edaphos 1.4.0 — Pillar 1 on real Cerrado data

Summary

Takes Pillar 1 from the synthetic br_cerrado toy to real
Brazilian Cerrado data. Backdoor-adjusted direct effects on
1 095 WoSIS topsoil profiles, with a DAG built against the exact
v1.3.1 covariate stack and block-bootstrap confidence intervals that
respect the spatial clustering of the profiles.

New API

• causal_cerrado_real_dag() — a DAG over 12 nodes / 23
  directed edges on the column names of the v1.3.1 case-study
  bundle, encoding: relief → climate (orographic + lapse-rate) →
  land cover; relief → texture → density; climate + texture +
  slope + land cover → SOC.

Identification of direct effects uses the existing
causal_adjustment_set() + causal_estimate_effect() API — no new
estimator code, just a domain-specific DAG and a real dataset.

Identified direct effects (LM, block-bootstrap by cluster, B = 200)

Exposure	Naive slope	Identified direct	Bootstrap 95 % CI
wc_bio_12 (MAP, g/kg per mm)	+0.0072	+0.0071	[+0.0002, +0.0121]
wc_landcover_trees (g/kg per % trees)	+0.898	+2.048 (2.3×)	[−0.465, +6.901]
soilgrids_clay (g/kg per % clay)	+0.526	+0.195 (0.37×)	[−0.099, +0.688]

Confounding moves in both directions. Naive OLS under-estimates
the land-use causal effect by more than half (tree cover really
does matter in Cerrado SOC) and over-estimates clay's direct
effect by nearly 3× (its apparent SOC lift is mostly slope / texture
confounding). Without DAG-guided adjustment all three numbers would
be reported wrong — exactly the kind of mistake Pearl's framework
is supposed to prevent, now demonstrated on a real Brazilian
dataset instead of a synthetic cube.

Deliverables

• data-raw/causal_cerrado_real.R — fully reproducible analysis.
• inst/extdata/causal_cerrado_real.rds — 62 KB slim results
  bundle.
• Vignette pilar1-causal-real — narrative walk-through with the
  DAG rendered via ggdag and the naive-vs-identified summary
  table.

Quality

• 11 new tests pinning the DAG structure and the adjustment sets
  for all three exposures.
• R CMD check --as-cran: 0 errors / 0 warnings / 2 harmless
  NOTEs.