{ "_id": "6ac6c415ca1b382b34ef427e", "Package": "NeStage", "Type": "Package", "Title": "Effective Population Size from Stage-Structured Populations", "Version": "0.8.1.9000", "Date": "2026-10-07", "Authors@R": "person(\"Raymond L.\", \"Tremblay\",\nemail = \"raymond.tremblay@gmail.com\",\nrole = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0002-8588-4372\"))", "Author": "Raymond L. Tremblay [aut, cre]\n()", "Maintainer": "Raymond L. Tremblay ", "Description": "Computes effective population size (Ne) and the Ne/N ratio\nfor stage-structured populations using the matrix population\nmodel framework of Yonezawa (2000)\n. Functions are\nprovided for sexually reproducing, clonally reproducing, and\nmixed (sexual + clonal) populations. Includes sensitivity and\nelasticity analyses for Ne/N with respect to vital rates.", "License": "GPL-3", "Encoding": "UTF-8", "Language": "en-US", "Roxygen": "list(markdown = TRUE)", "VignetteBuilder": "knitr", "URL": "https://github.com/RaymondLTremblay/NeStage", "BugReports": "https://github.com/RaymondLTremblay/NeStage/issues", "Config/roxygen2/version": "8.1.0", "Repository": "https://raymondltremblay.r-universe.dev", "Date/Publication": "2026-10-07 20:21:13 UTC", "RemoteUrl": "https://github.com/raymondltremblay/nestage", "RemoteRef": "HEAD", "RemoteSha": "5cb6dfc15643fa86622a567aee21d67b2208467d", "NeedsCompilation": "no", "Packaged": { "Date": "2026-10-07 22:10:57 UTC", "User": "root" }, "_user": "raymondltremblay", "_type": "src", "_file": "NeStage_0.8.1.9000.tar.gz", "_fileid": "https://r2.ropensci.org/515b46c42489bad7d92e7b2cf15ce5b582c8a84a73e5b58d6fb7ce5eb6f728e8", "_filesize": 1142086, "_sha256": "515b46c42489bad7d92e7b2cf15ce5b582c8a84a73e5b58d6fb7ce5eb6f728e8", "_expires": "2027-01-15T22:13:38.000Z", "_created": "2026-10-07T22:10:57.000Z", "_published": "2026-10-07T22:13:41.286Z", "_buildurl": "https://github.com/r-universe/raymondltremblay/actions/runs/37694065290", "_status": "success", "_host": "GitHub-Actions", "_jobs": [ { "job": 113042823737, "time": 125, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "11514389305" }, { "job": 113042823545, "time": 112, "config": "linux-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "11514433623" }, { "job": 113042823648, "time": 123, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "11514671944" }, { "job": 113042823561, "time": 123, "config": "macos-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "11515280870" }, { "job": 113041265325, "time": 234, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "11515245673" }, { "job": 113042823490, "time": 104, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "11515495165" }, { "job": 113042823780, "time": 79, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "11514159428" }, { "job": 113042823806, "time": 62, "config": "windows-oldrel-x86_64", "r": "4.5.3", "check": "OK", "artifact": "11514278965" }, { "job": 113042823579, "time": 69, "config": "windows-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "11515021302" } ], "_upstream": "https://github.com/raymondltremblay/nestage", "_commit": { "id": "5cb6dfc15643fa86622a567aee21d67b2208467d", "author": "Raymond L. Tremblay ", "committer": "Raymond L. Tremblay ", "message": "selecte CRAN submission\n", "time": 1791404473 }, "_maintainer": { "name": "Raymond L. Tremblay", "email": "raymond.tremblay@gmail.com", "orcid": "0000-0002-8588-4372" }, "_distro": "resolute", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.1.0", "role": "Depends" }, { "package": "ggplot2", "role": "Imports" }, { "package": "dplyr", "role": "Suggests" }, { "package": "tidyr", "role": "Suggests" }, { "package": "purrr", "role": "Suggests" }, { "package": "expm", "role": "Suggests" }, { "package": "gt", "version": ">= 0.9.0", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "popbio", "role": "Suggests" }, { "package": "popdemo", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" } ], "_owner": "raymondltremblay", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2026-10", "n": 30 }, { "week": "2026-11", "n": 2 }, { "week": "2026-13", "n": 1 }, { "week": "2026-41", "n": 3 } ], "_tags": [ { "name": "v0.7.0", "date": "2026-03-06" }, { "name": "v0.8.0", "date": "2026-03-07" }, { "name": "v0.8.1", "date": "2026-10-07" } ], "_topics": [ "conservation-biology", "demographic-matrix", "effective-population-size", "evolution", "fritillaria", "genetic-drift", "population-ecology", "population-genetics", "stage-structured" ], "_stars": 0, "_contributors": [ { "user": "raymondltremblay", "count": 36, "uuid": 29467955 } ], "_userbio": { "uuid": 29467955, "type": "user", "name": "Raymond L. Tremblay", "followers": 3 }, "_downloads": { "count": 312, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/NeStage" }, "_devurl": "https://github.com/raymondltremblay/nestage", "_searchresults": 38, "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/manual.pdf", "extra/NeStage.html", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md" ], "_homeurl": "https://github.com/raymondltremblay/nestage", "_realowner": "raymondltremblay", "_cranurl": true, "_releases": [ { "version": "0.8.0", "date": "2026-03-17" } ], "_exports": [ "Ne_clonal_Y2000", "Ne_clonal_Y2000_both", "Ne_mixed_Y2000", "Ne_mixed_Y2000_both", "Ne_sensitivity_d", "Ne_sensitivity_L", "Ne_sensitivity_Vc", "Ne_sensitivity_Vk", "Ne_sexual_Y2000" ], "_help": [ { "page": "Ne_clonal_Y2000", "title": "Variance effective population size for 100% clonal stage-structured populations", "topics": [ "Ne_clonal_Y2000" ] }, { "page": "Ne_clonal_Y2000_both", "title": "Run Ne_clonal_Y2000 with both observed and expected stage fractions", "topics": [ "Ne_clonal_Y2000_both" ] }, { "page": "Ne_mixed_Y2000", "title": "Variance effective population size for mixed sexual/clonal stage-structured populations", "topics": [ "Ne_mixed_Y2000" ] }, { "page": "Ne_mixed_Y2000_both", "title": "Run Ne_mixed_Y2000 with both observed and expected stage fractions", "topics": [ "Ne_mixed_Y2000_both" ] }, { "page": "Ne_sensitivity_d", "title": "Sensitivity of Ne/N to clonal fraction d_i in one stage", "topics": [ "Ne_sensitivity_d" ] }, { "page": "Ne_sensitivity_L", "title": "Sensitivity of Ne/N to generation time L", "topics": [ "Ne_sensitivity_L" ] }, { "page": "Ne_sensitivity_Vc", "title": "Sensitivity of Ne/N to clonal reproductive variance in one stage", "topics": [ "Ne_sensitivity_Vc" ] }, { "page": "Ne_sensitivity_Vk", "title": "Sensitivity of Ne/N to sexual reproductive variance in one stage", "topics": [ "Ne_sensitivity_Vk" ] }, { "page": "Ne_sexual_Y2000", "title": "Variance effective population size for 100% sexual stage-structured populations", "topics": [ "Ne_sexual_Y2000" ] } ], "_readme": "https://github.com/raymondltremblay/nestage/raw/HEAD/README.md", "_rundeps": [ "cli", "cpp11", "farver", "ggplot2", "glue", "gtable", "isoband", "labeling", "lifecycle", "R6", "RColorBrewer", "rlang", "S7", "scales", "vctrs", "viridisLite", "withr" ], "_vignettes": [ { "source": "NeStage_functions.Rmd", "filename": "NeStage_functions.html", "title": "NeStage Functions: A User Guide", "author": "Raymond L. 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": "2026-10-07 15:59:04", "commits": 6 }, { "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": 5.482873583608754, "_indexed": true, "_nocasepkg": "nestage", "_universes": [ "raymondltremblay" ], "_previous": "0.8.0", "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "0.8.1.9000", "date": "2026-10-07T22:13:02.000Z", "distro": "resolute", "commit": "5cb6dfc15643fa86622a567aee21d67b2208467d", "fileid": "https://r2.ropensci.org/7b86c88eb029b46b71369564416d9890b1e8cb320daa9be3d53272d52265a6ed", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/raymondltremblay/actions/runs/37694065290" }, { "r": "4.6.1", "os": "linux", "version": "0.8.1.9000", "date": "2026-10-07T22:12:55.000Z", "distro": "resolute", "commit": "5cb6dfc15643fa86622a567aee21d67b2208467d", "fileid": "https://r2.ropensci.org/2ad9ce35361be3d6c38ae8339e63c54ff8352ccd110409052b4eb2a38b8a31cb", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/raymondltremblay/actions/runs/37694065290" }, { "r": "4.5.3", "os": "mac", "version": "0.8.1.9000", "date": "2026-10-07T22:13:05.000Z", "commit": "5cb6dfc15643fa86622a567aee21d67b2208467d", "fileid": "https://r2.ropensci.org/07de51448b337b1c1dfb0bef91c57f974f9818f1e482a887b59bfe97649866aa", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/raymondltremblay/actions/runs/37694065290" }, { "r": "4.6.1", "os": "mac", "version": "0.8.1.9000", "date": "2026-10-07T22:13:04.000Z", "commit": "5cb6dfc15643fa86622a567aee21d67b2208467d", "fileid": "https://r2.ropensci.org/e1bcb6a746960f02692c0ec86b92b60f80d9578e9fe2682cf6dae695214cfa90", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/raymondltremblay/actions/runs/37694065290" }, { "r": "4.6.0", "os": "wasm", "version": "0.8.1.9000", "date": "2026-10-07T22:12:57.000Z", "commit": "5cb6dfc15643fa86622a567aee21d67b2208467d", "fileid": "https://r2.ropensci.org/2c2405577928cbce284782d7bff3d45989b2cd657fe52feb7cc71244a72072be", "status": "success", "buildurl": "https://github.com/r-universe/raymondltremblay/actions/runs/37694065290" }, { "r": "4.7.0", "os": "win", "version": "0.8.1.9000", "date": "2026-10-07T22:12:11.000Z", "commit": "5cb6dfc15643fa86622a567aee21d67b2208467d", "fileid": "https://r2.ropensci.org/05e4ad089036a72a84f70d436badf2119e044c07ccf6c485a66d8e26903e88ed", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/raymondltremblay/actions/runs/37694065290" }, { "r": "4.5.3", "os": "win", "version": "0.8.1.9000", "date": "2026-10-07T22:12:00.000Z", "commit": "5cb6dfc15643fa86622a567aee21d67b2208467d", "fileid": "https://r2.ropensci.org/399af1f15144df138c4a765651819ecde128229a8b337758c9537327bda8cd72", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/raymondltremblay/actions/runs/37694065290" }, { "r": "4.6.1", "os": "win", "version": "0.8.1.9000", "date": "2026-10-07T22:12:06.000Z", "commit": "5cb6dfc15643fa86622a567aee21d67b2208467d", "fileid": "https://r2.ropensci.org/e18e3f168051d0fea05bc60cc5d3bd06052ae16711d9c0a4643e13ad6fed6fc8", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/raymondltremblay/actions/runs/37694065290" } ] }