Fix R CMD check: clean to Status OK#39
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Two changes to src/GM99.cpp: 1. Tighter Poisson truncation in estab(): reduce Kmax from N + 10*sqrt(N+1) + 20 to N + 6*sqrt(N+1) + 6. The tail beyond the new cutoff is < 1e-10, so accuracy is unchanged but each dimension of the Cartesian odometer has ~2x fewer terms (e.g. N=1: 31 -> 16). 2. Replace the fixed-point iteration N_i <- N_i * W_i (up to 10000 steps, absolute tolerance) in gm99_equilibrium() with Newton's method on log W_i(N) = 0 in log-N space, using a numerical Jacobian computed by forward differences. Newton converges quadratically so only ~10-30 steps are needed vs thousands for the old fixed-point, which could oscillate slowly for multi-resident systems. Competitive exclusion is handled by removing near-zero residents (N < 1e-8, log W < 0) from the active Jacobian system. Before/after benchmarks (alpha=7, beta=15, R=1): 2-resident equilibrium: ~3.5 ms -> 0.11 ms (>30x) 3-resident equilibrium: ~1100 ms -> 4.7 ms (>230x, target was <100 ms) assembler step at 3 residents: ~6000 ms -> <0.1 ms (>60000x) All 218 tests pass unchanged. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Adapt the plant-family build conventions to regnans: - Makefile: adapted from plant/Makefile, dropping RcppR6/vignettes/ website targets (regnans uses plain Rcpp::compileAttributes and has no vignettes or pkgdown). Targets: compile, attributes, roxygen, test, install, build, check, clean. - .github/workflows/R-CMD-check.yaml: adapted from plant-dev2's modern r-lib/actions workflow (plant itself only has legacy Travis/AppVeyor). Runs R CMD check on Windows + macOS. - DESCRIPTION: add Remotes (traitecoevo/plant, smbache/loggr) so CI can install the GitHub-only dependencies. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
Resolve the install failure and all R CMD check warnings/notes:
- man/harness_gm99.Rd: reword apostrophes in roxygen (R 4.6 parse_Rd
read them as quote delimiters -> "unexpected end of input")
- community_demography.R: drop stray `ctrl = ctrl` arg (unused-argument
byte-compile note / latent runtime error)
- NAMESPACE: add @importFrom for stats/utils/ggplot2/dplyr/tibble/purrr
+ utils::globalVariables for NSE column names; move dplyr/tidyr/
mlr3learners from Depends to Imports; declare bbotk/data.table/loggr/
mlr3/mlr3mbo/paradox; drop unused progress; requireNamespace(mlr3learners)
- roxygen @param: sync community_start / community_solve_singularity_1D /
community_fitness_landscape with signatures; describe empty `@param ...`;
make community_fitness_landscape_bayesopt internal (no Rd)
- regenerate stale generated files to match committed GM99.cpp (Newton):
RcppExports.R + gm99_equilibrium.Rd defaults (200L / 1e-10)
- fix broken \link{assembler_stochastic_naive} cross-reference
- DESCRIPTION: complete-sentence Description; drop LazyData (no data/)
- .Rbuildignore: .claude, .github, .plant-interface-version, AGENTS.md,
dev Makefile (GNU-extensions warning)
- move WIP vignettes (assembly_fitmax, assembly_stochastic,
solving_attractors) out to overstorey_staging as .qmd
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
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R CMD checkto Status: OK (was 6 WARNINGs + 3 NOTEs, plus an install failure and a CI vignette-build error on macOS).Fixes
man/harness_gm99.Rdreworded so R 4.6'sparse_Rdno longer reads apostrophes (x',paper's,Daniel's) as quote delimiters (was: "unexpected end of input").ctrl = ctrlarg indemography_solve_equilibrium_solve()(unused-argument byte-compile note).@importFromfor stats/utils/ggplot2/dplyr/tibble/purrr +utils::globalVariables()for NSE columns; moveddplyr/tidyr/mlr3learnersfrom Depends to Imports; declaredbbotk/data.table/loggr/mlr3/mlr3mbo/paradox; dropped unusedprogress;requireNamespace(mlr3learners)instead ofrequire().@paramblocks with signatures (community_start,community_solve_singularity_1D,community_fitness_landscape); described empty@param ...; madecommunity_fitness_landscape_bayesoptinternal; fixed broken\link{assembler_stochastic_naive}.RcppExports.R+gm99_equilibrium.Rdto match the committed NewtonGM99.cpp(200L/1e-10). Master currently still has the old10000L/1e-12in these generated files, so this also clears the codoc mismatch now present on master.Description; removedLazyData(nodata/)..claude,.github,.plant-interface-version,AGENTS.md, devMakefile(GNU-extensions warning).Vignettes → staging
The three WIP vignettes (
assembly_fitmax,assembly_stochastic,solving_attractors) ran the full plant SCM on every build (the source of the macOS CIcreating vignettes ... ERROR). Moved out tooverstorey_staging/as.qmd.Not touched
loggris left as-is (Imports +Remotes: smbache/loggr), matchingplant, which uses it and passes on Windows. The earlier Windowspkgdependsresolution error on #35 looks like a transient/knock-on solve failure rather than a real loggr problem.🤖 Generated with Claude Code