{ "_id": "6a1ff06eb401979e734420c8", "Package": "drcSeedGerm", "Date": "2023-04-20", "Type": "Package", "Title": "Utilities for Data Analyses in Seed Germination/Emergence Assays", "Version": "1.1.1", "Author": "Andrea Onofri ", "Maintainer": "Andrea Onofri ", "Description": "Utility functions to be used to analyse datasets obtained\nfrom seed germination/emergence assays. Fits several types of\nseed germination/emergence models, including those reported in\nOnofri et al. (2018) \"Hydrothermal-time-to-event models for\nseed germination\", European Journal of Agronomy, 101, 129-139\n. Contains several datasets for\npracticing.", "URL": "https://www.statforbiology.com", "License": "GPL (>= 2)", "Encoding": "UTF-8", "LazyData": "true", "RoxygenNote": "7.2.0", "Config/pak/sysreqs": "cmake make libicu-dev", "Repository": "https://onofriandreapg.r-universe.dev", "Date/Publication": "2025-01-10 14:09:30 UTC", "RemoteUrl": "https://github.com/onofriandreapg/drcseedgerm", "RemoteRef": "HEAD", "RemoteSha": "d68b6e2e8b3b6ed20597f1d86d08c703db54630d", "NeedsCompilation": "no", "Packaged": { "Date": "2026-06-03 09:10:27 UTC", "User": "root" }, "MD5sum": "259c1003b22daf974e034acbecc3aac8", "_user": "onofriandreapg", "_type": "src", "_file": "drcSeedGerm_1.1.1.tar.gz", "_fileid": "b647cb4db04dc4a194d02825dc425dcefd453cba9d67a89315682525de6313a2", "_filesize": 378469, "_sha256": "b647cb4db04dc4a194d02825dc425dcefd453cba9d67a89315682525de6313a2", "_created": "2026-06-03T09:10:27.000Z", "_published": "2026-06-03T09:14:22.267Z", "_distro": "noble", "_jobs": [ { "job": 79260154617, "time": 186, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7380417765" }, { "job": 79260154600, "time": 172, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7380411734" }, { "job": 79260154580, "time": 115, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7380391416" }, { "job": 79260154583, "time": 160, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7380408180" }, { "job": 79259604398, "time": 190, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7380347225" }, { "job": 79260154521, "time": 127, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7380395964" }, { "job": 79260154664, "time": 136, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7380400068" }, { "job": 79260154615, "time": 126, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7380395747" }, { "job": 79260154629, "time": 123, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7380394828" } ], "_buildurl": "https://github.com/r-universe/onofriandreapg/actions/runs/26874926646", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/onofriandreapg/drcseedgerm", "_commit": { "id": "d68b6e2e8b3b6ed20597f1d86d08c703db54630d", "author": "Andrea ", "committer": "Andrea ", "message": "Minor edits\n", "time": 1736518170 }, "_maintainer": { "name": "Andrea Onofri", "email": "andrea.onofri@unipg.it", "login": "onofriandreapg", "description": "", "uuid": 36607650 }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.5.0", "role": "Depends" }, { "package": "drc", "role": "Depends" }, { "package": "drcte", "role": "Depends" }, { "package": "plyr", "role": "Imports" }, { "package": "dplyr", "role": "Imports" }, { "package": "mvtnorm", "role": "Imports" }, { "package": "survival", "role": "Imports" } ], "_owner": "onofriandreapg", "_selfowned": true, "_usedby": 