{ "_id": "6a104823acfb0bcc41c9f211", "Package": "cvasi", "Type": "Package", "Title": "Calibration, Validation, and Simulation of TKTD Models", "Version": "1.5.1", "Authors@R": "c(\nperson(\"Nils\", \"Kehrein\", email=\"nils.kehrein@gmail.com\", role=c(\"aut\", \"cre\")),\nperson(\"Dirk\", \"Nickisch\", role=\"aut\"),\nperson(\"Peter\", \"Vermeiren\", role=\"aut\"),\nperson(\"Torben\", \"Wittwer\", role=\"ctb\"),\nperson(\"Johannes\", \"Witt\", role=\"ctb\"),\nperson(\"Andre\", \"Gergs\", role=\"ctb\")\n)", "Description": "Eases the use of ecotoxicological effect models. Can\nsimulate common toxicokinetic-toxicodynamic (TK/TD) models such\nas General Unified Threshold models of Survival (GUTS) and\nLemna. It can derive effects and effect profiles (EPx) from\nscenarios. It supports the use of 'tidyr' workflows employing\nthe pipe symbol. Time-consuming tasks can be parallelized.", "URL": "https://github.com/cvasi-tktd/cvasi", "BugReports": "https://github.com/cvasi-tktd/cvasi/issues", "License": "GPL (>= 3)", "Encoding": "UTF-8", "LazyData": "true", "RoxygenNote": "7.3.3", "Roxygen": "list(markdown = TRUE, roclets = c(\"collate\", \"namespace\",\n\"rd\", \"roxyglobals::global_roclet\"))", "Config/testthat/edition": "3", "Collate": "'batch.R' 'cache.R' 'class-CalibrationSet.R'\n'class-ExposureSeries.R' 'class-EffectScenario.R' 'sequence.R'\n'calibrate.R' 'class-ParameterSet.R' 'class-Transferable.R'\n'data.R' 'dose_response.R' 'effect.R' 'epx.R' 'explore_space.R'\n'fx.R' 'solver.R' 'man-lemna.R' 'model-lemna_setac.R'\n'model-magma.R' 'model-lemna_schmitt.R' 'fit_growth.R'\n'fit_tktd.R' 'get.R' 'get_param.R' 'get_tag.R' 'get_times.R'\n'globals.R' 'has.R' 'import_morse.R' 'import_toxswa.R' 'is.R'\n'lik_profile.R' 'log.R' 'man-deb.R' 'man-macrophytes.R'\n'model-algae.R' 'model-deb_abj.R' 'model-debtox.R'\n'model-deb_daphnia.R' 'model-guts.R' 'model-guts_red.R'\n'numerics.R' 'package.R' 'pll.R' 'plot.R' 'plotting.r' 'pull.R'\n'set.R' 'set_bounds.R' 'set_exposure.R' 'set_forcings.R'\n'set_init.R' 'set_param.R' 'set_times.R' 'set_transfer.R'\n'set_window.R' 'show.R' 'simulate.R' 'survival.R' 'tox_data.R'\n'utils-pipe.R'", "VignetteBuilder": "knitr", "Config/roxyglobals/filename": "globals.R", "Config/roxyglobals/unique": "FALSE", "Config/pak/sysreqs": "libicu-dev libssl-dev libudunits2-dev", "Repository": "https://cvasi-tktd.r-universe.dev", "Date/Publication": "2026-04-10 14:19:34 UTC", "RemoteUrl": "https://github.com/cvasi-tktd/cvasi", "RemoteRef": "HEAD", "RemoteSha": "4f9cbd39fe98351d15b77a5d34e8b5025bf0d55e", "NeedsCompilation": "yes", "Packaged": { "Date": "2026-05-10 09:15:10 UTC", "User": "root" }, "Author": "Nils Kehrein [aut, cre],\nDirk Nickisch [aut],\nPeter Vermeiren [aut],\nTorben Wittwer [ctb],\nJohannes Witt [ctb],\nAndre Gergs [ctb]", "Maintainer": "Nils Kehrein ", "MD5sum": "6379bce780948d211e233d73079990e9", "_user": "cvasi-tktd", "_type": "src", "_file": "cvasi_1.5.1.tar.gz", "_fileid": "e97bd96c1f4fda8a9f88be0bf7def24952d169542572807c78162bfabd8bf2b3", "_filesize": 1907788, "_sha256": "e97bd96c1f4fda8a9f88be0bf7def24952d169542572807c78162bfabd8bf2b3", "_created": "2026-05-10T09:15:10.000Z", "_published": "2026-05-22T12:12:19.480Z", "_distro": "noble", "_jobs": [ { "job": 77376862844, "time": 196, "config": "linux-devel-arm64", "r": "4.7.0", "check": "OK", "artifact": "6902602430" }, { "job": 77376869743, "time": 189, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "6902601764" }, { "job": 77376846607, "time": 204, "config": "linux-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "6902603155" }, { "job": 77376846592, "time": 186, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "6902601576" }, { "job": 77376846977, "time": 150, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "6902669983" }, { "job": 