v0.2.0

.Rbuildignore

@@ -12,3 +12,4 @@
 ^README\.Rmd$
 ^GeoTwilightR\.Rproj$
 ^codemeta\.json$
+^LICENSE$

CITATION.cff

@@ -8,7 +8,7 @@ message: 'To cite package "GeoPathSampleR" in publications use:'
 type: software
 license: GPL-3.0-or-later
 title: 'GeoPathSampleR: Posterior Sampling of Geolocator Paths'
-version: 0.1.0.9000
+version: 0.2.0
 doi: 10.5281/zenodo.21944194
 abstract: Reconstructs bird migration trajectories from stationary-period likelihood
   maps built with GeoPressureR. A Gibbs sampler combines residence-dependent departure,
@@ -89,8 +89,8 @@ references:
     given-names: Mathieu
     email: mathieu@mgravey.com
     orcid: https://orcid.org/0000-0002-0871-1507
-  year: '2026'
   version: '>= 3.6.0'
+  year: '2026'
 - type: software
   title: ggplot2
   abstract: 'ggplot2: Create Elegant Data Visualisations Using the Grammar of Graphics'

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: GeoPathSampleR
 Title: Posterior Sampling of Geolocator Paths
-Version: 0.1.0.9000
+Version: 0.2.0
 Authors@R:
     person("Raphaël", "Nussbaumer", , "rafnuss@gmail.com", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0002-8185-1020"))

NEWS.md

@@ -2,12 +2,20 @@
 
 ## Main
 
+- [Add boundary sweeps to resample movement timing while retaining residence-segment locations](https://github.com/GeoPressure/GeoPathSampleR/commit/f15e91e), enabled every iteration by default with `boundary_interval = 1`. Use `0` or `Inf` to disable them.
+
 - [Update the default ground-speed and residence-dependent departure parameters](https://github.com/GeoPressure/GeoPathSampleR/commit/d40999d) from the pooled multi-sensor calibration. Results sampled with the previous defaults should be recomputed before comparison.
 - [Replace the route-detour model with a Gamma prior on route excess](https://github.com/GeoPressure/GeoPathSampleR/commit/7d4fb3f) whose scale depends on interval duration and direct endpoint distance ([3798978](https://github.com/GeoPressure/GeoPathSampleR/commit/3798978)). The prior applies to intervals with at least two movement days and endpoints at least 300 km apart, with predictors limited to the empirical calibration support.
 - Export `sampling_path_default_movement()` and document the movement model, `route_detour` and the modular cut of `long_period_light_only` in `sampling_path()`.
 
 ## Minor
 
+- Exclude the redundant repository GPL text from the R source package to resolve its package-check note.
+
+- [Fix known locations on water cells, stabilise the prior for direct routes, and reject excluded stationary periods](https://github.com/GeoPressure/GeoPathSampleR/commit/49e7735).
+- [Speed up route-prior evaluation, path summaries and diagnostics](https://github.com/GeoPressure/GeoPathSampleR/commit/6da2d15), and [avoid replicating scalar movement endpoints](https://github.com/GeoPressure/GeoPathSampleR/commit/0b989d1).
+- Document boundary sweeps, the complete sampler update schedule, route-prior support and computational controls in the function reference and getting-started vignette.
+
 - [Fix the diagnostic report rendering and browser opening](https://github.com/GeoPressure/GeoPathSampleR/commit/fb0d61f), and [declare its optional report dependencies](https://github.com/GeoPressure/GeoPathSampleR/commit/3ff7a89).
 - [Align the README and vignette with the movement model and sampler controls](https://github.com/GeoPressure/GeoPathSampleR/commit/ae3f0de), and add a provisional citation for the submitted methods manuscript alongside the software citation.
 - [Format the elapsed time compactly in the sampling message](https://github.com/GeoPressure/GeoPathSampleR/commit/38fe161).

R/path_collapse.R

@@ -11,7 +11,7 @@
 #' @param stap A stationary-period data frame containing `stap_id`, `start`,
 #'   and `end`. If `NULL`, these columns are taken from `paths`.
 #' @param label_stap_id logical; if `TRUE`, replace `stap_id` in the output
-#'   with a character label of the form `"{stap_id_start}->{stap_id_end}`.
+#'   with a character label of the form `"{stap_id_start}->{stap_id_end}"`.
 #'   The numeric `stap_id_start` and `stap_id_end` columns are always kept.
 #'
 #' @return A data frame with one row per collapsed stay and columns

R/path_summary.R

@@ -80,23 +80,31 @@ path_summary <- function(
   }
 
   if (by == "stap") {
+    row_by_stap <- split(
+      seq_len(nrow(paths)),
+      factor(paths$stap_id, levels = stap_id)
+    )
     out <- do.call(
       rbind,
-      lapply(stap_id, function(id) {
-        df <- paths[paths$stap_id == id, , drop = FALSE]
-        pos <- position_summary(df)
-        data.frame(
-          stap_id = id,
-          stap_id_start = id,
-          stap_id_end = id,
-          ind = as.integer(pos[["ind"]]),
-          lat = pos[["lat"]],
-          lon = pos[["lon"]],
-          start = stap$start[match(id, stap$stap_id)],
-          end = stap$end[match(id, stap$stap_id)],
-          n_path = length(unique(path_id[paths$stap_id == id]))
-        )
-      })
+      Map(
+        function(id, row_i) {
+          df <- paths[row_i, , drop = FALSE]
+          pos <- position_summary(df)
+          data.frame(
+            stap_id = id,
+            stap_id_start = id,
+            stap_id_end = id,
+            ind = as.integer(pos[["ind"]]),
+            lat = pos[["lat"]],
+            lon = pos[["lon"]],
+            start = stap$start[match(id, stap$stap_id)],
+            end = stap$end[match(id, stap$stap_id)],
+            n_path = length(unique(path_id[row_i]))
+          )
+        },
+        stap_id,
+        row_by_stap
+      )
     )
     row.names(out) <- NULL
     return(out)
@@ -114,11 +122,16 @@ path_summary <- function(
   group_start <- match(seq_len(max(group)), group)
   group_end <- c(group_start[-1L] - 1L, n_stap)
 
+  row_by_group <- split(
+    seq_len(nrow(paths)),
+    group[match(paths$stap_id, stap_id)]
+  )
+
   out <- do.call(
     rbind,
     lapply(seq_along(group_start), function(i) {
       ids <- stap_id[group_start[i]:group_end[i]]
-      df <- paths[paths$stap_id %in% ids, , drop = FALSE]
+      df <- paths[row_by_group[[i]], , drop = FALSE]
       pos <- position_summary(df)
       data.frame(
         stap_id = ids[1L],