freqTLS copyright and provenance notes freqTLS is released under GPL (>= 3), as declared in DESCRIPTION. This file records code and patterns adapted from other GPL-compatible packages, and the licence of the vendored benchmark data. Any further reuse must be recorded here, with the source file and the nature of the adaptation, before the change is treated as complete (AGENTS.md design rule 9). == Provenance == freqTLS is the frequentist sibling of bayesTLS, forked from the profileTLS package at commit 6f963a9 (v0.3.3), which it supersedes; profileTLS is now a private, archived predecessor. Both are GPL (>= 3). == Engineering patterns adapted from drmTMB (GPL-3) == Source: https://github.com/itchyshin/drmTMB (local sibling package). - src/init.c: the Boolean.h pre-include guard that lets the package compile cleanly under R 4.5's Apple clang is adapted from drmTMB::src/init.c. - src/profile_tls.cpp: the same Boolean.h pre-include guard (cf. drmTMB::src/drmTMB.cpp:1-14); the beta-binomial lgamma density form (cf. drmTMB::src/drmTMB.cpp:1319-1328); and the branch-free CppAD::CondExp probability clamp and the beta-binomial shape floor (cf. drmTMB::src/drmTMB.cpp:1302-1314). - src/profile_tls_numeric.h: the series-vs-direct CondExp switching for a stable log1p(exp()) is adapted from drmTMB::src/drm_numeric.h. - R/formula.R: the shape of the brms/drmTMB-style formula parser -- variadic capture of per-sub-parameter formulas via substitute(), the small formula-walking primitives (LHS/RHS extraction, additive flattening), and random-effect-bar detection -- is adapted from drmTMB's drm_formula() / parse_drm_formula_entry() (cf. drmTMB::R/parse-formula.R). freqTLS writes its own grammar: the time() / temp() axis markers, the five fixed sub-parameter handles (low, up, log_k, CTmax, log_z), the successes | trials(total) and cbind() response idioms. The initial port used intercept-only shapes and shared CTmax/log_z designs; freqTLS subsequently implemented independent shape designs and the limited random-intercept structures documented in the current package. - The agent-kit, dev-log discipline, and the optimizer/profile plumbing patterns implemented in R/fit_engine.R, R/profile.R, and R/confint.R follow drmTMB's governance and R/profile.R patterns. freqTLS writes independent code for the 4PL thermal-load-sensitivity likelihood and its direct CTmax/z parameterisation; only the numerical-stability and registration patterns above are adapted. == Confidence-Eye geometry adapted from gllvmTMB (GPL-3) == Source: https://github.com/JenniNiku/gllvmTMB (or the local sibling package). - R/plotting.R (Phase 4): the Confidence-Eye lens geometry in the helper tls_eye_polygon_df() adapts gllvmTMB's .eye_polygon_df(width_max = 0.70) from gllvmTMB/R/loading-uncertainty-helpers.R (the Gaussian-width lens taper and the CI-half-width fallback for a missing SE), and plot_confidence_eye() adapts the structure of gllvmTMB's plot_loadings_confidence_eye() from gllvmTMB/R/plot-loadings-confidence-eye.R (pale geom_polygon lens at alpha 0.35, hollow geom_point at shape 21, the reliability fill palette, and the honest fallback that refuses to draw a lens when no finite (lower, upper) interval exists -- here keyed off the profile conf.status so a non-closing profile renders a hollow point only). freqTLS writes its own forward-prediction and survival/TDT/surface plots; only the lens geometry and eye structure are adapted. == Bundled data and generated evidence == The file-by-file source, rights holder, licence or permission status, transformation, consumer, and CRAN ship/block decision are recorded in the repository-only docs/design/47-data-license-ledger.md. That build-excluded ledger is the release gate; a licence on one upstream package or repository must not be generalized to a component with a more specific licence. The brown-shrimp and life-stage zebrafish CSVs were obtained from bayesTLS, whose package distribution is CC BY 4.0. The model-ready .rda files apply the cleaning documented in R/data.R. The Drosophila suzukii assay data are from Orsted et al. (2024), Zenodo record 10602268, CC BY 4.0. The oxygen-gradient zebrafish data are from Saruhashi et al. (2026), Zenodo record 20075355, CC BY 4.0. The cereal-aphid data are from Li et al. (2023), Dryad 10.5061/dryad.mcvdnck4j, CC0 1.0. Two unused environmental traces derived from Open-Meteo/ERA5 and an Orsted et al. NicheMapR/NCEP workflow were reviewed for this release. The available records did not establish a complete redistribution chain for every underlying environmental-data provider, so neither trace is installed. They remain only in the build-excluded data-raw/licensing-pending/environmental-traces tree pending compatible primary terms or written permission. No installed vignette, example, or cache consumes them. The snow-gum PSII data are not CC BY 4.0. Arnold et al. (2026), doi:10.64898/2026.04.09.717599, release the source material under CC BY-NC 4.0. Written permission or compatible relicensing for unrestricted redistribution is pending. Therefore the snow-gum raw CSVs, derived snowgum_psii.rda, and its case-study source are retained only under the build-excluded data-raw/licensing-pending tree. Snow-gum rows were removed from the installed benchmark cache on 2026-07-11. Attribution does not remove the non-commercial restriction. The Kristineberg hourly station extract has no explicit redistribution licence in the source page reviewed for this release, and that page asks users to contact the station before publication use. It must be excluded from the CRAN source tarball unless the University of Gothenburg / Sven Loven Centre provides written redistribution permission and any required attribution terms. The extract and its provenance note are retained only under the build-excluded data-raw/licensing-pending tree. The remaining .rds files are outputs produced by freqTLS maintainers from package simulations or fits. They are covered by the freqTLS package licence except where a cache incorporates third-party data; the component ledger records those dependencies explicitly. freqTLS code remains GPL (>= 3); third-party data retain their stated licences. The cross-case-study cache `inst/extdata/case_study_summary_cache.rds` is built by `data-raw/build_case_study_summary_cache.R` from the shipped brown-shrimp, life-stage zebrafish, and Drosophila suzukii datasets. It stores freqTLS profile and documented bootstrap-fallback summaries plus version, configuration, and input-checksum metadata. The cache compilation is package-generated evidence; the three input datasets retain their CC BY 4.0 attribution and terms recorded in the component ledger.