{ "_id": "6a1ec2a6b25058d4daae1def", "Package": "hagis", "Title": "Analysis of Plant Pathogen Pathotype Complexities, Distributions\nand Diversity", "Version": "4.0.0.9000", "Authors@R": "c(\nperson(\"Austin G.\", \"McCoy\", , \"mccoyaus@msu.edu\", role = c(\"aut\", \"ccp\"),\ncomment = c(ORCID = \"0000-0003-2483-4184\")),\nperson(\"Zachary\", \"Noel\", , \"noelzach@msu.edu\", role = c(\"aut\", \"ccp\"),\ncomment = c(ORCID = \"0000-0001-6375-8300\")),\nperson(\"Adam H.\", \"Sparks\", , \"adamhsparks@gmail.com\", role = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0002-0061-8359\")),\nperson(\"Martin\", \"Chilvers\", , \"chilvers@msu.edu\", role = c(\"aut\", \"ths\"),\ncomment = c(ORCID = \"0000-0001-8832-1666\")),\nperson(\"Jari\", \"Oksanen\", , \"jhoksane@gmail.com\", role = \"aut\",\ncomment = \"Contributed fix for the use of 'vegan' in betadiversity vignette.\"),\nperson(\"Zhian N.\", \"Kamvar\", role = c(\"ctb\", \"rev\"),\ncomment = c(ORCID = \"0000-0003-1458-7108\")),\nperson(\"Michigan Soybean Promotion Committee\", role = c(\"fnd\", \"cph\")),\nperson(\"Project GREEEN\", role = c(\"fnd\", \"cph\")),\nperson(\"North Central Soybean Research Program\", role = c(\"fnd\", \"cph\")),\nperson(\"Grains Research and Development Corporation\", role = c(\"fnd\", \"cph\"),\ncomment = c(\"GRDC Project DAQ00186 and GRDC Project CUR2210-005OPX\\n (AAGI-CU)\", ROR = \"02xwr1996\")),\nperson(\"Michigan State University\", role = c(\"fnd\", \"cph\"),\ncomment = c(\"MSU AgBioResearch and MSU Extension\", ROR = \"05hs6h993\")),\nperson(\"University of Southern Queensland\", role = c(\"fnd\", \"cph\"),\ncomment = c(ROR = \"04sjbnx57\")),\nperson(\"Curtin University\", role = c(\"fnd\", \"cph\"),\ncomment = c(ROR = \"02n415q13\"))\n)", "Description": "Analysis of plant pathogen pathotype survey data.\nFunctions provided calculate distribution of susceptibilities,\ndistribution of complexities with statistics, pathotype\nfrequency distribution, as well as diversity indices for\npathotypes. This package is meant to be a direct replacement\nfor Herrmann, Löwer and Schachtel's (1999)\n Habgood-Gilmour\nSpreadsheet, 'HaGiS', previously used for pathotype analysis.", "License": "MIT + file LICENSE", "URL": "https://github.com/openplantpathology/hagis,\nhttps://openplantpathology.github.io/hagis/", "BugReports": "https://github.com/openplantpathology/hagis/issues", "VignetteBuilder": "knitr", "Config/Needs/build": "moodymudskipper/devtag", "Config/roxyglobals/filename": "globals.R", "Config/roxyglobals/unique": "FALSE", "Encoding": "UTF-8", "Language": "en-US", "LazyData": "true", "Roxygen": "list(markdown = TRUE, roclets = c(\"collate\", \"namespace\",\n\"rd\", \"roxyglobals::global_roclet\", \"devtag::dev_roclet\"))", "RoxygenNote": "7.3.3", "Repository": "https://openplantpathology.r-universe.dev", "Date/Publication": "2026-06-02 09:04:56 UTC", "RemoteUrl": "https://github.com/openplantpathology/hagis", "RemoteRef": "HEAD", "RemoteSha": "a8ecfd647877cc21c40b58c6f69145b2d62c4464", "NeedsCompilation": "no", "Packaged": { "Date": "2026-06-02 11:43:39 UTC", "User": "root" }, "Author": "Austin G. McCoy [aut, ccp] (ORCID:\n),\nZachary Noel [aut, ccp] (ORCID:\n),\nAdam H. Sparks [aut, cre] (ORCID:\n),\nMartin Chilvers [aut, ths] (ORCID:\n),\nJari Oksanen [aut] (Contributed fix for the use of 'vegan' in\nbetadiversity vignette.),\nZhian N. Kamvar [ctb, rev] (ORCID:\n),\nMichigan Soybean Promotion Committee [fnd, cph],\nProject GREEEN [fnd, cph],\nNorth Central Soybean Research Program [fnd, cph],\nGrains Research and Development Corporation [fnd, cph] (GRDC Project\nDAQ00186 and GRDC Project CUR2210-005OPX (AAGI-CU), ROR:\n),\nMichigan State University [fnd, cph] (MSU AgBioResearch and MSU\nExtension, ROR: ),\nUniversity of Southern Queensland [fnd, cph] (ROR:\n),\nCurtin University [fnd, cph] (ROR: )", "Maintainer": "Adam H. Sparks ", "MD5sum": "cdee038a258363e86af9f3b9467e5524", "_user": "openplantpathology", "_type": "src", "_file": "hagis_4.0.0.9000.tar.gz", "_fileid": "3c6d5b296a2b33e46a5870fbab16322bd57a7a651fa1467c15d72dbe5a94154d", "_filesize": 868923, "_sha256": "3c6d5b296a2b33e46a5870fbab16322bd57a7a651fa1467c15d72dbe5a94154d", "_created": "2026-06-02T11:43:39.000Z", "_published": "2026-06-02T11:46:46.711Z", "_distro": "noble", "_jobs": [ { "job": 79062940813, "time": 150, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7356769041" }, { "job": 79062940814, "time": 149, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7356768844" }, { "job": 79062940823, "time": 145, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7356767155" }, { "job": 79062940810, "time": 115, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7356755912" }, { "job": 79062286057, "time": 234, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7356714311" }, { "job": 79062940774, "time": 114, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7356756409" }, { "job": 79062940837, "time": 112, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7356755069" }, { "job": 79062940821, "time": 87, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7356745982" }, { "job": 79062940828, "time": 85, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7356745556" } ], "_buildurl": "https://github.com/r-universe/openplantpathology/actions/runs/26817297755", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/openplantpathology/hagis", "_commit": { "id": "a8ecfd647877cc21c40b58c6f69145b2d62c4464", "author": "Adam H. Sparks ", "committer": "Adam H. Sparks ", "message": "chore: cleanup .Rbuildignore\n", "time": 1780391096 }, "_maintainer": { "name": "Adam H. Sparks", "email": "adamhsparks@gmail.com", "login": "adamhsparks", "mastodon": "@adamhsparks@rstats.me", "orcid": "0000-0002-0061-8359", "description": "Professor of Biometry and Agricultural Data Analytics.\nEditor at @ropensci and Tropical Plant Pathology", "uuid": 3195906 }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.5.0", "role": "Depends" }, { "package": "data.table", "role": "Imports" }, { "package": "ggplot2", "role": "Imports" }, { "package": "pander", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "ape", "role": "Suggests" }, { "package": "dplyr", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "roxyglobals", "role": "Suggests" }, { "package": "testthat", "role": "Suggests" }, { "package": "vdiffr", "role": "Suggests" }, { "package": "vegan", "role": "Suggests" } ], "_owner": "openplantpathology", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-30", "n": 18 }, { "week": "2025-31", "n": 1 }, { "week": "2025-39", "n": 2 }, { "week": "2026-23", "n": 1 } ], "_tags": [ { "name": "v4.0.0", "date": "2025-07-26" } ], "_topics": [ "plant-pathology", "pathotype", "pathogen-survey", "virulence analysis", "differential set", "assessment scale", "pathotype-complexities", "plant-disease", "population-diversities" ], "_stars": 1, "_contributors": [ { "user": "adamhsparks", "count": 725, "uuid": 3195906 }, { "user": "agmccoy", "count": 24, "uuid": 46008155 }, { "user": "jarioksa", "count": 1, "uuid": 1432933 }, { "user": "zkamvar", "count": 1, "uuid": 3639446 } ], "_userbio": { "uuid": 27719812, "type": "organization", "name": "Open Plant Pathology", "description": "The Open Plant Pathology initiative has wrapped up, but all of our materials remain here in the spirit of openness and reproducibility" }, "_downloads": { "count": 199, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/hagis" }, "_devurl": "https://github.com/openplantpathology/hagis", "_pkgdown": "https://openplantpathology.github.io/hagis/", "_searchresults": 14, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/hagis.html", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_homeurl": "https://github.com/openplantpathology/hagis", "_realowner": "openplantpathology", "_cranurl": true, "_releases": [ { "version": "2.0.0", "date": "2019-06-24" }, { "version": "3.0.0", "date": "2019-08-26" }, { "version": "3.0.1", "date": "2019-11-18" }, { "version": "3.1.0", "date": "2020-10-07" }, { "version": "3.1.1", "date": "2020-12-09" }, { "version": "3.1.2", "date": "2021-09-30" }, { "version": "3.1.3", "date": "2021-10-14" }, { "version": "3.1.4", "date": "2022-08-15" }, { "version": "3.1.6", "date": "2023-04-25" }, { "version": "3.1.11", "date": "2023-09-06" }, { "version": "3.1.12", "date": "2024-05-16" }, { "version": "4.0.0", "date": "2025-07-26" } ], "_exports": [ "autoplot", "calculate_complexities", "calculate_diversities", "create_binary_matrix", "diversities_table", "individual_pathotypes", "summarize_gene" ], "_datasets": [ { "name": "P_sojae_survey", "title": "_Phytophthora sojae_ Survey Example Data", "object": "P_sojae_survey", "class": [ "data.table", "data.frame" ], "fields": [ "Isolate", "Line", "Rps", "Total", "HR (1)", "Lesion (2)", "Lesion to cotyledon (3)", "Dead (4)", "total.susc", "total.resis", "perc.susc", "perc.resis" ], "rows": 294, "table": true, "tojson": true }, { "name": "sample_meta", "title": "_Phytophthora sojae_ Survey Example Metadata", "object": "sample_meta", "class": [ "data.frame" ], "fields": [ "Sample", "Locale" ], "rows": 21, "table": true, "tojson": true } ], "_help": [ { "page": "autoplot.hagis.complexities", "title": "Plot hagis Complexities Objects", "topics": [ "autoplot.hagis.complexities" ] }, { "page": "autoplot.hagis.gene.summary", "title": "Plot hagis Summary Objects", "topics": [ "autoplot.hagis.gene.summary" ] }, { "page": "calculate_complexities", "title": "Calculate Distribution of Complexities by Sample", "topics": [ "calculate_complexities" ] }, { "page": "calculate_diversities", "title": "Calculate Diversities Indices", "topics": [ "calculate_diversities" ] }, { "page": "create_binary_matrix", "title": "Create Binary Data Matrix From Pathotype Data", "topics": [ "create_binary_matrix" ] }, { "page": "diversities_table", "title": "Custom Print for hagis Diversities Tables", "topics": [ "diversities_table" ] }, { "page": "individual_pathotypes", "title": "Prints Individual Pathotypes for Each Sample", "topics": [ "individual_pathotypes" ] }, { "page": "P_sojae_survey", "title": "_Phytophthora sojae_ Survey Example Data", "topics": [ "P_sojae_survey" ] }, { "page": "sample_meta", "title": "_Phytophthora sojae_ Survey Example Metadata", "topics": [ "sample_meta" ] }, { "page": "summarize_gene", "title": "Calculate and Summarize Distribution of Susceptibilities by Gene", "topics": [ "summarize_gene" ] } ], "_readme": "https://github.com/openplantpathology/hagis/raw/HEAD/README.md", "_rundeps": [ "cli", "cpp11", "data.table", "digest", "farver", "ggplot2", "glue", "gtable", "isoband", "labeling", "lifecycle", "pander", "R6", "RColorBrewer", "Rcpp", "rlang", "S7", "scales", "vctrs", "viridisLite", "withr" ], "_vignettes": [ { "source": "betadiversity.Rmd", "filename": "betadiversity.html", "title": "Beta-diversity Analysis with hagis", "author": "Austin McCoy", "engine": "knitr::rmarkdown", "headings": [ "Load Packages", "Convert the Dataset to a Binary Data Matrix", "Perform Principle Coordinates Analysis (PCOA)", "Add Metadata to your PCOA Data", "Statistical Tests for Beta Diversity", "Permutation Based Analysis of Variance (PERMANOVA) and Beta-dispersion Analyses", "Beta-Dispersion", "Permutation Based Analysis of Variance (PERMANOVA)", "Analysis of Similarity (ANOSIM)" ], "created": "2020-10-06 05:47:21", "modified": "2024-05-16 02:42:07", "commits": 14 }, { "source": "hagis.Rmd", "filename": "hagis.html", "title": "hagis: Tools for Analysis of Plant Pathogen Pathotype Complexities, Distributions and Diversity", "author": "Austin McCoy and Zachary Noel", "engine": "knitr::rmarkdown", "headings": [ "Getting Started With", "Function Arguments Used in", "Determination of Effective Resistance Genes", "Plotting Rps Summary Data", "Pathotype Complexities", "Plotting Complexities Data", "Diversity Indices, Frequency of Unique Pathotypes and Individual Isolate Pathotypes", "Table of Diversities", "Table of Individual Pathotypes", "Advanced Plotting", "{hagis} autoplot() Objects", "Changing the ggplot2 Theme", "Changing the Font", "Make a Horizontal Plot", "Use Colors in Autoplot Objects", "Sorting the x-axis" ], "created": "2019-01-09 00:33:26", "modified": "2025-02-05 04:13:22", "commits": 40 } ], "_score": 5.225309281725863, "_indexed": true, "_nocasepkg": "hagis", "_universes": [ "openplantpathology", "adamhsparks" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "4.0.0.9000", "date": "2026-06-02T11:46:04.000Z", "distro": "noble", "commit": "a8ecfd647877cc21c40b58c6f69145b2d62c4464", "fileid": "a6a0e293bb4911a31b21e32460846cd9191d7d036321c170baa026b86d6b05ba", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/openplantpathology/actions/runs/26817297755" }, { "r": "4.6.0", "os": "linux", "version": "4.0.0.9000", "date": "2026-06-02T11:46:03.000Z", "distro": "noble", "commit": "a8ecfd647877cc21c40b58c6f69145b2d62c4464", "fileid": "e3a3aff903dbcb83552ccf94ebec85a9abbe24966a449b65457fb082d714d510", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/openplantpathology/actions/runs/26817297755" }, { "r": "4.5.3", "os": "mac", "version": "4.0.0.9000", "date": "2026-06-02T11:45:59.000Z", "commit": "a8ecfd647877cc21c40b58c6f69145b2d62c4464", "fileid": "29a888d25e58219f52cffab9a34a808a126faf74bf921854c62b0a2aae1dd8ff", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/openplantpathology/actions/runs/26817297755" }, { "r": "4.6.0", "os": "mac", "version": "4.0.0.9000", "date": "2026-06-02T11:45:31.000Z", "commit": "a8ecfd647877cc21c40b58c6f69145b2d62c4464", "fileid": "6f5e12b8979e8d3254aa03abf1ce93600739afbd789e5b4fe29e4f9be00c136c", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/openplantpathology/actions/runs/26817297755" }, { "r": "4.6.0", "os": "wasm", "version": "4.0.0.9000", "date": "2026-06-02T11:45:57.000Z", "commit": "a8ecfd647877cc21c40b58c6f69145b2d62c4464", "fileid": "718237dff458a3489ba4535c57aa1b21f909cde5826374e66b307e13c266df78", "status": "success", "buildurl": "https://github.com/r-universe/openplantpathology/actions/runs/26817297755" }, { "r": "4.7.0", "os": "win", "version": "4.0.0.9000", "date": "2026-06-02T11:45:16.000Z", "commit": "a8ecfd647877cc21c40b58c6f69145b2d62c4464", "fileid": "05226c235aa3bf4a80a3d2109a5d550e3c8d59a14124ec778110418ef7763acb", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/openplantpathology/actions/runs/26817297755" }, { "r": "4.5.3", "os": "win", "version": "4.0.0.9000", "date": "2026-06-02T11:44:57.000Z", "commit": "a8ecfd647877cc21c40b58c6f69145b2d62c4464", "fileid": "7644a590981cc69a1152191ad9d6e42197bc694a1c64360e3d68b01126dca3c5", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/openplantpathology/actions/runs/26817297755" }, { "r": "4.6.0", "os": "win", "version": "4.0.0.9000", "date": "2026-06-02T11:44:55.000Z", "commit": "a8ecfd647877cc21c40b58c6f69145b2d62c4464", "fileid": "2fb217b384c27b77ee82e52b23eb442cccb5a38b8604b7566b4ed3e3ef3d2d9b", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/openplantpathology/actions/runs/26817297755" } ] }