{ "_id": "6a16a39dacfb0bcc41d81e09", "Package": "mkin", "Type": "Package", "Title": "Kinetic Evaluation of Chemical Degradation Data", "Version": "1.2.10", "Date": "2025-09-12", "Authors@R": "c(\nperson(\"Johannes\", \"Ranke\", role = c(\"aut\", \"cre\", \"cph\"),\nemail = \"johannes.ranke@jrwb.de\",\ncomment = c(ORCID = \"0000-0003-4371-6538\")),\nperson(\"Katrin\", \"Lindenberger\", role = \"ctb\", comment = \"contributed to mkinresplot()\"),\nperson(\"René\", \"Lehmann\", role = \"ctb\", comment = \"ilr() and invilr()\"),\nperson(\"Eurofins Regulatory AG\", role = \"cph\", comment = \"copyright for some of the contributions of JR 2012-2014\"))", "Description": "Calculation routines based on the FOCUS Kinetics Report\n(2006, 2014). Includes a function for conveniently defining\ndifferential equation models, model solution based on\neigenvalues if possible or using numerical solvers. If a C\ncompiler (on windows: 'Rtools') is installed, differential\nequation models are solved using automatically generated C\nfunctions. Non-constant errors can be taken into account using\nvariance by variable or two-component error models\n. Hierarchical degradation\nmodels can be fitted using nonlinear mixed-effects model\npackages as a back end .\nPlease note that no warranty is implied for correctness of\nresults or fitness for a particular purpose.", "License": "GPL", "LazyLoad": "yes", "LazyData": "yes", "Encoding": "UTF-8", "Language": "en-GB", "VignetteBuilder": "knitr", "BugReports": "https://github.com/jranke/mkin/issues/", "URL": "https://pkgdown.jrwb.de/mkin/", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.3.3", "Repository": "https://jranke.r-universe.dev", "Date/Publication": "2025-11-28 08:49:35 UTC", "RemoteUrl": "https://github.com/jranke/mkin", "RemoteRef": "HEAD", "RemoteSha": "1519d761ebb8c10350402b294907102d960b15a2", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-27 07:50:07 UTC", "User": "root" }, "Author": "Johannes Ranke [aut, cre, cph] (ORCID:\n),\nKatrin Lindenberger [ctb] (contributed to mkinresplot()),\nRené Lehmann [ctb] (ilr() and invilr()),\nEurofins Regulatory AG [cph] (copyright for some of the contributions\nof JR 2012-2014)", "Maintainer": "Johannes Ranke ", "MD5sum": "51cc071c9e5f7a41064358109eb71527", "_user": "jranke", "_type": "src", "_file": "mkin_1.2.10.tar.gz", "_fileid": "73b146c6748a2ce2c0a9305bbaa5009eff36ad058ebc3df2552780a17f7372ce", "_filesize": 5560290, "_sha256": "73b146c6748a2ce2c0a9305bbaa5009eff36ad058ebc3df2552780a17f7372ce", "_created": "2026-05-27T07:50:07.000Z", "_published": "2026-05-27T07:56:13.583Z", "_distro": "noble", "_jobs": [ { "job": 78031797579, "time": 319, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7234931258" }, { "job": 78031797569, "time": 275, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7234916949" }, { "job": 78031797603, "time": 222, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "WARNING", "artifact": "7234891676" }, { "job": 78031797580, "time": 271, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7234905020" }, { "job": 78031263364, "time": 209, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7234826886" }, { "job": 78031797607, "time": 139, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7234873226" }, { "job": 78031797602, "time": 294, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7234923521" }, { "job": 78031797594, "time": 297, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7234924592" }, { "job": 78031797622, "time": 304, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7234926276" } ], "_buildurl": "https://github.com/r-universe/jranke/actions/runs/26498090024", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/jranke/mkin", "_commit": { "id": "1519d761ebb8c10350402b294907102d960b15a2", "author": "Johannes Ranke ", "committer": "Johannes Ranke ", "message": "Add two-component error model to 2,4-D example\n\nAlso, explain the names of the metabolites.