sf st_buffer st_distance st_simplify st_bbox st_area
-#' @importFrom sf st_crs<- st_make_valid st_geometry st_sf st_within
-#' @importFrom sf st_difference NA_crs_
+#' @importFrom sf "st_crs<-" st_make_valid st_geometry st_sf st_within
+#' @importFrom sf st_difference NA_crs_ st_covered_by
 fit_spatial_mask <- function(
   coords,
 
@@ -178,7 +178,7 @@ fit_spatial_mask <- function(
   if (n_pts < 3L)
     stop("Need at least 3 coordinate pairs to fit a mask (got ", n_pts, ").")
   if (n_pts > 50000L && method == "kde" && verbose)
-    message("Large n = ", n_pts, " with method='kde' — consider method='raster'.")
+    message("Large n = ", n_pts, " with method='kde' -- consider method='raster'.")
 
   # ---- 2. Fit mask -----------------------------------------------------------
   mask_poly <- switch(method,
@@ -235,20 +235,20 @@ fit_spatial_mask <- function(
       .build_sf_with_holes(bands, crs)
     },
 
-    # -- Raster: Gaussian sum → threshold → cell union -------------------------
+    # -- Raster: Gaussian sum -> threshold -> cell union -----------------------
     #
     # Algorithm:
-    #   1. Bin points onto a regular grid (raster_resolution × raster_resolution).
+    #   1. Bin points onto a regular grid (raster_resolution x raster_resolution).
     #   2. Convolve the binary occupancy grid with a 2-D Gaussian of width
     #      raster_sigma (coordinate units). Equivalent to placing an isotropic
     #      Gaussian at every point and summing them all.
-    #   3. Threshold at raster_threshold × max(field). Cells above threshold
+    #   3. Threshold at raster_threshold * max(field). Cells above threshold
     #      are "inside"; cells below are "outside".
     #   4. Convert each "inside" cell to an axis-aligned rectangle and dissolve
     #      via GEOS union. Holes and islands emerge from the geometry naturally
-    #      — no ring-winding logic required.
+    #      -- no ring-winding logic required.
     #   5. Smooth the staircase boundary with a morphological close
-    #      (buffer out then in by ~0.6 × cell diagonal).
+    #      (buffer out then in by ~0.6 * cell diagonal).
     "raster" = {
 
       # Grid cell edges
@@ -275,16 +275,29 @@ fit_spatial_mask <- function(
       sigma_cu <- if (is.null(raster_sigma)) 0.03 * domain_w else raster_sigma
       sigma_gc <- sigma_cu / hx   # grid-cell units for convolution kernel
 
+      # Clamp sigma_gc so the Gaussian kernel fits within the grid.
+      # stats::filter() requires filter length <= time series length.
+      # Kernel length = 2 * ceiling(3 * sigma_gc) + 1 <= raster_resolution
+      # => sigma_gc <= floor((raster_resolution - 1) / 2) / 3
+      max_sigma_gc <- floor((raster_resolution - 1L) / 2L) / 3
+      if (sigma_gc > max_sigma_gc) {
+        if (verbose)
+          message("  raster_sigma clamped: sigma_gc = ", round(sigma_gc, 1),
+                  " exceeds grid limit (", round(max_sigma_gc, 1), " gc).",
+                  " Increase raster_resolution for finer control at large sigma.")
+        sigma_gc <- max_sigma_gc
+      }
+
       if (verbose)
         message("  raster_sigma = ", round(sigma_cu, 4),
                 " coord units  (", round(sigma_gc, 1), " grid cells)")
 
-      # Convolve binary occupancy with Gaussian — sum of point Gaussians
+      # Convolve binary occupancy with Gaussian -- sum of point Gaussians
       indicator <- (cm >= raster_min_pts) * 1.0
       sm        <- .gaussian_smooth_2d(indicator, sigma = sigma_gc,
                                        n_cores = n_cores)
 
-      # Threshold → binary
+      # Threshold -> binary
       thresh   <- raster_threshold * max(sm, na.rm = TRUE)
       binary   <- sm >= thresh
       on_cells <- which(binary, arr.ind = TRUE)   # [row = yi, col = xi]
@@ -307,11 +320,11 @@ fit_spatial_mask <- function(
         )))
       })
 
-      # GEOS dissolve — topology (holes, islands) emerges automatically
+      # GEOS dissolve -- topology (holes, islands) emerges automatically
       raw <- sf::st_union(sf::st_sfc(rects, crs = crs))
 
       # Morphological close: smooth staircase boundary.
-      # Buffer out then in by ~0.6 × cell diagonal.
+      # Buffer out then in by ~0.6 * cell diagonal.
       cell_diag <- sqrt(hx^2 + hy^2)
       raw <- sf::st_buffer(raw, dist =  cell_diag * 0.6)
       raw <- sf::st_buffer(raw, dist = -cell_diag * 0.6)
@@ -329,14 +342,17 @@ fit_spatial_mask <- function(
     mask_poly <- sf::st_buffer(mask_poly, dist = buffer_dist)
 
   # ---- 4. Containment guarantee ----------------------------------------------
+  # Use st_covered_by (not st_within): boundary points count as covered.
+  # st_within is strict interior containment and returns FALSE for hull vertices,
+  # which would trigger a zero-distance corrective buffer that does nothing.
   pts_sfc   <- sf::st_geometry(
     sf::st_as_sf(coords, coords = c("x", "y"), crs = crs))
-  contained <- sf::st_within(pts_sfc, sf::st_union(mask_poly), sparse = FALSE)
-  n_out     <- sum(!contained[, 1L])
+  mask_union <- sf::st_union(mask_poly)
+  contained  <- sf::st_covered_by(pts_sfc, mask_union, sparse = FALSE)
+  n_out      <- sum(!contained[, 1L])
   if (n_out > 0L) {
-    warning(n_out, " point(s) outside mask — applying corrective buffer.")
-    dists     <- sf::st_distance(pts_sfc[!contained[, 1L]],
-                                 sf::st_union(mask_poly))
+    warning(n_out, " point(s) outside mask - applying corrective buffer.")
+    dists     <- sf::st_distance(pts_sfc[!contained[, 1L]], mask_union)
     mask_poly <- sf::st_buffer(mask_poly,
                                dist = max(as.numeric(dists)) * 1.05)
   }
@@ -387,7 +403,7 @@ fit_spatial_mask <- function(
         ggplot2::coord_sf(datum = NA) +
         ggplot2::labs(
           title    = paste0("TissueMask | method = '", method, "'"),
-          subtitle = paste0(n_pts, " points  \u00b7  area = ",
+          subtitle = paste0(n_pts, " points | area = ",
                             round(suppressWarnings(
                               as.numeric(sf::st_area(mask_poly))), 2)),
           x = "X", y = "Y") +