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Release 3.7.0: seedable MCMC runs - #52
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Bump version to 3.7.0 and close out the NEWS entry for run_mcmc(seed =).
Use \doi{} for the namibia_data source so CRAN incoming checks are clean.
Add runnable examples and @return documentation to every exported function, cite the Bioinformatics paper in Description, declare parallel in Imports, drop the unused markdown Suggest, and credit the bundled spline.h author as cph. Fix swapped epsilon_pos/epsilon_neg docs in simulate_observed_allele(). Add cran-comments.md.
adapt_temp() now interpolates temperature as a function of cumulative communication barrier (Fritsch-Carlson / PCHIP slopes) and reads the new ladder off an even barrier grid, so there is no root solving, no monotonicity post-fix, and no band-matrix LU. Adjacent chains with zero barrier collapse into a single knot; if no barrier has been observed the update is skipped. Removes src/include/spline (GPL-2 third-party, locally modified without a change notice) and the cph entry for it. Adds testthat coverage for the adapted ladder.
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Cuts 3.7.0 from master after #51. This is the release intended for first CRAN submission.
Release
Versionto 3.7.0 and close out the NEWS entry forrun_mcmc(seed =).CRAN prep
@examplesand@returndocs on all 24 exported functions (slowest example 0.16 s).Descriptioncites Murphy & Greenhouse (2024)<doi:10.1093/bioinformatics/btae619>.paralleldeclared inImports; unusedmarkdowndropped fromSuggests.\doi{}for thenamibia_datasource;@formatforsimulated_data/mcmc_results.epsilon_pos/epsilon_negdescriptions insimulate_observed_allele().cran-comments.mdadded (build-ignored).Replace bundled
spline.hadapt_temp()now interpolates temperature as a function of cumulative communication barrier with a monotone cubic Hermite scheme (src/monotone_interpolator.h, ~100 lines, ours) and reads the new ladder off an even barrier grid. No root solving, no monotonicity post-fix, no band-matrix LU.src/include/spline(GPL-2 third-party, locally modified tofloatwithout a change notice). Nocphentry needed.test-adapt-temp.Rcovers finiteness, monotonicity, fixed endpoints,adapt_temp = FALSE, and user-supplied temperature vectors.Local
R CMD check --as-cran --run-donttest(R 4.5.2, macOS arm64): CRAN incoming feasibility OK, compiled code OK, examples/tests (46)/vignettes OK, tarball 3.96 MB. Remaining findings are local-toolchain only (-Wfixed-enum-extensionfromR_ext/Boolean.hunder Apple clang 21; HTML Tidy version).After merge: tag
v3.7.0, thendevtools::release()/devtools::submit_cran().