\n", "time": 1764319775 }, "_maintainer": { "name": "Johannes Ranke", "email": "johannes.ranke@jrwb.de", "login": "jranke", "description": "2023-present: Agroscope Switzerland; 2014-2022: https://jrwb.de; 2008-2014: Consultant at Harlan, then Eurofins; 1998-2008: University of Bremen", "uuid": 3621037, "orcid": "0000-0003-4371-6538" }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.1.0", "role": "Depends" }, { "package": "stats", "role": "Imports" }, { "package": "graphics", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "parallel", "role": "Imports" }, { "package": "deSolve", "version": ">= 1.35", "role": "Imports" }, { "package": "R6", "role": "Imports" }, { "package": "inline", "version": ">= 0.3.19", "role": "Imports" }, { "package": "numDeriv", "role": "Imports" }, { "package": "lmtest", "role": "Imports" }, { "package": "pkgbuild", "role": "Imports" }, { "package": "nlme", "version": ">= 3.1-151", "role": "Imports" }, { "package": "saemix", "version": ">= 3.2", "role": "Imports" }, { "package": "rlang", "role": "Imports" }, { "package": "vctrs", "role": "Imports" }, { "package": "knitr", "role": "Suggests" }, { "package": "rbenchmark", "role": "Suggests" }, { "package": "tikzDevice", "role": "Suggests" }, { "package": "testthat", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "covr", "role": "Suggests" }, { "package": "vdiffr", "role": "Suggests" }, { "package": "benchmarkme", "role": "Suggests" }, { "package": "tibble", "role": "Suggests" }, { "package": "stats4", "role": "Suggests" }, { "package": "readxl", "role": "Suggests" } ], "_owner": "jranke", "_selfowned": true, "_usedby": 1, "_updates": [ { "week": "2025-37", "n": 3 }, { "week": "2025-48", "n": 2 } ], "_tags": [], "_topics": [ "degradation", "focus-kinetics", "kinetic-models", "kinetics", "ode", "ode-model" ], "_stars": 12, "_contributors": [ { "user": "jranke", "count": 1436, "uuid": 3621037 }, { "user": "wibeasley", "count": 1, "uuid": 1372890 } ], "_userbio": { "uuid": 3621037, "type": "user", "name": "Johannes Ranke", "description": "2023-present: Agroscope Switzerland; 2014-2022: https://jrwb.de; 2008-2014: Consultant at Harlan, then Eurofins; 1998-2008: University of Bremen" }, "_downloads": { "count": 294, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/mkin" }, "_mentions": 2, "_devurl": "https://github.com/jranke/mkin", "_pkgdown": "https://pkgdown.jrwb.de/mkin/", "_searchresults": 69, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/mkin.html", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_homeurl": "https://github.com/jranke/mkin", "_realowner": "jranke", "_cranurl": true, "_releases": [ { "version": "0.7-1", "date": "2010-05-18" }, { "version": "0.7-2", "date": "2010-05-19" }, { "version": "0.7-5", "date": "2010-06-04" }, { "version": "0.7-6", "date": "2010-06-09" }, { "version": "0.7-8", "date": "2010-08-27" }, { "version": "0.8-05", "date": "2010-12-23" }, { "version": "0.8-08", "date": "2011-05-06" }, { "version": "0.8-11", "date": "2011-10-20" }, { "version": "0.9-05", "date": "2012-06-29" }, { "version": "0.9-06", "date": "2012-07-23" }, { "version": "0.9-10", "date": "2013-02-17" }, { "version": "0.9-12", "date": "2013-02-18" }, { "version": "0.9-14", "date": "2013-02-22" }, { "version": "0.9-18", "date": "2013-04-12" }, { "version": "0.9-20", "date": "2013-09-26" }, { "version": "0.9-22", "date": "2013-10-25" }, { "version": "0.9-24", "date": "2013-11-06" }, { "version": "0.9-27", "date": "2014-05-09" }, { "version": "0.9-28", "date": "2014-05-20" }, { "version": "0.9-29", "date": "2014-06-27" }, { "version": "0.9-30", "date": "2014-07-11" }, { "version": "0.9-31", "date": "2014-07-14" }, { "version": "0.9-32", "date": "2014-07-24" }, { "version": "0.9-33", "date": "2014-10-11" }, { "version": "0.9-34", "date": "2014-11-21" }, { "version": "0.9-35", "date": "2015-05-15" }, { "version": "0.9-36", "date": "2015-06-21" }, { "version": "0.9-38", "date": "2015-06-23" }, { "version": "0.9-39", "date": "2015-06-26" }, { "version": "0.9-40", "date": "2015-07-21" }, { "version": "0.9-41", "date": "2015-11-09" }, { "version": "0.9.42", "date": "2016-03-24" }, { "version": "0.9.43", "date": "2016-06-28" }, { "version": "0.9.44", "date": "2016-06-28" }, { "version": "0.9.45", "date": "2016-12-08" }, { "version": "0.9.45.2", "date": "2017-07-22" }, { "version": "0.9.46", "date": "2017-07-29" }, { "version": "0.9.46.1", "date": "2017-09-14" }, { "version": "0.9.46.2", "date": "2017-10-10" }, { "version": "0.9.46.3", "date": "2017-11-16" }, { "version": "0.9.47.1", "date": "2018-02-06" }, { "version": "0.9.47.2", "date": "2018-07-19" }, { "version": "0.9.47.5", "date": "2018-09-14" }, { "version": "0.9.48.1", "date": "2019-03-04" }, { "version": "0.9.49.5", "date": "2019-07-04" }, { "version": "0.9.49.6", "date": "2019-10-31" }, { "version": "0.9.49.7", "date": "2019-11-02" }, { "version": "0.9.49.8", "date": "2020-01-09" }, { "version": "0.9.49.9", "date": "2020-03