77376846739, "time": 313, "config": "macos-oldrel-x86_64", "r": "4.5.3", "check": "OK", "artifact": "6902648487" }, { "job": 77376846529, "time": 203, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "6902660927" }, { "job": 77376846337, "time": 620, "config": "macos-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "6902675670" }, { "job": 77376846123, "time": 281, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "6902584268" }, { "job": 77376845761, "time": 124, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7160169701" }, { "job": 77376869626, "time": 178, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "6902600822" }, { "job": 77376864617, "time": 178, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "6902600654" }, { "job": 77376865507, "time": 164, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "6902599528" } ], "_buildurl": "https://github.com/r-universe/cvasi-tktd/actions/runs/25624868463", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/cvasi-tktd/cvasi", "_commit": { "id": "4f9cbd39fe98351d15b77a5d34e8b5025bf0d55e", "author": "Nils Kehrein ", "committer": "Nils Kehrein ", "message": "vignettes recompiled\n", "time": 1775830774 }, "_maintainer": { "name": "Nils Kehrein", "email": "nils.kehrein@gmail.com", "login": "nkehrein", "uuid": 74192425 }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.5.0", "role": "Depends" }, { "package": "cli", "role": "Imports" }, { "package": "rlang", "role": "Imports" }, { "package": "stringr", "role": "Imports" }, { "package": "dplyr", "role": "Imports" }, { "package": "tibble", "role": "Imports" }, { "package": "purrr", "role": "Imports" }, { "package": "furrr", "role": "Imports" }, { "package": "tidyr", "role": "Imports" }, { "package": "magrittr", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "grid", "role": "Imports" }, { "package": "gridExtra", "role": "Imports" }, { "package": "ggplot2", "role": "Imports" }, { "package": "GGally", "role": "Imports" }, { "package": "deSolve", "role": "Imports" }, { "package": "lubridate", "role": "Imports" }, { "package": "units", "role": "Imports" }, { "package": "lifecycle", "role": "Imports" }, { "package": "future", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "lemna", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "roxyglobals", "role": "Suggests" }, { "package": "testthat", "role": "Suggests" }, { "package": "withr", "role": "Suggests" } ], "_owner": "cvasi-tktd", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-19", "n": 4 }, { "week": "2025-20", "n": 1 }, { "week": "2025-21", "n": 5 }, { "week": "2025-27", "n": 2 }, { "week": "2025-31", "n": 2 }, { "week": "2025-34", "n": 7 }, { "week": "2025-37", "n": 3 }, { "week": "2025-38", "n": 2 }, { "week": "2025-46", "n": 1 }, { "week": "2026-15", "n": 3 } ], "_tags": [ { "name": "v1.5.0", "date": "2025-09-11" }, { "name": "v1.5.1", "date": "2026-04-10" } ], "_topics": [ "ecotoxicology", "modeling", "simulation" ], "_stars": 5, "_contributors": [ { "user": "nkehrein", "count": 172, "uuid": 74192425 }, { "user": "dnickisch", "count": 12, "uuid": 138426261 }, { "user": "peter-vermeiren", "count": 3, "uuid": 63152615 }, { "user": "torden81", "count": 3, "uuid": 9078222 } ], "_userbio": { "uuid": 167879370, "type": "organization", "name": "cvasi-tktd" }, "_downloads": { "count": 587, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/cvasi" }, "_devurl": "https://github.com/cvasi-tktd/cvasi", "_searchresults": 13, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/cvasi.html", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_homeurl": "https://github.com/cvasi-tktd/cvasi", "_realowner": "cvasi-tktd", "_cranurl": true, "_releases": [ { "version": "0.10.4", "date": "2024-05-02" }, { "version": "0.10.5", "date": "2024-05-03" }, { "version": "1.1.0", "date": "2024-05-30" }, { "version": "1.1.3", "date": "2024-07-25" }, { "version": "1.2.0", "date": "2024-09-23" }, { "version": "1.3.1", "date": "2024-11-22" }, { "version": "1.4.0", "date": "2025-02-28" }, { "version": "1.5.0", "date": "2025-09-11" }, { "version": "1.5.1", "date": "2026-04-11" } ], "_exports": [ "%>%", "Algae_Simple", "Algae_TKTD", "Algae_Weber", "batch", "cache_controls", "calibrate", "CalibrationSet", "caliset", "ci_from_hessian", "DEB_abj", "DEB_Daphnia", "DEBtox", "diagnostics", "dose_response", "effect", "epx", "epx_mtw", "explore_space", "ExposureSeries", "fit_growth", "fit_tktd", "fx", "get_model", "get_model_name", "get_param", "get_tag", "get_times", "GUTS_RED_IT", "GUTS_RED_SD", "GUTS_SD", "import_morse", "import_swash", "import_toxswa", "is_deb", "is_DEB", "is_guts", "is_GUTS", "is_guts_it", "is_GUTS_IT", "is_guts_sd", "is_GUTS_SD", "is_lemna", "is_Lemna", "is_LemnaThreshold", "is_scenario", "Lemna_Schmitt", "Lemna_SchmittThold", "Lemna_SETAC", "lik_profile", "log_disable", "log_enable", "log_envir", "log_lik", "log_msg", "log_scenarios", "Magma", "morse", "Myrio", "Myrio_log", "no_exposure", "num_info", "parameter_set", "pll_debug", "plot_epx", "plot_lik_profile", "plot_param_space", "plot_ppc", "plot_scenario", "plot_sd", "pull_metadata", "SamX", "sequence", "set_bounds", "set_endpoints", "set_exposure", "set_forcings", "set_init", "set_moa", "set_mode_of_action", "set_noexposure", "set_notransfer", "set_nowindow", "set_param", "set_tag", "set_times", "set_transfer", "set_window", "simulate", "simulate_batch", "solver", "survival", "td2cs", "tox_data" ], "_datasets": [ { "name": "americamysis", "title": "A DEB abj scenario of Americamysis bahia", "object": "americamysis", "class": [ "DebAbj" ], "fields": [], "table": false, "tojson": false }, { "name": "dmagna", "title": "A DEBtox scenario of Daphnia magna", "object": "dmagna", "class": [ "DebTox" ], "fields": [], "table": false, "tojson": false }, { "name": "focusd1", "title": "A Lemna_SETAC scenario with variable environment", "object": "focusd1", "class": [ "LemnaSetac" ], "fields": [], "table": false, "tojson": false }, { "name": "metsulfuron", "title": "Lemna model fitted to _metsulfuron_ effect data", "object": "metsulfuron", "class": [ "LemnaSchmitt" ], "fields": [], "table": false, "tojson": false }, { "name": "minnow_it", "title": "A fitted GUTS-RED-IT scenario of the fathead minnow", "object": "minnow_it", "class": [ "GutsRedIt" ], "fields": [], "table": false, "tojson": false }, { "name": "minnow_sd", "title": "A fitted GUTS-RED-SD scenario of the fathead minnow", "object": "minnow_sd", "class": [ "GutsRedSd" ], "fields": [], "table": false, "tojson": false }, { "name": "ringtest_c", "title": "EFSA Ringtest Dataset C", "object": "ringtest_c", "class": [ "data.frame" ], "fields": [ "time", "Nsurv", "replicate", "conc" ], "rows": 30, "table": true, "tojson": true }, { "name": "ringtest_it", "title": "EFSA Ringtest Dataset A SD", "object": "ringtest_it", "class": [ "data.frame" ], "fields": [ "time", "Nsurv", "replicate", "conc" ], "rows": 42, "table": true, "tojson": true }, { "name": "ringtest_sd", "title": "EFSA Ringtest Dataset A SD", "object": "ringtest_sd", "class": [ "data.frame" ], "fields": [ "time", "Nsurv", "replicate", "conc" ], "rows": 42, "table": true, "tojson": true }, { "name": "rsubcapitata", "title": "A Weber scenario of algae exposed to isoproturon", "object": "rsubcapitata", "class": [ "AlgaeWeber" ], "fields": [], "table": false, "tojson": false }, { "name": "schmitt2013", "title": "A Lemna effect study data set with multiple treatment levels", "object": "schmitt2013", "class": [ "data.frame" ], "fields": [ "time", "obs", "trial", "conc" ], "rows": 