Restructure dft_stac_config() so cube-capable sources carry a role->asset
map (red/nir/swir16/mask), mask values, and reflectance scale/offset, marked
with cube = TRUE. Categorical sources (io-lulc, esa-worldcover) keep their
flat 4-field shape verbatim (backward compat, pinned by expect_named); the
cube marker is absence = FALSE. Add sentinel-2-l2a (Planetary Computer band
names B04/B08/B11/SCL). Guard dft_stac_fetch() to reject cube sources with a
pointer to dft_stac_cube().

Relates to NewGraphEnvironment/sred#16

Co-Authored-By: Claude Opus 4.8 <[email protected]>

Phase 2 (index registry): inst/indices/indices.csv holds spectral-index
formulas over band roles in gdalcubes tinyexpr C syntax (pow(), not ^).
dft_index_table() reads it (mirrors dft_class_table); dft_index_expr()
resolves roles to per-source assets, folds the reflectance scale/offset into
each band token (a non-zero offset does not cancel in a ratio index), and
applies the expression to a cube.

Phase 3 (cube fetch): dft_stac_cube() is the trajectory sibling of
dft_stac_fetch() -- STAC query with intersects (unioned AOI) + eo:cloud_cover
scene pre-filter + items_fetch pagination, an explicit AOI-bounded cube_view,
SCL cloud masking, the index applied, and the masked index cube materialized
to <source>/cube_<key>.nc keyed by every cube-affecting parameter. Returns the
lazy cube for dft_rast_break().

Fresh-eyes code-check on each: the cube's intersects used only the first AOI
feature (silent NoData holes for multi-feature AOIs) -- fixed by unioning.

Relates to NewGraphEnvironment/sred#16

Co-Authored-By: Claude Opus 4.8 <[email protected]>

Reduces an index cube over time with bfast::bfastmonitor(), returning a
two-band SpatRaster of break date (decimal year) and magnitude (negative =
index drop = scour / veg loss).

Empirical gate (findings.md): the gdalcubes reduce_time R callback runs in a
spawned worker at EVERY parallel setting, and a closure over enclosing locals
fails there ("object 'band' not found"). The reducer is therefore built
self-contained -- build_break_reducer() embeds the testable .dft_break_pixel()
helper as a literal object (env detached to baseenv) and inlines every scalar
parameter via substitute(), with load_pkgs="bfast" -- proven correct at
parallel 1 and 2. ts start / seasonal frequency are derived from the cube time
axis in the main process; a caller frequency that disagrees with the cadence
errors. Degenerate pixels (all-NA / < min_obs) short-circuit before any bfast
call, so those paths test with no bfast dependency.

Relates to NewGraphEnvironment/sred#16

Co-Authored-By: Claude Opus 4.8 <[email protected]>

The real-Sentinel-2 end-to-end run produced an entirely-NA kNDVI cube (and
intermittently segfaulted the gdalcubes compute worker). Isolated to
gdalcubes::filter_geom(): stepping through the pipeline, the raw bands, SCL
masking, and the kNDVI index all yield valid data (kNDVI in 0..1) WITHOUT
filter_geom, and the proven sibling dft_stac_fetch() works on the same AOI.

Drop the in-pipeline polygon clip. The cube now spans the AOI bounding box
(cloud-masked); callers clip the reduced raster with terra::mask(), matching
how dft_stac_fetch() masks after reading. Verified end-to-end: 48-month cube
has valid kNDVI throughout and dft_rast_break() reduces it (no segfault) to a
plausible break raster (dates in the 2022-2023 monitoring window).

Relates to NewGraphEnvironment/sred#16

Co-Authored-By: Claude Opus 4.8 <[email protected]>

…config (#30)

For high-latitude floodplains the all-months fetch was slow (~30 min for 100 ha
-- the Sentinel-2 streaming, not the compute) and injected winter snow/low-sun
noise that has no vegetation signal. Focus the analysis on the growing season:

- dft_stac_cube() gains `months` (calendar-month filter, default NULL/all).
  Fetching only e.g. June-September streams ~3x fewer scenes AND sharpens the
  signal; empty months become NA so the monthly series stays regular at
  frequency 12 for bfast.
- Snow/ice (SCL 11) added to the default Sentinel-2 mask.
- A GDAL /vsicurl config block (DISABLE_READDIR_ON_OPEN etc.), restored on exit,
  trims per-COG open latency.
- dft_rast_break() gains `order` (bfastmonitor harmonic order); lower it for a
  growing-season-only series that samples a narrow part of the annual cycle.

