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Tremblay", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "What is effective population size and why does it matter?", "Why stage-structured models?", "The three NeStage functions", "MatU and MatF: the standard input format", "The study system: Lepanthes orchids in Puerto Rico", "The six-stage life cycle of L. rupestris", "Setting up the matrices", "L. rupestris population 1 — monthly matrices", "Stage frequency vector D", "Monthly vs annual matrices: does the time step matter?", "Converting monthly to annual matrices", "Comparing Ne/N from monthly vs annual matrices", "Interpreting the difference", "Running Ne_sexual_Y2000: a complete worked example", "All inputs explained", "Full output for L. rupestris population 1", "Reading the output", "All populations of all three species", "Entering all matrices", "Computing Ne/N for all 17 populations", "Comparing to Orive (1993) estimates", "Summary and conservation implications", "Key conservation messages", "Brief overview of the other two functions", "Ne_clonal_Y2000", "Ne_mixed_Y2000", "Session information", "References" ], "created": "2026-03-06 13:46:24", "modified": "2026-03-07 01:37:40", "commits": 2 }, { "source": "NeStage_quickstart.Rmd", "filename": "NeStage_quickstart.html", "title": "NeStage: Quick Start Guide", "author": "Raymond L. Tremblay", "engine": "knitr::rmarkdown", "headings": [ "Overview", "What data do you need?", "T_mat — Survival/transition matrix", "F_vec — Fecundity vector", "D — Stage frequency distribution", "L — Generation time (optional but recommended)", "Quick data checklist", "Ne_clonal_Y2000() — Purely clonal populations", "Key outputs", "Ne_sexual_Y2000() — Purely sexual populations", "Optional: adjust reproductive variance Vk_over_k", "Ne_mixed_Y2000() — Mixed sexual + clonal populations", "The d vector — most common source of confusion", "Which function should I use?", "Interpreting the results", "Next steps", "References" ], "created": "2026-03-06 23:58:09", "modified": "2026-03-12 18:09:50", "commits": 2 }, { "source": "Ne_Yonezawa2000.Rmd", "filename": "Ne_Yonezawa2000.html", "title": "Replicating Yonezawa et al. (2000) with NeStage", "author": "Raymond L. Tremblay", "engine": "knitr::rmarkdown", "headings": [ "Introduction: What the Yonezawa (2000) model does", "Purpose and scope", "What the model does", "Biological system", "Notation and key formulas", "Variables (for $s$ stages)", "The one-year variance of allele-frequency change (Eq. 5)", "General generation-time effective size $N_e$ (Eq. 6)", "Clonal-dominant Poisson special case (Eq. 10)", "Annual effective size $N_y$ (Eq. 11)", "Glossary of R objects", "Step 1 — Load packages and define pedagogical helpers", "Step 2 — Enter Table 2 data (Miz and Nan populations)", "Step 3 — Compute $\\lambda$, stable stage distribution, and generation time $L$", "Step 4 — Manual computation of Table 4 quantities", "Observed stage fractions", "Expected (equilibrium) stage fractions", "Step 5 — Replication check: computed vs. paper Table 4", "Step 6 — NeStage package: Ne_clonal_Y2000()", "Inputs explained", "Running Ne_clonal_Y2000() for both populations", "Print output for Miz (observed D)", "Comparing Ne_clonal_Y2000() output to paper Table 4", "Step 7 — General model: Ne_mixed_Y2000()", "Internal consistency: general model must match clonal shortcut", "Sensitivity to the clonal fraction $d_i$", "Final summary: full replication of Table 4", "Session information" ], "created": "2026-03-05 22:19:54", "modified": "2026-03-12 18:09:50", "commits": 5 }, { "source": "NeStage_sensitivity.Rmd", "filename": "NeStage_sensitivity.html", "title": "Sensitivity Analysis for Conservation Decision-Making", "author": "Raymond