56, "table": true, "tojson": true } ], "_help": [ { "page": "Algae_Simple", "title": "Simple algae model without environment (Rendal et al. 2023)", "concept": [ "algae models" ], "topics": [ "AlgaeSimple-class", "AlgaeSimpleScenario-class", "Algae_Simple" ] }, { "page": "Algae_TKTD", "title": "Algae model variant (Weber et al. 2012) with scaled damage", "concept": [ "algae models" ], "topics": [ "AlgaeTKTD-class", "AlgaeTKTDScenario-class", "Algae_TKTD" ] }, { "page": "Algae_Weber", "title": "Algae model, _SAM-X_ (Weber et al. 2012)", "concept": [ "algae models" ], "topics": [ "AlgaeWeber-class", "AlgaeWeberScenario-class", "Algae_Weber", "SAM-X", "SamX" ] }, { "page": "Algae-models", "title": "Algae models", "concept": [ "algae models", "models" ], "topics": [ "Algae-class", "Algae-models" ] }, { "page": "americamysis", "title": "A DEB abj scenario of Americamysis bahia", "topics": [ "americamysis" ] }, { "page": "batch", "title": "Batch simulation of multiple exposure levels", "topics": [ "batch" ] }, { "page": "cache_controls", "title": "Cache control simulations", "topics": [ "cache_controls" ] }, { "page": "calibrate", "title": "Fit model parameters to experimental data", "topics": [ "calibrate", "calibrate,CalibrationSet-method", "calibrate,EffectScenario-method", "calibrate,list-method", "calibrate,ScenarioSequence-method" ] }, { "page": "CalibrationSet", "title": "Calibration set", "topics": [ "CalibrationSet", "CalibrationSet-class", "caliset" ] }, { "page": "ci_from_hessian", "title": "Parameter confidence intervals from fit", "topics": [ "ci_from_hessian" ] }, { "page": "DEB_abj", "title": "DEB_abj", "concept": [ "DEB models" ], "topics": [ "DebAbj-class", "DEB_abj" ] }, { "page": "DEB-models", "title": "Dynamic Energy Budget (DEB) models", "concept": [ "DEB models", "models" ], "topics": [ "Deb-class", "DEB-models" ] }, { "page": "DEBtox", "title": "DEBtox model", "concept": [ "DEB models" ], "topics": [ "DebDaphnia-class", "DEBtox", "DebTox-class", "DEBtox2019", "DEB_Daphnia" ] }, { "page": "diagnostics", "title": "Diagnostics of solvers", "topics": [ "diagnostics", "diagnostics.cvasi_simulate", "diagnostics.default" ] }, { "page": "dmagna", "title": "A DEBtox scenario of Daphnia magna", "topics": [ "dmagna" ] }, { "page": "dose_response", "title": "Calculate a dose response curve", "topics": [ "dose_response" ] }, { "page": "effect", "title": "Effect level", "topics": [ "effect", "effect,EffectScenario-method", "effect,ScenarioSequence-method" ] }, { "page": "epx", "title": "Effect profiles (EPx values)", "topics": [ "epx" ] }, { "page": "epx_mtw", "title": "Calculate EPx values for a series of moving time window", "topics": [ "epx_mtw" ] }, { "page": "explore_space", "title": "Explore parameter space", "topics": [ "explore_space" ] }, { "page": "ExposureSeries", "title": "Exposure time-series", "topics": [ "ExposureSeries", "ExposureSeries-class", "NoExposureSeries-class" ] }, { "page": "fit_growth", "title": "Fit growth parameters", "topics": [ "fit_growth", "fit_growth,ANY,ANY-method", "fit_growth,EffectScenario,ANY-method", "fit_growth,LemnaSchmitt,missing-method", "fit_growth,LemnaSetac,missing-method", "fit_growth,list,missing-method", "fit_growth,Magma,missing-method", "fit_growth,ScenarioSequence,ANY-method" ] }, { "page": "fit_tktd", "title": "Fit TK/TD parameters", "topics": [ "fit_tktd", "fit_tktd,ANY,ANY-method", "fit_tktd,CalibrationSet,ANY-method", "fit_tktd,CalibrationSet,missing-method", "fit_tktd,cvasi_fit,ANY-method", "fit_tktd,EffectScenario,ANY-method", "fit_tktd,LemnaSchmitt,missing-method", "fit_tktd,LemnaSetac,missing-method", "fit_tktd,list,missing-method", "fit_tktd,Magma,missing-method", "fit_tktd,ScenarioSequence,ANY-method" ] }, { "page": "focusd1", "title": "A Lemna_SETAC scenario