{ "_id": "6ae32e1495ca2370cc8cdfbe", "Package": "hmde", "Title": "Hierarchical Methods for Differential Equations", "Version": "1.4.0", "Authors@R": "c(\nperson(given = \"Daniel\", family = \"Falster\", role = c(\"aut\", \"ctb\"), email = \"daniel.falster@unsw.edu.au\", comment = c(ORCID = \"0000-0002-9814-092X\")),\nperson(given = \"Tess\", family = \"O'Brien\", role = c(\"aut\", \"cre\", \"cph\"), email = \"tess_obrien@fastmail.com\", comment = c(ORCID = \"0009-0000-5821-8801\")),\nperson(given = \"Fonti\", family = \"Kar\", role = c(\"ctb\"), email = \"f.kar@unsw.edu.au\", comment = c(ORCID = \"0000-0002-2760-3974\")),\nperson(given = \"David\", family= \"Warton\", role = c(\"aut\", \"ctb\"), email = \"david.warton@unsw.edu.au\", comment = c(ORCID = \"0000-0002-1642-628X\"))\n)", "Description": "Wrapper for 'Stan' that offers a number of in-built models\nto implement a hierarchical Bayesian longitudinal model for\nrepeat observation data. Model choice selects the differential\nequation that is fit to the observations. Single and\nmulti-individual models are available. O'Brien et al. (2024)\n.", "License": "GPL (>= 3)", "Encoding": "UTF-8", "RoxygenNote": "7.3.3", "Biarch": "true", "SystemRequirements": "GNU make", "VignetteBuilder": "knitr", "Config/testthat/edition": "3", "LazyData": "true", "URL": "https://traitecoevo.github.io/hmde/", "BugReports": "https://github.com/traitecoevo/hmde/issues", "NeedsCompilation": "yes", "Packaged": { "Date": "2026-10-29 11:10:03 UTC", "User": "root" }, "Author": "Daniel Falster [aut, ctb] (ORCID:\n), Tess O'Brien [aut,\ncre, cph] (ORCID: ),\nFonti Kar [ctb] (ORCID:\n), David Warton [aut,\nctb] (ORCID: )", "Maintainer": "Tess O'Brien ", "Config/pak/sysreqs": "make", "Repository": "https://cran.r-universe.dev", "Date/Publication": "2026-05-04 07:29:26 UTC", "RemoteUrl": "https://github.com/cran/hmde", "RemoteRef": "HEAD", "RemoteSha": "f0cf93b448ce3ce8b9e2abb8d68015edb6453c82", "_user": "cran", "_type": "src", "_file": "hmde_1.4.0.tar.gz", "_fileid": "https://r2.ropensci.org/cf0c7a17861db2e2893cd9699d8f5a633cca5f8d6d91a3ad522877c097a9c7a9", "_filesize": 4983421, "_sha256": "cf0c7a17861db2e2893cd9699d8f5a633cca5f8d6d91a3ad522877c097a9c7a9", "_expires": "2027-02-06T11:29:22.000Z", "_created": "2026-10-29T11:10:03.000Z", "_published": "2026-10-29T11:29:24.836Z", "_upstream": "https://github.com/cran/hmde", "_status": "success", "_maintainer": { "name": "Tess OBrien", "email": "tess_obrien@fastmail.com", "login": "tess-lacoil", "description": "Applied mathematician with a focus on statistics to make the connection between a mathematical model and data.", "uuid": 36254282, "orcid": "0009-0000-5821-8801" }, "_jobs": [ { "job": 123414164861, "time": 461, "config": "linux-devel-arm64", "r": "4.7.0", "check": "OK", "artifact": "12893830298" }, { "job": 123414164979, "time": 451, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "12892848497" }, { "job": 123414164920, "time": 472, "config": "linux-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "12893586164" }, { "job": 123414164902, "time": 497, "config": "linux-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "12892584586" }, { "job": 123406564949, "time": 1026, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "12893420138" }, { "job": 123414164903, "time": 362, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "12892199320" }, { "job": 123414164939, "time": 535, "config": "windows-devel-arm64", "r": "4.7.0", "check": "OK", "artifact": "12893357144" }, { "job": 123414164913, "time": 779, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "12894165264" }, { "job": 123414165016, "time": 572, "config": "windows-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "12893312519" }, { "job": 123414164964, "time": 705, "config": "windows-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "12892804495" } ], "_buildurl": "https://github.com/r-universe/cran/actions/runs/40861722194", "_commit": { "id": "f0cf93b448ce3ce8b9e2abb8d68015edb6453c82", "author": "Tess