0, "_updates": [], "_tags": [], "_topics": [ "nonlinear-regression", "seed-germination-assays", "time-to-event" ], "_stars": 5, "_contributors": [ { "user": "onofriandreapg", "count": 55, "uuid": 36607650 } ], "_userbio": { "uuid": 36607650, "type": "user", "name": "Andrea Onofri" }, "_downloads": { "count": 166, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/drcSeedGerm" }, "_devurl": "https://github.com/onofriandreapg/drcseedgerm", "_searchresults": 42, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/drcSeedGerm.html", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_homeurl": "https://github.com/onofriandreapg/drcseedgerm", "_realowner": "onofriandreapg", "_cranurl": true, "_releases": [ { "version": "1.0.1", "date": "2023-05-16" } ], "_exports": [ "GRPsi.Lin", "GRPsi.Pol", "GRPsi.Pol2", "GRPsiLin", "GRPsiLin.fun", "GRPsiPol", "GRPsiPol.fun", "GRPsiPol2", "GRPsiPol2.fun", "GRT.BS", "GRT.BS.fun", "GRT.BSb", "GRT.BSb.fun", "GRT.Ex", "GRT.Ex.fun", "GRT.Exb", "GRT.Exb.fun", "GRT.GH", "GRT.GH.fun", "GRT.GH2", "GRT.GH2.fun", "GRT.M", "GRT.M.fun", "GRT.Mb", "GRT.Mb.fun", "GRT.RF", "GRT.RF.fun", "GRT.RFb", "GRT.RFb.fun", "GRT.YL", "GRT.YL.fun", "GRTPsi.BS", "GRTPsi.BS.fun", "GRTPsi.M", "GRTPsi.M.fun", "HaloTL", "HaloTL.fun", "HaloTLL", "HaloTLL.fun", "HaloTnorm", "HaloTnorm.fun", "HTE1", "HTE1.fun", "HTE2", "HTE2.fun", "HTE3", "HTE3.fun", "HTex", "HTex.fun", "HTG", "HTG.fun", "HTL", "HTL.fun", "HTLL", "HTLL.fun", "HTnorm", "HTnorm.fun", "HTTEM", "HTTEM.fun", "HTTLL.BS", "HTTLL.BS.fun", "HTTLL.M", "HTTLL.M.fun", "HTTnorm.BS", "HTTnorm.BS.fun", "HTTnorm.M", "HTTnorm.M.fun", "HTW1", "HTW1.fun", "HTW2", "HTW2.fun", "jackGroupSE", "makeDrm", "makeDrm2", "PmaxPsi1", "PmaxPsi1.fun", "PmaxT1", "PmaxT1.fun", "TTEM", "TTEM.fun", "TTERF", "TTERF.fun", "TTERFc", "TTERFc.fun" ], "_datasets": [ { "name": "alfalfaSG", "title": "Field-book for a germination assay with alfalfa", "object": "alfalfaSG", "class": [ "data.frame" ], "fields": [ "Dish", "Temp", "nViable", "1", "2", "3", "4", "5", "6", "7", "8", "9", "10", "11", "12", "13", "14", "15", "16", "17", "18", "19", "20", "21", "22", "23", "24", "27", "28", "29", "31", "34" ], "rows": 21, "table": true, "tojson": true }, { "name": "barley", "title": "A series of germination assays with barley", "object": "barley", "class": [ "data.frame" ], "fields": [ "Dish", "Temp", "timeBef", "timeAf", "nSeeds", "nCum", "propCum" ], "rows": 810, "table": true, "tojson": true }, { "name": "excalibur", "title": "Relationship between germination rate and water potential in oilseed rape (var. Excalibur)", "object": "excalibur", "class": [ "data.frame" ], "fields": [ "Perc", "Psi", "Tg", "SE", "GR" ], "rows": 27, "table": true, "tojson": true }, { "name": "festuca", "title": "Relationship between germination rate and water potential in Festuca arundinacea L.", "object": "festuca", "class": [ "data.frame" ], "fields": [ "g", "Psi", "GR" ], "rows": 36, "table": true, "tojson": true }, { "name": "hordeum", "title": "Germination of Hordeum spontaneum at different temperatures and water potentials", "object": "hordeum", "class": [ "data.frame" ], "fields": [ "temp", "water", "Dish", "timeBef", "timeAf", "nViable", "nSeeds", "nCum" ], "rows": 