-31" }, { "version": "0.9.49.10", "date": "2020-04-18" }, { "version": "0.9.49.11", "date": "2020-04-20" }, { "version": "0.9.50.1", "date": "2020-05-11" }, { "version": "0.9.50.2", "date": "2020-05-12" }, { "version": "0.9.50.3", "date": "2020-10-08" }, { "version": "1.0.0", "date": "2021-02-03" }, { "version": "1.0.1", "date": "2021-02-10" }, { "version": "1.0.3", "date": "2021-02-15" }, { "version": "1.0.4", "date": "2021-04-20" }, { "version": "1.0.5", "date": "2021-09-15" }, { "version": "1.1.0", "date": "2022-03-14" }, { "version": "1.1.1", "date": "2022-07-12" }, { "version": "1.2.0", "date": "2022-11-17" }, { "version": "1.2.1", "date": "2022-11-19" }, { "version": "1.2.3", "date": "2023-04-17" }, { "version": "1.2.4", "date": "2023-05-19" }, { "version": "1.2.5", "date": "2023-08-09" }, { "version": "1.2.6", "date": "2023-10-14" }, { "version": "1.2.9", "date": "2025-02-13" }, { "version": "1.2.10", "date": "2025-05-13" } ], "_exports": [ "add_err", "aw", "backtransform_odeparms", "best", "CAKE_export", "create_deg_func", "DFOP.solution", "endpoints", "f_time_norm_focus", "FOMC.solution", "get_deg_func", "hierarchical_kinetics", "HS.solution", "html_listing", "illparms", "ilr", "intervals", "invilr", "IORE.solution", "llhist", "loftest", "logistic.solution", "lrtest", "max_twa_dfop", "max_twa_fomc", "max_twa_hs", "max_twa_parent", "max_twa_sfo", "mean_degparms", "mhmkin", "mixed", "mkin_long_to_wide", "mkin_wide_to_long", "mkinds", "mkindsg", "mkinerrmin", "mkinerrplot", "mkinfit", "mkinmod", "mkinparplot", "mkinplot", "mkinpredict", "mkinresplot", "mkinsub", "mmkin", "multistart", "nafta", "nlme", "nlme_data", "nlme_function", "parms", "parplot", "plot_err", "plot_res", "plot_sep", "read_spreadsheet", "saem", "saemix_data", "saemix_model", "set_nd_nq", "set_nd_nq_focus", "SFO.solution", "SFORB.solution", "sigma_twocomp", "status", "summary_listing", "tex_listing", "transform_odeparms", "which.best" ], "_datasets": [ { "name": "D24_2014", "title": "Aerobic soil degradation data on 2,4-D from the EU assessment in 2014", "object": "D24_2014", "class": [ "mkindsg", "R6" ], "fields": [], "table": false, "tojson": false }, { "name": "dimethenamid_2018", "title": "Aerobic soil degradation data on dimethenamid and dimethenamid-P from the EU assessment in 2018", "object": "dimethenamid_2018", "class": [ "mkindsg", "R6" ], "fields": [], "table": false, "tojson": false }, { "name": "ds_dfop", "title": "Synthetic data for hierarchical kinetic degradation models", "object": "ds_mixed", "class": [ "list" ], "fields": [], "table": true, "tojson": true }, { "name": "ds_dfop_sfo", "title": "Synthetic data for hierarchical kinetic degradation models", "object": "ds_mixed", "class": [ "list" ], "fields": [], "table": true, "tojson": true }, { "name": "ds_fomc", "title": "Synthetic data for hierarchical kinetic degradation models", "object": "ds_mixed", "class": [ "list" ], "fields": [], "table": true, "tojson": true }, { "name": "ds_hs", "title": "Synthetic data for hierarchical kinetic degradation models", "object": "ds_mixed", "class": [ "list" ], "fields": [], "table": true, "tojson": true }, { "name": "ds_sfo", "title": "Synthetic data for hierarchical kinetic degradation models", "object": "ds_mixed", "class": [ "list" ], "fields": [], "table": true, "tojson": true }, { "name": "experimental_data_for_UBA_2019", "title": "Experimental datasets used for development and testing of error models", "object": "experimental_data_for_UBA_2019", "class": [ "list" ], "fields": [], "table": false, "tojson": false }, { "name": "FOCUS_2006_A", "title": "Datasets A to F from the FOCUS Kinetics report from 2006", "object": "FOCUS_2006_datasets", "class": [ "data.frame" ], "fields": [ "name", "time", "value" ], "rows": 8, "table": true, "tojson": true }, { "name": "FOCUS_2006_B", "title": "Datasets A to F from the FOCUS Kinetics report from 2006", "object": "FOCUS_2006_datasets", "class": [ "data.frame" ], "fields": [ "name", "time", "value" ], "rows": 8, "table": true, "tojson": true }, { "name": "FOCUS_2006_C", "title": "Datasets A to F from the FOCUS Kinetics report from 2006", "object": "FOCUS_2006_datasets", "class": [ "data.frame" ], "fields": [ "name", "time", "value" ], "rows": 9, "table": true, "tojson": true }, { "name": "FOCUS_2006_D", "title": "Datasets A to F from the FOCUS Kinetics report from 2006", "object": "FOCUS_2006_datasets", "class": [ "data.frame" ], "fields": [ "name", "time", "value" ], "rows": 44, "table": true, "tojson": true }, { "name": "FOCUS_2006_DFOP_ref_A_to_B", "title": "Results of fitting the DFOP model to Datasets A to B of FOCUS (2006)", "object": "FOCUS_2006_DFOP_ref_A_to_B", "class": [ "data.frame" ], "fields": [ "package", "M0", "f", "k1", "k2", "DT50", "DT90", "dataset" ], "rows": 15, "table": true, "tojson": true }, { "name": "FOCUS_2006_E", "title": "Datasets A to F from the FOCUS Kinetics report from 2006", "object": "FOCUS_2006_datasets", "class": [ "data.frame" ], "fields": [ "name", "time", "value" ], "rows": 18, "table": true, "tojson": true }, { "name": "FOCUS_2006_F", "title": "Datasets A to F from the FOCUS Kinetics report from 2006", "object": "FOCUS_2006_datasets", "class": [ "data.frame" ], "fields": [ "name", "time", "value" ], "rows": 27, "table": true, "tojson": true }, { "name": "FOCUS_2006_FOMC_ref_A_to_F", "title": "Results of fitting the FOMC model to Datasets A to F of FOCUS (2006)", "object": "FOCUS_2006_FOMC_ref_A_to_F", "class": [ "data.frame" ], "fields": [ "package", "M0", "alpha", "beta", "DT50", "DT90", "dataset" ], "rows": 45, "table": true, "tojson": true }, { "name": "FOCUS_2006_HS_ref_A_to_F", "title": "Results of fitting the HS model to Datasets A to F of FOCUS (2006)", "object": "FOCUS_2006_HS_ref_A_to_F", "class": [ "data.frame" ], "fields": [ "package", "M0", "tb", "k1", "k2", "DT50", "DT90", "dataset" ], "rows": 36, "table": true, "tojson": true }, { "name": "FOCUS_2006_SFO_ref_A_to_F", "title": "Results of fitting the SFO model to Datasets A to F of FOCUS (2006)", "object": "FOCUS_2006_SFO_ref_A_to_F", "class": [ "data.frame" ], "fields": [ "package", "M0", "k", "DT50", "DT90", "dataset" ], "rows": 50, "table": true, "tojson": true }, { "name": "focus_soil_moisture", "title": "FOCUS default values for soil moisture contents at field capacity, MWHC and 1/3 bar", "object": "focus_soil_moisture", "class": [ "matrix", "array" ], "fields": [ "pF1", "pF2", "pF2.5" ], "rows": 12, "table": true, "tojson": true }, { "name": "mccall81_245T", "title": "Datasets on aerobic soil metabolism of 2,4,5-T in six soils", "object": "mccall81_245T", "class": [ "data.frame" ], "fields": [ "name", "time", "value", "soil" ], "rows": 141, "table": true, "tojson": true }, { "name": "NAFTA_SOP_Appendix_B", "title": "Example datasets from the NAFTA SOP published 2015", "object": "NAFTA_SOP_2015", "class": [ "data.frame" ], "fields": [ "name", "time", "value" ], "rows": 14, "table": true, "tojson": true }, { "name": "NAFTA_SOP_Appendix_D", "title": "Example datasets from the NAFTA SOP published 2015", "object": "NAFTA_SOP_2015", "class": [ "data.frame" ], "fields": [ "name", "time", "value" ], "rows": 18, "table": true, "tojson": true }, { "name": "NAFTA_SOP_Attachment", "title": "Example datasets from Attachment 1 to the NAFTA SOP published 2015", "object": "NAFTA_SOP_Attachment", "class": [ "list" ], "fields": [], "table": false, "tojson": true }, { "name": "schaefer07_complex_case", "title": "Metabolism data set used for checking the software quality of KinGUI", "object": "schaefer07_complex_case", "class": [ "data.frame" ], "fields": [ "time", "parent", "A1", "B1", "C1", "A2" ], "rows": 8, "table": true, "tojson": true }, { "name": "schaefer07_complex_results", "title": "Metabolism data set used for checking the software quality of KinGUI", "object": "schaefer07_complex_case", "class": [ "data.frame" ], "fields": [ "compound", "parameter", "KinGUI", "ModelMaker", "deviation" ], "rows": 14, "table": true, "tojson": true }, { "name": "synthetic_data_for_UBA_2014", "title": "Synthetic datasets for one parent compound with two metabolites", "object": "synthetic_data_for_UBA_2014", "class": [ "list" ], "fields": [], "table": false, "tojson": false }, { "name": "test_data_from_UBA_2014", "title": "Three experimental datasets from two water sediment systems and one soil", "object": "test_data_from_UBA_2014", "class": [ "list" ], "fields": [], "table": false, "tojson": false } ], "_help": [ { "page": "Extract.mmkin", "title": "Subsetting method for mmkin objects", "topics": [ "[.mmkin" ] }, { "page": "add_err", "title": "Add normally distributed errors to simulated kinetic degradation data", "topics": [ "add_err" ] }, { "page": "AIC.mmkin", "title": "Calculate the AIC for a column of an mmkin object", "topics": [ "AIC.mmkin", "BIC.mmkin" ] }, { "page": "anova.saem.mmkin", "title": "Anova method for saem.mmkin