O'\"'\"'Brien ", "committer": "cran-robot ", "message": "version 1.4.0\n", "time": 1777879766 }, "_distro": "resolute", "_host": "GitHub-Actions", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.1.0", "role": "Depends" }, { "package": "BH", "version": ">= 1.66.0", "role": "LinkingTo" }, { "package": "Rcpp", "version": ">= 0.12.19", "role": "LinkingTo" }, { "package": "RcppEigen", "version": ">= 0.3.3.3.0", "role": "LinkingTo" }, { "package": "RcppParallel", "version": ">= 5.0.1", "role": "LinkingTo" }, { "package": "rstan", "version": ">= 2.18.1", "role": "LinkingTo" }, { "package": "StanHeaders", "version": ">= 2.18.0", "role": "LinkingTo" }, { "package": "methods", "role": "Imports" }, { "package": "dplyr", "role": "Imports" }, { "package": "ggplot2", "role": "Imports" }, { "package": "Rcpp", "version": ">= 0.12.19", "role": "Imports" }, { "package": "RcppParallel", "version": ">= 5.0.1", "role": "Imports" }, { "package": "rlang", "role": "Imports" }, { "package": "rstan", "version": ">= 2.18.1", "role": "Imports" }, { "package": "rstantools", "version": ">= 2.3.1.1", "role": "Imports" }, { "package": "tibble", "role": "Imports" }, { "package": "cowplot", "role": "Imports" }, { "package": "knitr", "role": "Imports" }, { "package": "purrr", "version": ">= 1.2.0", "role": "Imports" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" }, { "package": "withr", "role": "Suggests" }, { "package": "mnormt", "role": "Suggests" }, { "package": "here", "role": "Suggests" }, { "package": "patchwork", "role": "Suggests" }, { "package": "deSolve", "role": "Suggests" }, { "package": "mixtools", "role": "Suggests" }, { "package": "MASS", "role": "Suggests" } ], "_owner": "cran", "_selfowned": false, "_usedby": 0, "_updates": [ { "week": "2025-48", "n": 1 }, { "week": "2025-52", "n": 1 }, { "week": "2026-19", "n": 1 } ], "_tags": [ { "name": "1.3", "date": "2025-11-27" }, { "name": "1.3.1", "date": "2025-12-23" }, { "name": "1.4.0", "date": "2026-05-04" } ], "_stars": 0, "_contributors": [ { "user": "tess-lacoil", "count": 5, "uuid": 36254282 } ], "_userbio": { "uuid": 6899542, "type": "organization", "name": "cran", "followers": 634, "description": "Unofficial read-only mirror of all CRAN R packages" }, "_downloads": { "count": 419, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/hmde" }, "_devurl": "https://github.com/traitecoevo/hmde", "_pkgdown": "https://traitecoevo.github.io/hmde/", "_searchresults": 0, "_topics": [ "onetbb", "cpp" ], "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/hmde.html", "extra/manual.pdf", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md" ], "_homeurl": "https://github.com/traitecoevo/hmde", "_realowner": "traitecoevo", "_cranurl": false, "_releases": [ { "version": "1.2.1", "date": "2025-07-04" }, { "version": "1.2.2", "date": "2025-10-03" }, { "version": "1.3", "date": "2025-11-27" }, { "version": "1.3.1", "date": "2025-12-23" }, { "version": "1.4.0", "date": "2026-05-04" } ], "_exports": [ "error_ests", "error_ests<-", "fit_summary", "fit_summary<-", "hmde_affine_de", "hmde_canham_de", "hmde_const_de", "hmde_data_template", "hmde_estimates", "hmde_extract_Rhat", "hmde_model", "hmde_model_des", "hmde_model_names", "hmde_model_pars", "hmde_plot_de_pieces", "hmde_plot_obs_est_inds", "hmde_plot_Rhat_hist", "hmde_run", "hmde_vb_de", "individual_ests", "individual_ests<-", "measurement_ests", "measurement_ests<-", "method", "method<-", "model_level", "model_level<-", "model_name", "model_name<-", "obs_data", "obs_data<-", "par_names", "par_names<-", "plot", "population_ests", "population_ests<-", "print", "prior_pars", "prior_pars<-", "runtime", "runtime<-", "show", "summary" ], "_datasets": [ { "name": "Lizard_Size_Data", "title": "Skink size data - Lampropholis delicata", "object": "Lizard_Size_Data", "class": [ "tbl_df", "tbl", "data.frame" ], "fields": [ "ind_id", "time", "y_obs", "obs_index" ], "rows": 328, "table": true, "tojson": true }, { "name": "Tree_Size_Data", "title": "Garcinia recondita - Barro Colorado Island data", "object": "Tree_Size_Data", "class": [ "tbl_df", "tbl", "data.frame" ], "fields": [ "ind_id", "time", "y_obs", "obs_index" ], "rows": 300, "table": true, "tojson": true }, { "name": "Tree_Size_Ests", "title": "Garcinia recondita model estimates - Barro Colorado Island data", "object": "Tree_Size_Ests", "class": [ "hmde_estimates" ], "fields": [], "table": false, "tojson": false }, { "name": "Trout_Size_Data", "title": "SUSTAIN Salmo trutta data", "object": "Trout_Size_Data", "class": [ "tbl_df", "tbl", "data.frame" ], "fields": [ "ind_id", "time", "y_obs", "obs_index" ], "rows": 135, "table": true, "tojson": true } ], "_help": [ { "page": "hmde-package", "title": "The 'hmde' package.", "topics": [ "hmde-package", "hmde" ] }, { "page": "error_ests-generic", "title": "generic error_ests getter", "topics": [ "error_ests", "error_ests<-" ] }, { "page": "fit_summary-generic", "title": "generic fit_summary getter", "topics": [ "fit_summary", "fit_summary<-" ] }, { "page": "hmde_affine_de", "title": "Differential equation for affine growth single individual model", "topics": [ "hmde_affine_de" ] }, { "page": "hmde_canham_de", "title": "Differential equation for Canham growth single and multi- individual models", "topics": [ "hmde_canham_de" ] }, { "page": "hmde_const_de", "title": "Differential equation for constant growth single and multi- individual models", "topics": [ "hmde_const_de" ] }, { "page": "hmde_extract_Rhat", "title": "Calculate Rhat statistics for a hmde_fit object", "topics": [ "hmde_extract_Rhat" ] }, { "page": "hmde_model", "title": "helper function for hmde_data_template that provides data structure for model, Also used to guide the user on the required structure for the model they want.", "topics": [ "hmde_model" ] }, { "page": "hmde_model_des", "title": "Function to select DE given model name", "topics": [ "hmde_model_des" ] }, { "page": "hmde_model_names", "title": "Returns names of available models.", "topics": [ "hmde_model_names" ] }, { "page": "hmde_model_pars", "title": "Show parameter list for hmde supported model", "topics": [ "hmde_model_pars" ] }, { "page": "hmde_plot_de_pieces", "title": "Plot pieces of chosen differential equation model for each individual. Structured to take the individual data tibble that is built by the hmde_estimates function using the ind_par_name_mean estimates. Function piece will go from the first fitted size to the last. Accepted ggplot arguments will change the axis labels, title, line colour, alpha", "topics": [ "hmde_plot_de_pieces" ] }, { "page": "hmde_plot_obs_est_inds", "title": "Plot estimated and observed values over time for a chosen number of individuals based on posterior estimates. Structured to take in the measurement_data tibble constructed by the hmde_extract_estimates function.", "topics": [ "hmde_plot_obs_est_inds" ] }, { "page": "hmde_plot_Rhat_hist", "title": "Plot histogram of R_hat values for hmde_fit object.", "topics": [ "hmde_plot_Rhat_hist" ] }, { "page": "hmde_run", "title": "Run chosen pre-built model in Stan", "topics": [ "hmde_run" ] }, { "page": "hmde_vb_de", "title": "Differential equation for von Bertalanffy growth single and multi- individual models", "topics": [ "hmde_vb_de" ] }, { "page": "individual_ests-generic", "title": "generic individual_ests getter", "topics": [ "individual_ests", "individual_ests<-" ] }, { "page": "Lizard_Size_Data", "title": "Skink size data - Lampropholis delicata", "topics": [ "Lizard_Size_Data" ] }, { "page": "measurement_ests-generic", "title": "generic measurement_ests getter", "topics": [ "measurement_ests", "measurement_ests<-" ] }, { "page": "method-generic", "title": "generic method getter", "topics": [ "method", "method<-" ] }, { "page": "model_level-generic", "title": "generic model_level setter", "topics": [ "model_level", "model_level<-", "obs_data", "obs_data<-" ] }, { "page": "model_name-generic", "title": "generic model_name getter", "topics": [ "model_name", "model_name<-" ] }, { "page": "par_names-generic", "title": "generic par_names getter", "topics": [ "par_names", "par_names<-" ] }, { "page": "population_ests-generic", "title": "generic population_ests setter", "topics": [ "population_ests", "population_ests<-" ] }, { "page": "prior_pars-generic", "title": "generic prior_pars getter", "topics": [ "prior_pars", "prior_pars<-" ] }, { "page": "runtime-generic", "title": "generic runtime getter", "topics": [ "runtime", "runtime<-" ] }, { "page": "Tree_Size_Data", "title": "Garcinia recondita - Barro Colorado Island data", "topics": [ "Tree_Size_Data" ] }, { "page": "Tree_Size_Ests", "title": "Garcinia recondita model estimates - Barro Colorado Island data", "topics": [ "Tree_Size_Ests" ] }, { "page": "Trout_Size_Data", "title": "SUSTAIN Salmo trutta data", "topics": [ "Trout_Size_Data" ] } ], "_readme": "https://github.com/cran/hmde/raw/HEAD/README.md", "_rundeps": [ "abind", "backports", "BH", "callr", "checkmate", "cli", "cowplot", "cpp11", "desc", "distributional", "dplyr", "evaluate", "farver", "generics", "ggplot2", "glue", "gridExtra", "gtable", "highr", "inline", "isoband", "knitr", "labeling", "lifecycle", "loo", "magrittr", "matrixStats", "numDeriv", "otel", "pillar", "pkgbuild", "pkgconfig", "posterior", "processx", "ps", "purrr", "QuickJSR", "R6", "RColorBrewer", "Rcpp", "RcppEigen", "RcppParallel", "rlang", "rstan", "rstantools", "S7", "scales", "StanHeaders", "tensorA", "tibble", "tidyselect", "utf8", "vctrs", "viridisLite", "withr", "xfun", "yaml" ], "_sysdeps": [ { "shlib": "libtbb", "package": "libtbb12", "headers": "libtbb-dev", "source": "onetbb", "version": "2022.3.0-2", "name": "onetbb", "homepage": "https://uxlfoundation.github.io/oneTBB/", "description": "parallelism library for C++ - runtime files" }, { "shlib": "libstdc++", "package": "libstdc++6", "source": "gcc", "version": "16-20260322-1ubuntu1", "name": "c++", "homepage": "http://gcc.gnu.org/", "description": "GNU Standard C++ Library v3" } ], "_vignettes": [ { "source": "canham.Rmd", "filename": "canham.html", "title": "Case study 3: Canham function growth with tree data from Barro Colorado Island", "engine": "knitr::rmarkdown", "headings": [ "References" ], "created": "2025-07-04 19:20:06", "modified": "2026-05-04 07:29:26", "commits": 2 }, { "source": "constant-growth.Rmd", "filename": "constant-growth.html", "title": "Case study 1: Constant growth with SUSTAIN Trout data", "engine": "knitr::rmarkdown", "headings": [ "Overview", "Load dependencies", "Priors", "Simulate data", "Visualise data", "SUSTAIN trout data", "Transform data", "Visualise raw data", "Fit model using", "Inspect estimates", "$R^2$", "Individual growth functions ($\\beta$)", "Population hyper-parameters", "References" ], "created": "2025-07-04 19:20:06", "modified": "2026-05-04 07:29:26", "commits": 3 }, { "source": "here_be_dragons.Rmd", "filename": "here_be_dragons.html", "title": "Here be dragons", "engine": "knitr::rmarkdown", "headings": [ "Load dependencies", "The model", "Simulating data", "Implementing models and collecting posterior estimates", "Step size data", "Analysis", "Second cluster analysis", "Where to from here?" ], "created": "2025-07-04 19:20:06", "modified": "2026-05-04 07:29:26", "commits": 2 }, { "source": "hmde.Rmd", "filename": "hmde.html", "title": "hmde", "engine": "knitr::rmarkdown", "headings": [ "Installation", "Overview", "Notation", "hmde supported growth functions", "Workflow", "References" ], "created": "2025-07-04 19:20:06", "modified": "2025-07-04 19:20:06", "commits": 1 }, { "source": "hmde_for_mathematicians.Rmd", "filename": "hmde_for_mathematicians.html", "title": "hmde for Mathematicians", "engine": "knitr::rmarkdown", "headings": [ "Getting started with", "The Theory", "The Maths", "The