Prototype reverse-mode AD of SCM outputs

.gitignore

@@ -23,6 +23,8 @@ Meta
 *.pdf
 *.png
 *.RDS
+# ...except committed test fixtures (the AD-gradient regression baseline).
+!tests/testthat/fixtures/gradient-baseline.rds
 
 # Overstorey guide preview figures — regenerated when the guide builds in the
 # Overstorey repo; not version-controlled here.

Makefile

@@ -32,6 +32,13 @@ roxygen:
 test: all
 	Rscript -e 'library(methods); devtools::test()'
 
+# AD tests self-skip under load_all (pkgload DLL). Run against the INSTALLED
+# package: library(plant) loads the installed .so so the skip-gate passes;
+# test_dir (not test_local) avoids re-loading via load_all; the namespace-parented
+# env exposes unexported internals; parallel off so callr workers inherit the load.
+test-ad: install
+	TESTTHAT_PARALLEL=false Rscript -e 'library(plant); e <- new.env(parent = asNamespace("plant")); testthat::test_dir("tests/testthat", filter = "ad", env = e)'
+
 benchmark:
 	Rscript scripts/benchmark.R
 
@@ -49,4 +56,4 @@ check: build
 clean:
 	rm -f src/*.o src/*.so src/*.o.tmp
 
-.PHONY: all compile doc clean test attributes roxygen install build check
+.PHONY: all compile doc clean test test-ad attributes roxygen install build check

NAMESPACE

@@ -43,6 +43,7 @@ export(TF24f_hyperpar)
 export(Weibull_Disturbance_Regime)
 export(add_mutant)
 export(add_strategies)
+export(birth_rate_gradient)
 export(control)
 export(control_accurate)
 export(environment_type)
@@ -52,6 +53,7 @@ export(export_patch_state)
 export(generate_strategy)
 export(grow_individual_to_height)
 export(grow_individual_to_size)
+export(grow_individual_to_size_gradient)
 export(grow_individual_to_time)
 export(hyperpar)
 export(integrate_over_size_distribution)
@@ -65,6 +67,7 @@ export(make_hyperpar)
 export(make_initial_state)
 export(mutant_parameters)
 export(node_schedule_times_default)
+export(offspring_production_gradient)
 export(optimise_individual_rate_at_height_by_trait)
 export(optimise_individual_rate_at_size_by_trait)
 export(param_hyperpar)
@@ -79,6 +82,8 @@ export(seq_log)
 export(seq_log_range)
 export(seq_range)
 export(set_initial_state)
+export(stand_gradient)
+export(stand_state_jacobian)
 export(strategy_list)
 export(tidy_individual)
 export(trait_matrix)