with variable environment", "topics": [ "focusd1" ] }, { "page": "fx", "title": "Generic to calculate effects for a particular scenario", "topics": [ "fx", "fx,Algae-method", "fx,ANY-method", "fx,GutsIt-method", "fx,GutsRedIt-method", "fx,GutsRedSd-method", "fx,GutsSd-method", "fx,Lemna-method", "fx,Magma-method", "fx,ScenarioSequence-method" ] }, { "page": "get_model", "title": "Get model name", "topics": [ "get_model", "get_model,ANY-method", "get_model,EffectScenario-method", "get_model,list-method", "get_model,ParameterSet-method", "get_model_name" ] }, { "page": "get_param", "title": "Get scenario parameters", "topics": [ "get_param", "get_param,ANY-method", "get_param,EffectScenario-method", "get_param,list-method", "get_param,ParameterSet-method", "get_param,ScenarioSequence-method" ] }, { "page": "get_tag", "title": "Get scenario tag", "topics": [ "get_tag", "get_tag,ANY-method", "get_tag,EffectScenario-method", "get_tag,list-method", "get_tag,ParameterSet-method", "get_tag,ScenarioSequence-method" ] }, { "page": "get_times", "title": "Get output times", "topics": [ "get_times", "get_times,ANY-method", "get_times,EffectScenario-method", "get_times,list-method", "get_times,ScenarioSequence-method" ] }, { "page": "GUTS_IT", "title": "GUTS-IT scenario", "concept": [ "GUTS models" ], "topics": [ "GUTS-IT", "GutsIt-class", "GUTS_IT" ] }, { "page": "GUTS_RED_IT", "title": "GUTS-RED-IT scenario", "concept": [ "GUTS-RED models" ], "topics": [ "GUTS-RED-IT", "GutsRedIt-class", "GUTS_RED_IT" ] }, { "page": "GUTS_RED_SD", "title": "GUTS-RED-SD scenario", "concept": [ "GUTS-RED models" ], "topics": [ "GUTS-RED-SD", "GutsRedSd-class", "GUTS_RED_SD" ] }, { "page": "GUTS_SD", "title": "GUTS-SD scenario", "concept": [ "GUTS models" ], "topics": [ "Guts-class", "GUTS-SD", "GutsSd-class", "GUTS_SD" ] }, { "page": "GUTS-RED-models", "title": "GUTS-RED models", "concept": [ "GUTS-RED models", "models" ], "topics": [ "GUTS-RED-models" ] }, { "page": "import_morse", "title": "Import 'morse' model parameters", "topics": [ "import_morse", "morse" ] }, { "page": "import_swash", "title": "SWASH project exposure profile import", "topics": [ "import_swash" ] }, { "page": "import_toxswa", "title": "Import _TOXSWA_ exposure series", "topics": [ "import_toxswa" ] }, { "page": "is_deb", "title": "Test if argument is a DEB scenario", "topics": [ "is_DEB", "is_deb" ] }, { "page": "is_guts", "title": "Test if argument is a GUTS scenario", "topics": [ "is_GUTS", "is_guts", "is_GUTS_IT", "is_guts_it", "is_GUTS_SD", "is_guts_sd" ] }, { "page": "is_lemna", "title": "Test if argument is a Lemna scenario", "topics": [ "is_Lemna", "is_lemna" ] }, { "page": "is_LemnaThreshold", "title": "Test if argument is a LemnaThreshold scenario", "topics": [ "is_LemnaThreshold" ] }, { "page": "is_scenario", "title": "Test if argument is an effect scenario", "topics": [ "is_scenario" ] }, { "page": "Lemna_Schmitt", "title": "Lemna model (Schmitt et al. 2013)", "concept": [ "Lemna models", "macrophyte models" ], "topics": [ "LemnaSchmitt-class", "LemnaSchmittScenario-class", "Lemna_Schmitt", "Lemna_SchmittThold" ] }, { "page": "Lemna_SETAC", "title": "Lemna model v1.3 (Klein et al. 2021)", "concept": [ "Lemna models", "macrophyte models" ], "topics": [ "LemnaSetac-class", "LemnaSetacScenario-class", "Lemna_SETAC" ] }, { "page": "Lemna-models", "title": "Lemna models", "concept": [ "Lemna models", "models" ], "topics": [ "Lemna-class", "Lemna-models" ] }, { "page": "lik_profile", "title": "Likelihood profiling", "topics": [ "lik_profile" ] }, { "page": "log_enable", "title": "Start and stop logging", "topics": [ "log_disable", "log_enable" ] }, { "page": "log_envir", "title": "Log R environment properties", "topics": [ "log_envir" ] }, { "page": "log_lik", "title": "Calculate