3024, "table": true, "tojson": true }, { "name": "phalaris", "title": "A series of germination assays with Phalaris minor", "object": "phalaris", "class": [ "data.frame" ], "fields": [ "temp", "water", "Dish", "timeBef", "timeAf", "nViable", "nSeeds", "nCum", "propCum" ], "rows": 3024, "table": true, "tojson": true }, { "name": "rape", "title": "Germination data from an assay of rapeseed at decreasing water potential levels", "object": "rape", "class": [ "data.frame" ], "fields": [ "Psi", "Dish", "timeBef", "timeAf", "nSeeds", "nCum", "propCum" ], "rows": 294, "table": true, "tojson": true }, { "name": "rape2G", "title": "Germination data from an assay of rapeseed at decreasing water potential levels", "object": "rape2G", "class": [ "data.frame" ], "fields": [ "CV", "Psi", "Dish", "timeBef", "timeAf", "nSeeds", "nCum", "Prop" ], "rows": 588, "table": true, "tojson": true } ], "_help": [ { "page": "alfalfaSG", "title": "Field-book for a germination assay with alfalfa", "topics": [ "alfalfaSG" ] }, { "page": "barley", "title": "A series of germination assays with barley", "topics": [ "barley" ] }, { "page": "excalibur", "title": "Relationship between germination rate and water potential in oilseed rape (var. Excalibur)", "topics": [ "excalibur" ] }, { "page": "festuca", "title": "Relationship between germination rate and water potential in Festuca arundinacea L.", "topics": [ "festuca" ] }, { "page": "GRPsi_models", "title": "Hydro-time models based on the germination rate", "topics": [ "GRPsi.Lin", "GRPsi.Pol", "GRPsi.Pol2", "GRPsiLin", "GRPsiLin.fun", "GRPsiPol", "GRPsiPol.fun", "GRPsiPol2", "GRPsiPol2.fun" ] }, { "page": "GRT_models", "title": "Thermal-time models based on the germination rate", "topics": [ "GRT.BS", "GRT.BS.fun", "GRT.BSb", "GRT.BSb.fun", "GRT.Ex", "GRT.Ex.fun", "GRT.Exb", "GRT.Exb.fun", "GRT.GH", "GRT.GH.fun", "GRT.GH2", "GRT.GH2.fun", "GRT.M", "GRT.M.fun", "GRT.Mb", "GRT.Mb.fun", "GRT.RF", "GRT.RF.fun", "GRT.RFb", "GRT.RFb.fun", "GRT.YL", "GRT.YL.fun" ] }, { "page": "GRTPsi_models", "title": "Hydro-Thermal-time models based on the germination rate", "topics": [ "GRTPsi.BS", "GRTPsi.BS.fun", "GRTPsi.M", "GRTPsi.M.fun" ] }, { "page": "HaloTL", "title": "Halotime model with logistic distribution of base salt concentration (derived from Bakhshandeh et al., 2020)", "topics": [ "HaloTL", "HaloTL.fun" ] }, { "page": "HaloTLL", "title": "Halotime model with log-logistic distribution of base salt concentration (derived from Bakhshandeh et al., 2020)", "topics": [ "HaloTLL", "HaloTLL.fun" ] }, { "page": "HaloTnorm", "title": "Halotime model with normal distribution of base salt concentration (derived from Bakhshandeh et al., 2020)", "topics": [ "HaloTnorm", "HaloTnorm.fun" ] }, { "page": "hordeum", "title": "Germination of Hordeum spontaneum at different temperatures and water potentials", "topics": [ "hordeum" ] }, { "page": "HTE1", "title": "Hydrotime model with log-logistic distribution of germination time (Onofri et al., 2018)", "topics": [ "HTE1", "HTE1.fun" ] }, { "page": "HTE2", "title": "Hydrotime model with log-logistic distribution of germination time (Onofri et al., 2018)", "topics": [ "HTE2", "HTE2.fun" ] }, { "page": "HTE3", "title": "Hydrotime model with log-logistic distribution of