Stats", "Integration of time series", "Demonstration: Canham Growth - Multiple Individuals" ], "created": "2025-07-04 19:20:06", "modified": "2026-05-04 07:29:26", "commits": 2 }, { "source": "von-bertalanffy.Rmd", "filename": "von-bertalanffy.html", "title": "Case study 2: von Bertalanffy growth with lizard size data", "engine": "knitr::rmarkdown", "headings": [ "Load dependencies", "Overview", "Priors", "Visualise model", "Lizard size data", "Implementation", "References" ], "created": "2025-07-04 19:20:06", "modified": "2026-05-04 07:29:26", "commits": 2 } ], "_score": 3.954242509439325, "_indexed": false, "_nocasepkg": "hmde", "_universes": [ "cran" ], "_indexurl": "https://traitecoevo.r-universe.dev/hmde", "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.4.0", "date": "2026-10-29T11:17:56.000Z", "distro": "resolute", "arch": "aarch64", "commit": "f0cf93b448ce3ce8b9e2abb8d68015edb6453c82", "fileid": "https://r2.ropensci.org/df3c678eb74f03382715bd68d7ad0ae03c7ec28ab1f4599f4dc96aa6d23ffda3", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cran/actions/runs/40861722194" }, { "r": "4.7.0", "os": "linux", "version": "1.4.0", "date": "2026-10-29T11:18:04.000Z", "distro": "resolute", "arch": "x86_64", "commit": "f0cf93b448ce3ce8b9e2abb8d68015edb6453c82", "fileid": "https://r2.ropensci.org/ad6d34d64fa6b3e2afbec276c0430f29c0137323ef86152d01438722e23837dd", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cran/actions/runs/40861722194" }, { "r": "4.6.1", "os": "linux", "version": "1.4.0", "date": "2026-10-29T11:17:57.000Z", "distro": "resolute", "arch": "aarch64", "commit": "f0cf93b448ce3ce8b9e2abb8d68015edb6453c82", "fileid": "https://r2.ropensci.org/0db2375332be10d5446291d245dadbd8c118148a618285c48d82b4c5babae0fd", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cran/actions/runs/40861722194" }, { "r": "4.6.1", "os": "linux", "version": "1.4.0", "date": "2026-10-29T11:18:44.000Z", "distro": "resolute", "arch": "x86_64", "commit": "f0cf93b448ce3ce8b9e2abb8d68015edb6453c82", "fileid": "https://r2.ropensci.org/96812a5b337587f4c1dc4489af6bf12b166faa886685f8d68baea8195ee8bc2e", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cran/actions/runs/40861722194" }, { "r": "4.6.0", "os": "wasm", "version": "1.4.0", "date": "2026-10-29T11:18:21.000Z", "arch": "emscripten", "commit": "f0cf93b448ce3ce8b9e2abb8d68015edb6453c82", "fileid": "https://r2.ropensci.org/701c23f3be73047208fb5f2d71bdb56f9273b58586298845750e3b533f111199", "status": "success", "buildurl": "https://github.com/r-universe/cran/actions/runs/40861722194" }, { "r": "4.7.0", "os": "win", "version": "1.4.0", "date": "2026-10-29T11:19:09.000Z", "arch": "aarch64", "commit": "f0cf93b448ce3ce8b9e2abb8d68015edb6453c82", "fileid": "https://r2.ropensci.org/3ae5b7d48090fcbcfcae3675bfa72ea373ece734beb4ee6b48f1ea82fa53f6a5", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cran/actions/runs/40861722194" }, { "r": "4.7.0", "os": "win", "version": "1.4.0", "date": "2026-10-29T11:17:34.000Z", "arch": "x86_64", "commit": "f0cf93b448ce3ce8b9e2abb8d68015edb6453c82", "fileid": "https://r2.ropensci.org/63a59956d18d8d91896fefb07b811b309aa65bfc10ff9235ad4b03008af32275", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cran/actions/runs/40861722194" }, { "r": "4.6.1", "os": "win", "version": "1.4.0", "date": "2026-10-29T11:19:29.000Z", "arch": "aarch64", "commit": "f0cf93b448ce3ce8b9e2abb8d68015edb6453c82", "fileid": "https://r2.ropensci.org/26f7009c3a3211498d60cec59b54b4c4a10cdebe3f7e12a8877e251d080be1db", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cran/actions/runs/40861722194" }, { "r": "4.6.1", "os": "win", "version": "1.4.0", "date": "2026-10-29T11:17:14.000Z", "arch": "x86_64", "commit": "f0cf93b448ce3ce8b9e2abb8d68015edb6453c82", "fileid": "https://r2.ropensci.org/a0da1c102d58da65a3512f7605fbc3d5253b00ef5682f96efd2464855a896267", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cran/actions/runs/40861722194" } ] }