log likelihood", "topics": [ "log_lik" ] }, { "page": "log_msg", "title": "Add a log message", "topics": [ "log_msg" ] }, { "page": "log_scenarios", "title": "Log scenario properties", "topics": [ "log_scenarios" ] }, { "page": "Macrophyte-models", "title": "Macrophyte models", "concept": [ "macrophyte models", "models" ], "topics": [ "Macrophyte-models" ] }, { "page": "Magma", "title": "Magma model (Witt et al., submitted)", "concept": [ "macrophyte models" ], "topics": [ "Magma", "Myrio", "Myrio_log" ] }, { "page": "Magma-class", "title": "Magma scenario class", "topics": [ "Magma-class" ] }, { "page": "metsulfuron", "title": "Lemna model fitted to _metsulfuron_ effect data", "topics": [ "metsulfuron" ] }, { "page": "minnow_it", "title": "A fitted GUTS-RED-IT scenario of the fathead minnow", "topics": [ "minnow_it" ] }, { "page": "minnow_sd", "title": "A fitted GUTS-RED-SD scenario of the fathead minnow", "topics": [ "minnow_sd" ] }, { "page": "no_exposure", "title": "Zero exposure", "topics": [ "no_exposure" ] }, { "page": "num_info", "title": "Print information about numerical solver result", "topics": [ "num_info", "num_info.cvasi_fit", "num_info.cvasi_simulate", "num_info.default" ] }, { "page": "parameter_set", "title": "Set of model parameters", "topics": [ "ParameterSet-class", "parameter_set", "parameter_set-class" ] }, { "page": "pll_debug", "title": "Disable parallelization for debugging", "topics": [ "pll_debug" ] }, { "page": "plot", "title": "S3 plotting functions", "topics": [ "plot", "plot.cvasi_drc", "plot.cvasi_simulate", "plot.lik_profile", "plot_lik_profile" ] }, { "page": "plot_epx", "title": "Plot EPx values", "topics": [ "plot_epx" ] }, { "page": "plot_ppc", "title": "Creates a PPC plot for a single dataset", "topics": [ "plot_ppc" ] }, { "page": "plot_ppc_combi", "title": "Create PPC plot for one or more datasets", "topics": [ "plot_ppc_combi" ] }, { "page": "plot_scenario", "title": "Creates a prediction plot for one effect scenario", "topics": [ "plot_scenario" ] }, { "page": "plot_sd", "title": "Creates plot of model results (uncertainties optional)", "topics": [ "plot_sd" ] }, { "page": "plot.param_space", "title": "Plot profiled parameter space", "topics": [ "plot.param_space", "plot_param_space" ] }, { "page": "pull_metadata", "title": "Pull metadata from scenarios", "topics": [ "pull_metadata" ] }, { "page": "ringtest_c", "title": "EFSA Ringtest Dataset C", "topics": [ "ringtest_c" ] }, { "page": "ringtest_it", "title": "EFSA Ringtest Dataset A SD", "topics": [ "ringtest_it" ] }, { "page": "ringtest_sd", "title": "EFSA Ringtest Dataset A SD", "topics": [ "ringtest_sd" ] }, { "page": "rsubcapitata", "title": "A Weber scenario of algae exposed to isoproturon", "topics": [ "rsubcapitata" ] }, { "page": "Scenarios", "title": "Effect scenario classes", "concept": [ "scenario-related" ], "topics": [ "EffectScenario-class", "scenario", "Scenarios", "scenarios" ] }, { "page": "schmitt2013", "title": "A Lemna effect study data set with multiple treatment levels", "topics": [ "schmitt2013" ] }, { "page": "sequence", "title": "Sequence of scenarios", "topics": [ "ScenarioSequence-class", "sequence" ] }, { "page": "sequence.extract", "title": "Extract and replace elements of a sequence", "topics": [ "length,ScenarioSequence-method", "sequence.extract", "[,ScenarioSequence,numeric,missing,missing-method", "[[,ScenarioSequence,numeric-method", "[[<-,ScenarioSequence,numeric,ANY,ANY-method", "[[<-,ScenarioSequence,numeric,missing,EffectScenario-method" ] }, { "page": "set_bounds", "title": "Set boundaries of model parameters", "topics": [ "set_bounds", "set_bounds,CalibrationSet,list-method", "set_bounds,EffectScenario,list-method", "set_bounds,list,list-method", "set_bounds,ScenarioSequence,list-method" ] }, { "page": "set_endpoints", "title": "Set