L. Tremblay", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "From a ratio to a decision", "The four sensitivity functions", "Elasticity: a standardised sensitivity measure", "Study populations", "Sensitivity to sexual reproductive variance: Ne_sensitivity_Vk()", "What is Vk/k̄ and why does it matter?", "Running Ne_sensitivity_Vk() for the reproductive stage", "Interpretation", "Sensitivity to generation time: Ne_sensitivity_L()", "Why L matters so much", "Sweeping L across a biologically plausible range", "Key insight: Ne/N is hyperbolic in L", "Sensitivity to clonal fraction: Ne_sensitivity_d()", "When does clonal fraction matter?", "Cross-parameter comparison: which lever matters most?", "Conservation prioritisation framework", "Priority 1 — Reduce uncertainty in L", "Priority 2 — Equalise reproductive output in high-fecundity stages", "Priority 3 — Augment census size in the lowest-Ne/N populations", "Session information", "References" ], "created": "2026-03-06 13:46:24", "modified": "2026-03-12 18:09:50", "commits": 3 } ], "_score": 4.924279286061882, "_indexed": true, "_nocasepkg": "nestage", "_universes": [ "raymondltremblay" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "0.8.0", "date": "2026-05-23T05:19:59.000Z", "distro": "noble", "commit": "84c25874014a91caa1cf0b430828dfa8464e4e9b", "fileid": "38dfea59c1bab8dde518164a6baa0f622a4a18a7d218782207b5aec1793dda34", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/raymondltremblay/actions/runs/26324345505" }, { "r": "4.6.0", "os": "linux", "version": "0.8.0", "date": "2026-05-23T05:20:01.000Z", "distro": "noble", "commit": "84c25874014a91caa1cf0b430828dfa8464e4e9b", "fileid": "56702681cbd81ccac0dc5092310aa423b816065b5411c64818705f3905bc5113", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/raymondltremblay/actions/runs/26324345505" }, { "r": "4.5.3", "os": "mac", "version": "0.8.0", "date": "2026-05-23T05:20:10.000Z", "commit": "84c25874014a91caa1cf0b430828dfa8464e4e9b", "fileid": "9d96ebe8f88efd536d940016a8677041ce6124320fc3a5d3c869d17d46ff1c95", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/raymondltremblay/actions/runs/26324345505" }, { "r": "4.6.0", "os": "mac", "version": "0.8.0", "date": "2026-05-23T05:20:14.000Z", "commit": "84c25874014a91caa1cf0b430828dfa8464e4e9b", "fileid": "c5edd348442568ddd76fdac72ebdf238b459ed067994fe4e740ab62e3e682eb8", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/raymondltremblay/actions/runs/26324345505" }, { "r": "4.6.0", "os": "wasm", "version": "0.8.0", "date": "2026-05-23T05:20:08.000Z", "commit": "84c25874014a91caa1cf0b430828dfa8464e4e9b", "fileid": "1b773b5e343d4438b1b518edb46c2fd6221d9c77c5b62d7739b821b145f19843", "status": "success", "buildurl": "https://github.com/r-universe/raymondltremblay/actions/runs/26324345505" }, { "r": "4.7.0", "os": "win", "version": "0.8.0", "date": "2026-05-23T05:19:18.000Z", "commit": "84c25874014a91caa1cf0b430828dfa8464e4e9b", "fileid": "1746bf2f4a7c587fdecb55b820f6033ef43ee7ef7cbfb8137d647c455df525e3", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/raymondltremblay/actions/runs/26324345505" }, { "r": "4.5.3", "os": "win", "version": "0.8.0", "date": "2026-05-23T05:19:19.000Z", "commit": "84c25874014a91caa1cf0b430828dfa8464e4e9b", "fileid": "46d3d750ad05c188f68631d9e0038ec26b257de829c5bc4eb60c112ff820a872", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/raymondltremblay/actions/runs/26324345505" }, { "r": "4.6.0", "os": "win", "version": "0.8.0", "date": "2026-05-23T05:19:15.000Z", "commit": "84c25874014a91caa1cf0b430828dfa8464e4e9b", "fileid": "e795e20eac9ea4fcd0b3c6159f515e67144856edd1d5f1bb3da39d0fe638de02", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/raymondltremblay/actions/runs/26324345505" } ] }