{ "_id": "6a13ea6eacfb0bcc41d2dfea", "Package": "PSRICalcSM", "Type": "Package", "Title": "Plant Stress Response Index Calculator - Softmax Method", "Version": "1.0.0", "Authors@R": "c(\nperson(\"Richard\", \"Feiss\",\nemail = \"feiss026@umn.edu\",\nrole = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0009-0008-0409-6042\")),\nperson(\"University of Minnesota\",\nrole = \"cph\")\n)", "Description": "Implements the softmax aggregation method for calculating\nPlant Stress Response Index (PSRI) from time-series germination\ndata under environmental stressors including prions,\nxenobiotics, osmotic stress, heavy metals, and chemical\ncontaminants. Provides zero-robust PSRI computation through\nadaptive softmax weighting of germination components (Maximum\nStress-adjusted Germination, Maximum Rate of Germination,\ncomplementary Mean Time to Germination, and Radicle Vigor\nScore), eliminating the zero-collapse failure mode of the\ngeometric mean approach implemented in 'PSRICalc'. Includes\nperplexity-based temperature parameter calibration and modular\ncomponent functions for transparent germination analysis. Built\non the methodological foundation of the Osmotic Stress Response\nIndex (OSRI) framework developed by Walne et al. (2020)\n. Note: This package implements\nmethodology currently under peer review. Please contact the\nauthor before publication using this approach. Development\nfollowed an iterative human-machine collaboration where all\nalgorithmic design, statistical methodologies, and biological\nvalidation logic were conceptualized, tested, and iteratively\nrefined by Richard A. Feiss through repeated cycles of running\nexperimental data, evaluating analytical outputs, and selecting\namong candidate algorithms and approaches. AI systems\n(Anthropic Claude and OpenAI GPT) served as coding assistants\nand analytical sounding boards under continuous human\ndirection. The selection of statistical methods, evaluation of\nbiological plausibility, and all final methodology decisions\nwere made by the human author. AI systems did not independently\noriginate algorithms, statistical approaches, or scientific\nmethodologies.", "License": "MIT + file LICENSE", "Encoding": "UTF-8", "LazyData": "true", "RoxygenNote": "7.3.2", "URL": "https://github.com/RFeissIV/PSRICalcSM", "BugReports": "https://github.com/RFeissIV/PSRICalcSM/issues", "Config/testthat/edition": "3", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-25 06:19:14 UTC", "User": "root" }, "Author": "Richard Feiss [aut, cre] (ORCID:\n), University of\nMinnesota [cph]", "Maintainer": "Richard Feiss ", "Repository": "https://rfeissiv.r-universe.dev", "Date/Publication": "2026-02-20 11:30:07 UTC", "RemoteUrl": "https://github.com/cran/PSRICalcSM", "RemoteRef": "HEAD", "RemoteSha": "cb38bb0c3b73507d79a113be26f57a4581c971ef", "MD5sum": "ba1314111da60fd00b6caff6b4751245", "_user": "rfeissiv", "_type": "src", "_file": "PSRICalcSM_1.0.0.tar.gz", "_fileid": "a237714a909ca7310bb1df6bfcc093dcb35fdfb6ee4ad3fecffcdc32c61a1f63", "_filesize": 188922, "_sha256": "a237714a909ca7310bb1df6bfcc093dcb35fdfb6ee4ad3fecffcdc32c61a1f63", "_created": "2026-05-25T06:19:14.000Z", "_published": "2026-05-25T06:21:34.905Z", "_distro": "noble", "_jobs": [ { "job": 77666001270, "time": 104, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7192762359" }, { "job": 77666001276, "time": 106, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7192762835" }, { "job": 77666001261, "time": 88, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7192759183" }, { "job": 77666001271, "time": 85, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7192758672" }, { "job": 77665704503, "time": 180, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7192741338" }, { "job": 77666001295, "time": 84, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7192758713" }, { "job": 77666001289, "time": 85, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7192758552" }, { "job": 77666001320, "time": 66, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7192754878" }, { "job": 77666001292, "time": 100, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7192761668" } ], "_buildurl": "https://github.com/r-universe/rfeissiv/actions/runs/26386378166", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/cran/PSRICalcSM", "_commit": { "id": "cb38bb0c3b73507d79a113be26f57a4581c971ef", "author": "Richard Feiss ", "committer": "cran-robot ", "message": "version 1.0.0\n", "time": 1771587007 }, "_maintainer": { "name": "Richard Feiss", "email": "feiss026@umn.edu", "login": "rfeissiv", "description": "", "uuid": 173518863 }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.0.0", "role": "Depends" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" } ], "_owner": "cran", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2026-08", "n": 1 } ], "_tags": [ { "name": "1.0.0", "date": "2026-02-20" } ], "_stars": 