Both cache keys extended with the new params. Growing-season E2E (months=6:9,
2018-2023): 12 min vs 30, 24 clean summer observations per pixel, breaks dated
to summer months.

Relates to NewGraphEnvironment/sred#16

Co-Authored-By: Claude Opus 4.8 <[email protected]>

The Planetary Computer +1000 DN reflectance offset only applies from processing
baseline 04.00 (2022-01-25 on); earlier scenes have no offset. A uniform
offset was therefore wrong for pre-2022 scenes and produced a false
whole-AOI index step at the boundary (validated: 99% of pixels showed a
negative "break" dated to exactly the boundary -- an artifact, not vegetation).

Fix (baseline-conditional split):
- dft_stac_config() sentinel-2-l2a gains offset_boundary = "2022-01-25" and
  offset_before = 0.
- dft_stac_cube() splits items at the boundary, corrects each side with its own
  offset, and coalesces onto the shared monthly grid. It now returns a terra
  SpatRaster stack (materialized GeoTIFF, time per layer) instead of a gdalcubes
  cube -- gdalcubes cannot read a terra-written NetCDF, so the coalesce lives in
  terra.
- dft_rast_break() reduces the stack per pixel via parallel::mclapply (forked
  workers inherit the namespace and closures, so the whole gdalcubes reduce_time
  worker-serialization machinery -- build_break_reducer, load_pkgs -- is gone;
  .dft_break_pixel is unchanged). ts start / frequency derive from the layer
  times.

Validated end-to-end on 2018-2023 growing-season Sentinel-2: split fired
75 pre / 85 post, per-year kNDVI now aligns across 2022 (2021=0.52, 2022=0.53),
and breaks fell from 99% to 25% of usable pixels -- real change, not the
boundary artifact. Addresses the offset half of #32.

Relates to NewGraphEnvironment/sred#16

Co-Authored-By: Claude Opus 4.8 <[email protected]>

Flag that the Sentinel-2 (and Landsat template) cube sources read free
Planetary Computer / Azure Open Data with no egress charge, prompting anyone
adding a new source to check egress terms before shipping a requester-pays one.

Relates to NewGraphEnvironment/sred#16

Co-Authored-By: Claude Opus 4.8 <[email protected]>

vignettes/trajectory-break-detection.Rmd demonstrates the continuous
index-trajectory pipeline on the same Neexdzii Kwa reach as the land-cover
vignette. Following drift's data-raw pattern, data-raw/vignette_data_break.R
does the network + bfast work (growing-season Sentinel-2 kNDVI 2018-2023 with
the baseline-conditional offset split, reduced to break date + magnitude) and
saves a small committed artifact (inst/testdata/neexdzii_break.rds, 132 KB) so
every vignette chunk runs live under pkgdown with no network or bfast.

The vignette shows the break-magnitude map (negative = scour / veg loss), the
break-year map, and scour-vs-stable pixel kNDVI trajectories with the detected
break marked. Renders clean.

Relates to NewGraphEnvironment/sred#16

Co-Authored-By: Claude Opus 4.8 <[email protected]>

- .Rbuildignore: exclude planning/ and .claude/ from the built package (they
  belong in git for the SRED trail but are not package sources).
- .gitignore: data-raw/.break_cache/ (local STAC cube cache).
- Declare the rlang .data pronoun as a global (pre-existing note in
  dft_rast_classify's apply_remap), alongside eo:cloud_cover.

Relates to NewGraphEnvironment/sred#16

Co-Authored-By: Claude Opus 4.8 <[email protected]>

Continuous index-trajectory change detection (Sentinel-2 + BFAST) for
floodplain reaches (#30). R CMD check: 0 errors / 0 warnings / 0 notes.

Relates to NewGraphEnvironment/sred#16

Co-Authored-By: Claude Opus 4.8 <[email protected]>

Continuous index-trajectory change detection shipped as v0.3.0. See the archive
README for the outcome and the three empirical findings that reshaped the plan
(worker-closure failure, filter_geom segfault, Sentinel-2 offset boundary).

Co-Authored-By: Claude Opus 4.8 <[email protected]>

Continuation of the archived #30 cycle (v0.3.0 / PR #33). Refines the trajectory
vignette example to 2017-2023 (apples-to-apples with the LULC vignette) and to
surface the known 2022-2023 logging cut, which the shipped 2018-2023 /
monitor-from-2022 example did not (region-wide 2023 dip dominated). PWF headers
carry the prior journey forward and reference the archive.