objects", "topics": [ "anova.saem.mmkin" ] }, { "page": "aw", "title": "Calculate Akaike weights for model averaging", "topics": [ "aw", "aw.mixed.mmkin", "aw.mkinfit", "aw.mmkin", "aw.multistart" ] }, { "page": "CAKE_export", "title": "Export a list of datasets format to a CAKE study file", "topics": [ "CAKE_export" ] }, { "page": "check_failed", "title": "Check if fit within an mhmkin object failed", "topics": [ "check_failed" ] }, { "page": "confint.mkinfit", "title": "Confidence intervals for parameters of mkinfit objects", "topics": [ "confint.mkinfit" ] }, { "page": "create_deg_func", "title": "Create degradation functions for known analytical solutions", "topics": [ "create_deg_func" ] }, { "page": "D24_2014", "title": "Aerobic soil degradation data on 2,4-D from the EU assessment in 2014", "topics": [ "D24_2014" ] }, { "page": "DFOP.solution", "title": "Double First-Order in Parallel kinetics", "concept": [ "parent solutions" ], "topics": [ "DFOP.solution" ] }, { "page": "dimethenamid_2018", "title": "Aerobic soil degradation data on dimethenamid and dimethenamid-P from the EU assessment in 2018", "topics": [ "dimethenamid_2018" ] }, { "page": "ds_mixed", "title": "Synthetic data for hierarchical kinetic degradation models", "topics": [ "ds_dfop", "ds_dfop_sfo", "ds_fomc", "ds_hs", "ds_mixed", "ds_sfo" ] }, { "page": "endpoints", "title": "Function to calculate endpoints for further use from kinetic models fitted with mkinfit", "topics": [ "endpoints" ] }, { "page": "experimental_data_for_UBA", "title": "Experimental datasets used for development and testing of error models", "topics": [ "experimental_data_for_UBA_2019" ] }, { "page": "f_time_norm_focus", "title": "Normalisation factors for aerobic soil degradation according to FOCUS guidance", "topics": [ "f_time_norm_focus", "f_time_norm_focus.mkindsg", "f_time_norm_focus.numeric" ] }, { "page": "FOCUS_2006_datasets", "title": "Datasets A to F from the FOCUS Kinetics report from 2006", "topics": [ "FOCUS_2006_A", "FOCUS_2006_B", "FOCUS_2006_C", "FOCUS_2006_D", "FOCUS_2006_E", "FOCUS_2006_F" ] }, { "page": "FOCUS_2006_DFOP_ref_A_to_B", "title": "Results of fitting the DFOP model to Datasets A to B of FOCUS (2006)", "topics": [ "FOCUS_2006_DFOP_ref_A_to_B" ] }, { "page": "FOCUS_2006_FOMC_ref_A_to_F", "title": "Results of fitting the FOMC model to Datasets A to F of FOCUS (2006)", "topics": [ "FOCUS_2006_FOMC_ref_A_to_F" ] }, { "page": "FOCUS_2006_HS_ref_A_to_F", "title": "Results of fitting the HS model to Datasets A to F of FOCUS (2006)", "topics": [ "FOCUS_2006_HS_ref_A_to_F" ] }, { "page": "FOCUS_2006_SFO_ref_A_to_F", "title": "Results of fitting the SFO model to Datasets A to F of FOCUS (2006)", "topics": [ "FOCUS_2006_SFO_ref_A_to_F" ] }, { "page": "focus_soil_moisture", "title": "FOCUS default values for soil moisture contents at field capacity, MWHC and 1/3 bar", "topics": [ "focus_soil_moisture" ] }, { "page": "FOMC.solution", "title": "First-Order Multi-Compartment kinetics", "concept": [ "parent solutions" ], "topics": [ "FOMC.solution" ] }, { "page": "get_deg_func", "title": "Retrieve a degradation function from the mmkin namespace", "topics": [ "get_deg_func" ] }, { "page": "hierarchical_kinetics", "title": "Hierarchical kinetics template", "topics": [ "hierarchical_kinetics" ] }, { "page": "HS.solution", "title": "Hockey-Stick kinetics", "concept": [ "parent solutions" ], "topics": [ "HS.solution" ] }, { "page": "illparms", "title": "Method to get the names of ill-defined parameters", "topics": [ "illparms", "illparms.mhmkin", "illparms.mkinfit", "illparms.mmkin", "illparms.saem.mmkin", "print.illparms.mhmkin", "print.illparms.mkinfit", "print.illparms.mmkin", "print.illparms.saem.mmkin" ] }, { "page": "ilr", "title": "Function to perform isometric log-ratio transformation", "topics": [ "ilr", "invilr" ] }, { "page": "intervals.saem.mmkin", "title": "Confidence intervals for parameters in saem.mmkin objects", "topics": [ "intervals.saem.mmkin" ] }, { "page": "IORE.solution", "title": "Indeterminate order rate equation kinetics", "concept": [ "parent solutions" ], "topics": [ "IORE.solution" ] }, { "page": "llhist", "title": "Plot the distribution of log likelihoods from multistart objects", "topics": [ "llhist" ] }, { "page": "loftest", "title": "Lack-of-fit test for models fitted to data with replicates", "topics": [ "loftest", "loftest.mkinfit" ] }, { "page": "logistic.solution", "title": "Logistic