0, "_contributors": [ { "user": "rfeissiv", "count": 1, "uuid": 173518863 } ], "_userbio": { "uuid": 173518863, "type": "user", "name": "RFeissIV" }, "_downloads": { "count": 146, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/PSRICalcSM" }, "_devurl": "https://github.com/rfeissiv/psricalcsm", "_searchresults": 0, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/NEWS.html", "extra/NEWS.txt", "extra/PSRICalcSM.html", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_realowner": "rfeissiv", "_cranurl": false, "_releases": [ { "version": "1.0.0", "date": "2026-02-20" } ], "_exports": [ "calibrate_temperature", "compute_cmtg", "compute_mrg", "compute_msg", "compute_psri_sm", "compute_rvs", "softmax_weights" ], "_datasets": [ { "name": "germination_example", "title": "Example Germination Data for PSRI Softmax Calculation", "object": "germination_example", "class": [ "data.frame" ], "fields": [ "species", "treatment", "replicate", "total_seeds", "day3", "day5", "day7", "radicle_count" ], "rows": 40, "table": true, "tojson": true } ], "_help": [ { "page": "PSRICalcSM-package", "title": "Plant Stress Response Index Calculator - Softmax Method", "topics": [ "PSRICalcSM-package", "PSRICalcSM" ] }, { "page": "calibrate_temperature", "title": "Calibrate Softmax Temperature Parameter", "topics": [ "calibrate_temperature" ] }, { "page": "compute_cmtg", "title": "Compute Complementary Mean Time to Germination (cMTG)", "topics": [ "compute_cmtg" ] }, { "page": "compute_mrg", "title": "Compute Maximum Rate of Germination (MRG)", "topics": [ "compute_mrg" ] }, { "page": "compute_msg", "title": "Compute Maximum Stress-adjusted Germination (MSG)", "topics": [ "compute_msg" ] }, { "page": "compute_psri_sm", "title": "Compute Softmax Plant Stress Response Index (PSRI_SM)", "topics": [ "compute_psri_sm" ] }, { "page": "compute_rvs", "title": "Compute Radicle Vigor Score (RVS)", "topics": [ "compute_rvs" ] }, { "page": "germination_example", "title": "Example Germination Data for PSRI Softmax Calculation", "topics": [ "germination_example" ] }, { "page": "softmax_weights", "title": "Compute Softmax Weights", "topics": [ "softmax_weights" ] } ], "_readme": "https://github.com/cran/PSRICalcSM/raw/HEAD/README.md", "_rundeps": [], "_score": 1.6989700043360187, "_indexed": true, "_nocasepkg": "psricalcsm", "_universes": [ "rfeissiv" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.0.0", "date": "2026-05-25T06:21:08.000Z", "distro": "noble", "commit": "cb38bb0c3b73507d79a113be26f57a4581c971ef", "fileid": "d4ed70350f9135eb6e665bdc2b9ebec9599e0e98dd50b42740989552a229ea53", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/rfeissiv/actions/runs/26386378166" }, { "r": "4.6.0", "os": "linux", "version": "1.0.0", "date": "2026-05-25T06:21:10.000Z", "distro": "noble", "commit": "cb38bb0c3b73507d79a113be26f57a4581c971ef", "fileid": "69a7c2e1bda9cdb1395f5a433fcb41b3298796be7c243241d7c6957411bd2fe0", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/rfeissiv/actions/runs/26386378166" }, { "r": "4.5.3", "os": "mac", "version": "1.0.0", "date": "2026-05-25T06:20:53.000Z", "commit": "cb38bb0c3b73507d79a113be26f57a4581c971ef", "fileid": "965301cdca6ff3a62bd66bbcd615688731b95b513f5e5ed88d0daff8924c0206", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/rfeissiv/actions/runs/26386378166" }, { "r": "4.6.0", "os": "mac", "version": "1.0.0", "date": "2026-05-25T06:20:52.000Z", "commit": "cb38bb0c3b73507d79a113be26f57a4581c971ef", "fileid": "c089d4ebbddc133d21806a7a30064cf1fffb5da65d342dbbbb8688b83d063809", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/rfeissiv/actions/runs/26386378166" }, { "r": "4.6.0", "os": "wasm", "version": "1.0.0", "date": "2026-05-25T06:21:00.000Z", "commit": "cb38bb0c3b73507d79a113be26f57a4581c971ef", "fileid": "5a5b1cd6493901557200a8596002e81af25c19707e506fc8fd085433ccb19a9e", "status": "success", "buildurl": "https://github.com/r-universe/rfeissiv/actions/runs/26386378166" }, { "r": "4.7.0", "os": "win", "version": "1.0.0", "date": "2026-05-25T06:20:43.000Z", "commit": "cb38bb0c3b73507d79a113be26f57a4581c971ef", "fileid": "3014a02cd204f2429c2b5a5c18da9d4477636537e3040de33d1077b9c3b994a4", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/rfeissiv/actions/runs/26386378166" }, { "r": "4.5.3", "os": "win", "version": "1.0.0", "date": "2026-05-25T06:20:27.000Z", "commit": "cb38bb0c3b73507d79a113be26f57a4581c971ef", "fileid": "5912370918a9acbad190ab6b03e415151ec0c98b2ff8976ac19a47c35874c918", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/rfeissiv/actions/runs/26386378166" }, { "r": "4.6.0", "os": "win", "version": "1.0.0", "date": "2026-05-25T06:21:00.000Z", "commit": "cb38bb0c3b73507d79a113be26f57a4581c971ef", "fileid": "68496a1b02fc35d19f5bd60d6493fab2e383b7bf0ee3f9cbcfec2ebe8f0043e9", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/rfeissiv/actions/runs/26386378166" } ] }