Relates to NewGraphEnvironment/sred#16

Co-Authored-By: Claude Opus 4.8 <[email protected]>

Redo of the trajectory vignette example so it is apples-to-apples with the
land-cover vignette (same Neexdzii Kwa reach, same 2017-2023 window) and
actually surfaces the logging the shipped 2018-start / monitor-from-2022
example buried under a region-wide 2023 dip.

- data-raw/vignette_data_break.R: fetch 2017-2023 growing-season kNDVI (offset
  split), monitor from 2022 with 2017-2021 history (longer baseline -> 13k
  breaks vs 25k), and precompute a LULC ground-truth grouping (Trees ->
  Rangeland/Bare vs intact forest vs background) + agreement stats into a
  140 KB artifact.
- vignette reframed as the complement to LULC: LULC says what and roughly when
  (annual snapshots), the trajectory says exactly when (monthly). Shows the
  break map with LULC tree-loss outlined, an agreement table (tree-loss stands
  break 2x as often, 2.7x stronger, dated summer 2023), and the grouped
  trajectory -- with the basin-wide 2023 dip honestly acknowledged.

Vignette re-builds clean under R CMD check; 286 tests pass. Lands on PR #33.

Relates to NewGraphEnvironment/sred#16

Co-Authored-By: Claude Opus 4.8 <[email protected]>

)

Reconciling why the bfast trajectory disagreed with LULC's dramatic
Trees->Rangeland *inside* the floodplain revealed the tool's real value for the
project goal (floodplain veg change to justify leave-standing / restoration):
the LULC "tree-loss" pixels were borderline (kNDVI baseline 0.43 vs 0.50 intact,
median drop 0.037, only 2% a real crash). On this deciduous-riparian reach the
categorical product overstates forest loss (label flips, not canopy removal),
and the continuous trajectory's job is to QA that and to catch gradual
degradation/recovery the annual labels cannot.

- dft_rast_trend(): new export. Per-pixel robust Theil-Sen slope (index/yr) +
  Mann-Kendall significance over the full stack, via forked mclapply like
  dft_rast_break. Resistant to a single anomalous season. Guards for <2 layers
  / min_obs<2. Code-check verified the statistics.
- Vignette rebuilt as "Trajectories as a Check on Land-Cover Change": a
  degradation/recovery trend map (floodplain is stable-to-greening), a QA table
  showing the mapped tree-loss carries a median trend of ~0 and only ~6%
  significant decline (a caution on the area numbers), the grouped trajectory,
  and an honest "when to use which" (strong on evergreen/abrupt/gradual, weak at
  deciduous-riparian-vs-grass). Fixed an inverted map palette in self-review.

302 tests pass; R CMD check clean (bar a spurious future-timestamp NOTE); lint
clean. Lands on PR #33.

Relates to NewGraphEnvironment/sred#16

Co-Authored-By: Claude Opus 4.8 <[email protected]>

…e map (#30)

Rework the vignette from patch-level ground truth: real cutblocks in the
floodplain coincide with red patches in the break/trend maps, and some red
falls outside the LULC Trees->Rangeland polygons -- the continuous trajectory
and the categorical map catch different real change, so they are complementary,
not one correcting the other.

- data-raw: derive the actual LULC Trees->Rangeland transition polygons
  (dft_rast_transition + dft_transition_vectors, filtered to the loss
  transition, not stable Trees->Trees) for the map + overlap check; drop the
  aggregate QA table and averaged group trajectory (whole-floodplain averaging
  hides the patchy signal).
- vignette: neutral methods-first framing; break-magnitude map with the
  transition polygons outlined (red in/out/absent = confirmed / LULC-missed /
  unsupported); trend map relabelled per-year 2017-2023; and an interactive
  leaflet mirroring the land-cover vignette (Light/Esri/Google basemaps, AOI
  centering) with toggleable break, trend, and beige Trees->Rangeland layers to
  inspect the cutblocks on satellite imagery.

R CMD check clean (bar the spurious future-timestamp NOTE); vignette builds;
302 tests pass; lint + code-check clean. Lands on PR #33.

Relates to NewGraphEnvironment/sred#16

Co-Authored-By: Claude Opus 4.8 <[email protected]>