kinetics", "concept": [ "parent solutions" ], "topics": [ "logistic.solution" ] }, { "page": "logLik.mkinfit", "title": "Calculated the log-likelihood of a fitted mkinfit object", "topics": [ "logLik.mkinfit" ] }, { "page": "logLik.saem.mmkin", "title": "logLik method for saem.mmkin objects", "topics": [ "logLik.saem.mmkin" ] }, { "page": "lrtest.mkinfit", "title": "Likelihood ratio test for mkinfit models", "topics": [ "lrtest.mkinfit", "lrtest.mmkin" ] }, { "page": "max_twa_parent", "title": "Function to calculate maximum time weighted average concentrations from kinetic models fitted with mkinfit", "topics": [ "max_twa_dfop", "max_twa_fomc", "max_twa_hs", "max_twa_parent", "max_twa_sfo" ] }, { "page": "mccall81_245T", "title": "Datasets on aerobic soil metabolism of 2,4,5-T in six soils", "topics": [ "mccall81_245T" ] }, { "page": "mean_degparms", "title": "Calculate mean degradation parameters for an mmkin row object", "topics": [ "mean_degparms" ] }, { "page": "mhmkin", "title": "Fit nonlinear mixed-effects models built from one or more kinetic degradation models and one or more error models", "topics": [ "mhmkin", "mhmkin.list", "mhmkin.mmkin", "print.mhmkin", "[.mhmkin" ] }, { "page": "mixed", "title": "Create a mixed effects model from an mmkin row object", "topics": [ "mixed", "mixed.mmkin", "print.mixed.mmkin" ] }, { "page": "mkin_long_to_wide", "title": "Convert a dataframe from long to wide format", "topics": [ "mkin_long_to_wide" ] }, { "page": "mkin_wide_to_long", "title": "Convert a dataframe with observations over time into long format", "topics": [ "mkin_wide_to_long" ] }, { "page": "mkinds", "title": "A dataset class for mkin", "topics": [ "mkinds", "print.mkinds" ] }, { "page": "mkindsg", "title": "A class for dataset groups for mkin", "topics": [ "mkindsg", "print.mkindsg" ] }, { "page": "mkinerrmin", "title": "Calculate the minimum error to assume in order to pass the variance test", "topics": [ "mkinerrmin" ] }, { "page": "mkinerrplot", "title": "Function to plot squared residuals and the error model for an mkin object", "topics": [ "mkinerrplot" ] }, { "page": "mkinfit", "title": "Fit a kinetic model to data with one or more state variables", "topics": [ "mkinfit" ] }, { "page": "mkinmod", "title": "Function to set up a kinetic model with one or more state variables", "topics": [ "mkinmod", "mkinsub", "print.mkinmod" ] }, { "page": "mkinparplot", "title": "Function to plot the confidence intervals obtained using mkinfit", "topics": [ "mkinparplot" ] }, { "page": "mkinplot", "title": "Plot the observed data and the fitted model of an mkinfit object", "topics": [ "mkinplot" ] }, { "page": "mkinpredict", "title": "Produce predictions from a kinetic model using specific parameters", "topics": [ "mkinpredict", "mkinpredict.mkinfit", "mkinpredict.mkinmod" ] }, { "page": "mkinresplot", "title": "Function to plot residuals stored in an mkin object", "topics": [ "mkinresplot" ] }, { "page": "mmkin", "title": "Fit one or more kinetic models with one or more state variables to one or more datasets", "topics": [ "mmkin", "print.mmkin" ] }, { "page": "multistart", "title": "Perform a hierarchical model fit with multiple starting values", "topics": [ "best", "best.default", "multistart", "multistart.saem.mmkin", "print.multistart", "which.best", "which.best.default" ] }, { "page": "nafta", "title": "Evaluate parent kinetics using the NAFTA guidance", "topics": [ "nafta", "print.nafta" ] }, { "page": "NAFTA_SOP_2015", "title": "Example datasets from the NAFTA SOP published 2015", "topics": [ "NAFTA_SOP_Appendix_B", "NAFTA_SOP_Appendix_D" ] }, { "page": "NAFTA_SOP_Attachment", "title": "Example datasets from Attachment 1 to the NAFTA SOP published 2015", "topics": [ "NAFTA_SOP_Attachment" ] }, { "page": "nlme", "title": "Helper functions to create nlme models from mmkin row objects", "topics": [ "nlme_data", "nlme_function" ] }, { "page": "nlme.mmkin", "title": "Create an nlme model for an mmkin row object", "topics": [ "nlme.mmkin", "print.nlme.mmkin", "update.nlme.mmkin" ] }, { "page": "nobs.mkinfit", "title": "Number of observations on which an mkinfit object was fitted", "topics": [ "nobs.mkinfit" ] }, { "page": "parms", "title": "Extract model parameters", "topics": [ "parms", "parms.mkinfit", "parms.mmkin", "parms.multistart", "parms.saem.mmkin" ] }, { "page": "parplot", "title": "Plot parameter variability of multistart objects", "topics": [ "parplot", "parplot.multistart.saem.mmkin" ] }, { "page": "plot.mixed.mmkin", "title": "Plot predictions from a fitted nonlinear mixed model obtained via an mmkin row object", "topics": [ "plot.mixed.mmkin" ] }, { "page": "plot.mkinfit", "title": "Plot the observed data and the fitted model of an mkinfit object", "topics": [ "plot.mkinfit", "plot_err", "plot_res", "plot_sep" ] }, { "page": "plot.mmkin", "title": "Plot model fits (observed and fitted) and the residuals for a row or column of an mmkin object", "topics": [ "plot.mmkin" ] }, { "page": "plot.nafta", "title": "Plot the results of the three models used in the NAFTA scheme.", "topics": [ "plot.nafta" ] }, { "page": "read_spreadsheet", "title": "Read datasets and relevant meta information from a spreadsheet file", "topics": [ "read_spreadsheet" ] }, { "page": "residuals.mkinfit", "title": "Extract residuals from an mkinfit model", "topics": [ "residuals.mkinfit" ] }, { "page": "saem", "title": "Fit nonlinear mixed models with SAEM", "topics": [ "print.saem.mmkin", "saem", "saem.mmkin", "saemix_data", "saemix_model" ] }, { "page": "schaefer07_complex_case", "title": "Metabolism data set used for checking the software quality of KinGUI", "topics": [ "schaefer07_complex_case", "schaefer07_complex_results" ] }, { "page": "set_nd_nq", "title": "Set non-detects and unquantified values in residue series without replicates", "topics": [ "set_nd_nq", "set_nd_nq_focus" ] }, { "page": "SFO.solution", "title": "Single First-Order kinetics", "concept": [ "parent solutions" ], "topics": [ "SFO.solution" ] }, { "page": "SFORB.solution", "title": "Single First-Order Reversible Binding kinetics", "concept": [ "parent solutions" ], "topics": [ "SFORB.solution" ] }, { "page": "sigma_twocomp", "title": "Two-component error model", "topics": [ "sigma_twocomp" ] }, { "page": "status", "title": "Method to get status information for fit array objects", "topics": [ "print.status.mhmkin", "print.status.mmkin", "status", "status.mhmkin", "status.mmkin" ] }, { "page": "summary_listing", "title": "Display the output of a summary function according to the output format", "topics": [ "html_listing", "summary_listing", "tex_listing" ] }, { "page": "summary.mkinfit", "title": "Summary method for class \"mkinfit\"", "topics": [ "print.summary.mkinfit", "summary.mkinfit" ] }, { "page": "summary.mmkin", "title": "Summary method for class \"mmkin\"", "topics": [ "print.summary.mmkin", "summary.mmkin" ] }, { "page": "summary.nlme.mmkin", "title": "Summary method for class \"nlme.mmkin\"", "topics": [ "print.summary.nlme.mmkin", "summary.nlme.mmkin" ] }, { "page": "summary.saem.mmkin", "title": "Summary method for class \"saem.mmkin\"", "topics": [ "print.summary.saem.mmkin", "summary.saem.mmkin" ] }, { "page": "synthetic_data_for_UBA_2014", "title": "Synthetic datasets for one parent compound with two metabolites", "topics": [ "synthetic_data_for_UBA_2014" ] }, { "page": "test_data_from_UBA_2014", "title": "Three experimental datasets from two water sediment systems and one soil", "topics": [ "test_data_from_UBA_2014" ] }, { "page": "transform_odeparms", "title": "Functions to transform and backtransform kinetic parameters for fitting", "topics": [ "backtransform_odeparms", "transform_odeparms" ] }, { "page": "update.mkinfit", "title": "Update an mkinfit model with different arguments", "topics": [ "update.mkinfit" ] } ], "_readme": "https://github.com/jranke/mkin/raw/HEAD/README.md", "_rundeps": [ "callr", "cli", "cpp11", "desc", "deSolve", "farver", "ggplot2", "glue", "gridExtra", "gtable", "inline", "isoband", "labeling", "lattice", "lifecycle", "lmtest", "MASS", "mclust", "nlme", "npde", "numDeriv", "pkgbuild", "processx", "ps", "R6", "RColorBrewer", "rlang", "S7", "saemix", "scales", "vctrs", "viridisLite", "withr", "zoo" ], "_vignettes": [ { "source": "twa.rmd", "filename": "twa.html", "title": "Calculation of time weighted average concentrations with mkin", "author": "Johannes Ranke", "engine": "knitr::rmarkdown", "headings": [], "created": "2017-03-04 08:58:00", "modified": "2021-02-15 14:20:53", "commits": 5 }, { "source": "FOCUS_D.rmd", "filename": "FOCUS_D.html", "title": "Example evaluation of FOCUS Example Dataset D", "author": "Johannes Ranke", "engine": "knitr::rmarkdown", "headings": [], "created": "2020-05-13 14:20:23", "modified": "2021-02-15 14:20:53", "commits": 2 }, { "source": "FOCUS_L.rmd", "filename": "FOCUS_L.html", "title": "Example evaluation of FOCUS