germination time (Onofri et al., 2018)", "topics": [ "HTE3", "HTE3.fun" ] }, { "page": "HTEx", "title": "Hydrotime model with Type II Extreme Value distribution of base water potential (Mesgaran et al., 2013)", "topics": [ "HTex", "HTex.fun" ] }, { "page": "HTG", "title": "Hydrotime model with Gumbel distribution of base water potential (Mesgaran et al., 2013)", "topics": [ "HTG", "HTG.fun" ] }, { "page": "HTL", "title": "Hydrotime model with logistic distribution of base water potential (Mesgaran et al., 2013)", "topics": [ "HTL", "HTL.fun" ] }, { "page": "HTLL", "title": "Hydrotime model with log-logistic distribution of base water potential (Mesgaran et al., 2013)", "topics": [ "HTLL", "HTLL.fun" ] }, { "page": "HTnorm", "title": "Hydrotime model with normal distribution of base water potential (Bradford, 2002)", "topics": [ "HTnorm", "HTnorm.fun" ] }, { "page": "HTTEM", "title": "Hydro-thermal-time model with log-logistic distribution of germination time (Onofri et al., 2018)", "topics": [ "HTTEM", "HTTEM.fun" ] }, { "page": "HTTLL", "title": "Hydro-thermal-time model with log-logistic distribution of base water potential (Mesgaran et al., 2017)", "topics": [ "HTTLL.BS", "HTTLL.BS.fun", "HTTLL.M", "HTTLL.M.fun" ] }, { "page": "HTTnorm", "title": "Hydro-thermal-time model with normal distribution of base water potential (Bradford, 2002)", "topics": [ "HTTnorm.BS", "HTTnorm.BS.fun", "HTTnorm.M", "HTTnorm.M.fun" ] }, { "page": "HTW1", "title": "Hydrotime model with Weibull Type I distribution of base water potential (Mesgaran et al., 2013)", "topics": [ "HTW1", "HTW1.fun" ] }, { "page": "HTW2", "title": "Hydrotime model with Weibull Type II distribution of base water potential (Mesgaran et al., 2013)", "topics": [ "HTW2", "HTW2.fun" ] }, { "page": "jackGroup", "title": "Delete-a-Petri-dish jackknife", "topics": [ "jackGroupSE" ] }, { "page": "makeDrm", "title": "Reshape a seed germination datasets for time-to-event analyses (deprecated)", "topics": [ "makeDrm" ] }, { "page": "makeDrm2", "title": "Reshape a seed germination datasets for time-to-event model fitting.", "topics": [ "makeDrm2" ] }, { "page": "phalaris", "title": "A series of germination assays with Phalaris minor", "topics": [ "phalaris" ] }, { "page": "Pmax_models", "title": "Effect of environmental water potential or temperature on the germination capability of a seed lot", "topics": [ "PmaxPsi1", "PmaxPsi1.fun", "PmaxT1", "PmaxT1.fun" ] }, { "page": "rape", "title": "Germination data from an assay of rapeseed at decreasing water potential levels", "topics": [ "rape" ] }, { "page": "rape2G", "title": "Germination data from an assay of rapeseed at decreasing water potential levels", "topics": [ "rape2G" ] }, { "page": "TTE_models", "title": "Thermal-time models with log-logistic distribution of germination time (Onofri et al., 2018)", "topics": [ "TTEM", "TTEM.fun", "TTERF", "TTERF.fun", "TTERFc", "TTERFc.fun" ] } ], "_readme": "https://github.com/onofriandreapg/drcseedgerm/raw/HEAD/README.md", "_rundeps": [ "abind", "backports", "boot", "broom", "car", "carData", "cli", "codetools", "colorspace", "cowplot", "cpp11", "Deriv", "doBy", "dplyr", "drc", "drcte", "farver", "forecast", "Formula", "fracdiff", "generics", "ggplot2", "glue", "gtable", "gtools", "isoband", "labeling", "lattice", "lifecycle", "lme4", "lmtest", "magrittr", "MASS", "Matrix", "MatrixModels", "mclust", "mgcv", "microbenchmark", "minqa", "modelr", "multcomp", "mvtnorm", "nlme", "nloptr", "nnet", "nor1mix", "numDeriv", "pbkrtest", "pillar", "pkgconfig", "plotrix", "plyr", "purrr", "quantreg", "R6", "rbibutils", "RColorBrewer", "Rcpp", "RcppArmadillo", "RcppEigen", "Rdpack", "reformulas", "rlang", "S7", "sandwich", "scales", "SparseM", "stringi", "stringr", "survival", "TH.data", "tibble", "tidyr", "tidyselect", "timeDate", "urca", "utf8", "vctrs", "viridisLite", "withr", "zoo" ], "_score": 4.021189299069938, "_indexed": true, "_nocasepkg": "drcseedgerm", "_universes": [ "onofriandreapg" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.1.1", "date": "2026-06-03T09:13:06.000Z", "distro": "noble", "commit": "d68b6e2e8b3b6ed20597f1d86d08c703db54630d", "fileid": "e8478048b48a541605cbe6689dbfcf554df11cd8b826d7757d86d57169c1f448", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/onofriandreapg/actions/runs/26874926646" }, { "r": "4.6.0", "os": "linux", "version": "1.1.1", "date": "2026-06-03T09:12:56.000Z", "distro": "noble", "commit": "d68b6e2e8b3b6ed20597f1d86d08c703db54630d", "fileid": "4956ee691fba8522838bc3a3e769651214b6ae63045d680188fa96c00a2fcd4b", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/onofriandreapg/actions/runs/26874926646" }, { "r": "4.5.3", "os": "mac", "version": "1.1.1", "date": "2026-06-03T09:12:16.000Z", "commit": "d68b6e2e8b3b6ed20597f1d86d08c703db54630d", "fileid": "21835527fee8448df1419e19f118f8311adf7b58bd8ca9f2d9ad01457d72e0ec", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/onofriandreapg/actions/runs/26874926646" }, { "r": "4.6.0", "os": "mac", "version": "1.1.1", "date": "2026-06-03T09:12:47.000Z", "commit": "d68b6e2e8b3b6ed20597f1d86d08c703db54630d", "fileid": "9ae589f135a493fd86571114e344aa7fb7bdde5616b4336346e51707fc95e2ab", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/onofriandreapg/actions/runs/26874926646" }, { "r": "4.6.0", "os": "wasm", "version": "1.1.1", "date": "2026-06-03T09:13:02.000Z", "commit": "d68b6e2e8b3b6ed20597f1d86d08c703db54630d", "fileid": "e9a53cca0c35b30720c78938ee45bc155382c0e405174f82b6c8a6f76882440c", "status": "success", "buildurl": "https://github.com/r-universe/onofriandreapg/actions/runs/26874926646" }, { "r": "4.7.0", "os": "win", "version": "1.1.1", "date": "2026-06-03T09:12:20.000Z", "commit": "d68b6e2e8b3b6ed20597f1d86d08c703db54630d", "fileid": "c175f02546b72eb9185dee1fd132e7932fc35fab09863a40a301d7d9d396956e", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/onofriandreapg/actions/runs/26874926646" }, { "r": "4.5.3", "os": "win", "version": "1.1.1", "date": "2026-06-03T09:11:58.000Z", "commit": "d68b6e2e8b3b6ed20597f1d86d08c703db54630d", "fileid": "d4061664d2076e83e4af8d7e1ddaad0163e6cdcb3cee1e7a1e443ef218845b04", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/onofriandreapg/actions/runs/26874926646" }, { "r": "4.6.0", "os": "win", "version": "1.1.1", "date": "2026-06-03T09:11:55.000Z", "commit": "d68b6e2e8b3b6ed20597f1d86d08c703db54630d", "fileid": "32495dcfd211d514fd35873e34fa1e47685b38c544a13cb7d9d4428e1d0f2b98", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/onofriandreapg/actions/runs/26874926646" } ] }