Laboratory Data L1 to L3", "author": "Johannes Ranke", "engine": "knitr::rmarkdown", "headings": [ "Laboratory Data L1", "Laboratory Data L2", "SFO fit for L2", "FOMC fit for L2", "DFOP fit for L2", "Laboratory Data L3", "Fit multiple models", "Accessing mmkin objects", "Laboratory Data L4", "References" ], "created": "2020-05-13 14:20:23", "modified": "2023-05-19 15:10:16", "commits": 5 }, { "source": "mkin.rmd", "filename": "mkin.html", "title": "Short introduction to mkin", "author": "Johannes Ranke", "engine": "knitr::rmarkdown", "headings": [ "Abstract", "Background", "Derived software tools", "Unique features", "Internal parameter transformations", "Confidence intervals based on transformed parameters", "Parameter t-test based on untransformed parameters", "References" ], "created": "2020-05-13 14:20:23", "modified": "2023-05-19 15:10:16", "commits": 5 }, { "source": "dmta_parent_2022_prebuilt.rnw", "filename": "dmta_parent_2022_prebuilt.pdf", "title": "Testing hierarchical parent degradation kinetics with residue data on dimethenamid and dimethenamid-P", "engine": "utils::Sweave", "headings": [], "created": "2023-02-13 04:19:08", "modified": "2023-02-17 08:30:37", "commits": 2 }, { "source": "cyan_pathway_2022_prebuilt.rnw", "filename": "cyan_pathway_2022_prebuilt.pdf", "title": "Testing hierarchical pathway kinetics with residue data on cyantraniliprole", "engine": "utils::Sweave", "headings": [], "created": "2025-02-14 06:19:15", "modified": "2025-02-14 06:19:15", "commits": 1 }, { "source": "dmta_pathway_2022_prebuilt.rnw", "filename": "dmta_pathway_2022_prebuilt.pdf", "title": "Testing hierarchical pathway kinetics with residue data on dimethenamid and dimethenamid-P", "engine": "utils::Sweave", "headings": [], "created": "2023-02-13 04:19:08", "modified": "2023-02-17 13:44:29", "commits": 2 } ], "_score": 7.5412796271827816, "_indexed": true, "_nocasepkg": "mkin", "_universes": [ "jranke" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.2.10", "date": "2026-05-27T07:53:17.000Z", "distro": "noble", "commit": "1519d761ebb8c10350402b294907102d960b15a2", "fileid": "978f535d55491439068e3f21468ecc16aabc941af2ccfd44ed2da98767256307", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/jranke/actions/runs/26498090024" }, { "r": "4.6.0", "os": "linux", "version": "1.2.10", "date": "2026-05-27T07:52:48.000Z", "distro": "noble", "commit": "1519d761ebb8c10350402b294907102d960b15a2", "fileid": "8cd317fef39f8a6c18aa4bbb20acc96e7ebad9bd206033dfb00cb255b78d78c9", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/jranke/actions/runs/26498090024" }, { "r": "4.5.3", "os": "mac", "version": "1.2.10", "date": "2026-05-27T07:52:19.000Z", "commit": "1519d761ebb8c10350402b294907102d960b15a2", "fileid": "edaf427b83cdafd1582b046de42c600d28c9bfadb10467612af326eb7bf8e2a2", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/jranke/actions/runs/26498090024" }, { "r": "4.6.0", "os": "mac", "version": "1.2.10", "date": "2026-05-27T07:52:38.000Z", "commit": "1519d761ebb8c10350402b294907102d960b15a2", "fileid": "0597b9a7007f0e25e1998c61839bcd9dfa755a82dd38ad226edb0401b22047a6", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/jranke/actions/runs/26498090024" }, { "r": "4.6.0", "os": "wasm", "version": "1.2.10", "date": "2026-05-27T07:52:53.000Z", "commit": "1519d761ebb8c10350402b294907102d960b15a2", "fileid": "ee6d12e95043dad0892595af0c113391af8529a383a76b8e2dd44c8e6802b963", "status": "success", "buildurl": "https://github.com/r-universe/jranke/actions/runs/26498090024" }, { "r": "4.7.0", "os": "win", "version": "1.2.10", "date": "2026-05-27T07:51:35.000Z", "commit": "1519d761ebb8c10350402b294907102d960b15a2", "fileid": "ece72f4d90084b8fa540946ad681690439dccd8e8d31ce2e2cf7840aba2ee63b", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/jranke/actions/runs/26498090024" }, { "r": "4.5.3", "os": "win", "version": "1.2.10", "date": "2026-05-27T07:51:47.000Z", "commit": "1519d761ebb8c10350402b294907102d960b15a2", "fileid": "c0a59d6a8f2919adf6b0d65f581147572166a84e5622829f2759485c69188bb5", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/jranke/actions/runs/26498090024" }, { "r": "4.6.0", "os": "win", "version": "1.2.10", "date": "2026-05-27T07:52:19.000Z", "commit": "1519d761ebb8c10350402b294907102d960b15a2", "fileid": "e398ea62b56b70d1d7f6ac07668e91470db3ca48edc9058b03ff0421c6b4b444", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/jranke/actions/runs/26498090024" } ] }