effect endpoints", "topics": [ "set_endpoints" ] }, { "page": "set_exposure", "title": "Set exposure time-series", "topics": [ "set_exposure", "set_exposure,ANY,ANY-method", "set_exposure,EffectScenario,data.frame-method", "set_exposure,EffectScenario,ExposureSeries-method", "set_exposure,EffectScenario,list-method", "set_exposure,EffectScenario,NoExposureSeries-method", "set_exposure,list,ANY-method", "set_exposure,list,list-method", "set_exposure,ScenarioSequence,ANY-method" ] }, { "page": "set_forcings", "title": "Set time-dependent parameters", "topics": [ "set_forcings", "set_forcings,EffectScenario-method", "set_forcings,list-method" ] }, { "page": "set_init", "title": "Set initial state", "topics": [ "set_init", "set_init,EffectScenario-method", "set_init,ScenarioSequence-method", "set_init,vector-method" ] }, { "page": "set_mode_of_action", "title": "Set mode of action", "topics": [ "set_moa", "set_mode_of_action" ] }, { "page": "set_noexposure", "title": "Set zero exposure", "topics": [ "set_noexposure" ] }, { "page": "set_param", "title": "Set scenario parameters", "topics": [ "set_param", "set_param,CalibrationSet,ANY-method", "set_param,EffectScenario,ParameterSet-method", "set_param,EffectScenario,vector-method", "set_param,list,ParameterSet-method", "set_param,list,vector-method", "set_param,ScenarioSequence,ANY-method" ] }, { "page": "set_tag", "title": "Set a tag", "topics": [ "set_tag" ] }, { "page": "set_times", "title": "Set output times", "topics": [ "set_times", "set_times,ANY-method", "set_times,EffectScenario-method", "set_times,list-method", "set_times,ScenarioSequence-method" ] }, { "page": "set_transfer", "title": "Set transfer events", "topics": [ "set_notransfer", "set_transfer", "set_transfer,ANY-method", "set_transfer,Transferable-method" ] }, { "page": "set_window", "title": "Set window length", "topics": [ "set_nowindow", "set_window" ] }, { "page": "simulate", "title": "Simulate an effect scenario", "topics": [ "simulate", "simulate,EffectScenario-method", "simulate,ScenarioSequence-method", "simulate,SimulationBatch-method", "simulate,Transferable-method" ] }, { "page": "simulate_batch", "title": "Batch simulation using multiple exposure series", "topics": [ "simulate_batch" ] }, { "page": "solver", "title": "Calls ODE solver for a particular model", "topics": [ "solver", "solver,AlgaeSimple-method", "solver,AlgaeTKTD-method", "solver,AlgaeWeber-method", "solver,ANY-method", "solver,DebAbj-method", "solver,DebDaphnia-method", "solver,DebTox-method", "solver,GutsIt-method", "solver,GutsRedIt-method", "solver,GutsRedSd-method", "solver,GutsSd-method", "solver,LemnaSchmitt-method", "solver,LemnaSetac-method", "solver,Magma-method" ] }, { "page": "survival", "title": "Survival rate", "topics": [ "survival" ] }, { "page": "td2cs", "title": "Create _calisets_ from _tox_data_", "topics": [ "td2cs" ] }, { "page": "tox_data", "title": "Prepare ecotox study data for fitting", "topics": [ "ToxData-class", "tox_data" ] }, { "page": "Transferable", "title": "Biomass transfer class", "concept": [ "scenario-related" ], "topics": [ "Biomass-transfer", "Transferable", "Transferable-class" ] } ], "_readme": "https://github.com/cvasi-tktd/cvasi/raw/HEAD/README.md", "_rundeps": [ "cli", "codetools", "cpp11", "crayon", "deSolve", "digest", "dplyr", "farver", "forcats", "furrr", "future", "generics", "GGally", "ggplot2", "ggstats", "globals", "glue", "gridExtra", "gtable", "hms", "isoband", "labeling", "lifecycle", "listenv", "lubridate", "magrittr", "parallelly", "patchwork", "pillar", "pkgconfig", "prettyunits", "progress", "purrr", "R6", "RColorBrewer", "Rcpp", "rlang", "S7", "scales", "stringi", "stringr", "tibble", "tidyr", "tidyselect", "timechange", "units", "utf8", "vctrs", "viridisLite", "withr" ], "_vignettes": [ { "source": "cvasi-2-howto.Rmd", "filename": "cvasi-2-howto.html", "title": "Modeling Howto", "author": "N. Kehrein and contributors", "engine": "knitr::rmarkdown", "headings": [ "How to access scenario properties", "Using tidyr syntax", "Predictions", "Moving exposure windows", "Simulating biomass transfers", "Fitting model parameters", "Obtaining confidence intervals for parameters", "Assessing parameter correlations and identifiability", "Changes in parameter values over time", "Decrease assessment runtime", "Implementing custom models", "Complete working example", "Setting up a scenario", "Simulating a scenario and plotting" ], "created": "2024-05-03 10:33:29", "modified": "2025-09-11 10:21:05", "commits": 19 }, { "source": "cvasi-1-manual.Rmd", "filename": "cvasi-1-manual.html", "title": "User Manual", "author": "N. Kehrein", "engine": "knitr::rmarkdown", "headings": [ "Required skills", "How to install", "Modeling and assessment workflow", "Overview", "Setting up a scenario", "Running a simulation", "Deriving assessment endpoints", "Data format of model inputs", "How to derive model inputs", "Description of model outputs", "Simulation results", "Effect levels", "Effect profiles", "References" ], "created": "2024-05-03 10:33:29", "modified": "2025-08-21 09:53:43", "commits": 11 } ], "_score": 6.290034611362518, "_indexed": true, "_nocasepkg": "cvasi", "_universes": [ "cvasi-tktd", "nkehrein" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.5.1", "date": "2026-05-10T09:17:48.000Z", "distro": "noble", "arch": "aarch64", "commit": "4f9cbd39fe98351d15b77a5d34e8b5025bf0d55e", "fileid": "78c14f829a7b0c2c31bb1f92f9e638289ede8d5df52f5121d7c7333aca80b3c9", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cvasi-tktd/actions/runs/25624868463" }, { "r": "4.7.0", "os": "linux", "version": "1.5.1", "date": "2026-05-10T09:17:50.000Z", "distro": "noble", "arch": "x86_64", "commit": "4f9cbd39fe98351d15b77a5d34e8b5025bf0d55e", "fileid": "bc08e0c76f58fe9b71fa115a6fc1c8b4947280571ad054b8c20354a1b5c0131e", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cvasi-tktd/actions/runs/25624868463" }, { "r": "4.6.0", "os": "linux", "version": "1.5.1", "date": "2026-05-10T09:18:02.000Z", "distro": "noble", "arch": "aarch64", "commit": "4f9cbd39fe98351d15b77a5d34e8b5025bf0d55e", "fileid": "e261cdadfb36225a7f89ae3eecedd09fbb28b123fc49858feb32f5ff5449d227", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cvasi-tktd/actions/runs/25624868463" }, { "r": "4.6.0", "os": "linux", "version": "1.5.1", "date": "2026-05-10T09:17:37.000Z", "distro": "noble", "arch": "x86_64", "commit": "4f9cbd39fe98351d15b77a5d34e8b5025bf0d55e", "fileid": "8f7d17f79b3e6a5a598ad5a4b0dce462761412c38d1a22d142bde6b146d289cb", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cvasi-tktd/actions/runs/25624868463" }, { "r": "4.5.3", "os": "mac", "version": "1.5.1", "date": "2026-05-10T09:30:11.000Z", "arch": "aarch64", "commit": "4f9cbd39fe98351d15b77a5d34e8b5025bf0d55e", "fileid": "6ffb8b3055bff20494bbb54f42f4d3d763e7ba6cb0d3443d8d580d2185f8b767", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cvasi-tktd/actions/runs/25624868463" }, { "r": "4.5.3", "os": "mac", "version": "1.5.1", "date": "2026-05-10T09:25:32.000Z", "arch": "x86_64", "commit": "4f9cbd39fe98351d15b77a5d34e8b5025bf0d55e", "fileid": "e4b262596724523db01f4897f55d36926afbc1791374ebe201eea0ea746490d9", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cvasi-tktd/actions/runs/25624868463" }, { "r": "4.6.0", "os": "mac", "version": "1.5.1", "date": "2026-05-10T09:28:38.000Z", "arch": "aarch64", "commit": "4f9cbd39fe98351d15b77a5d34e8b5025bf0d55e", "fileid": "5d0ce9466c739dc013774634fa3120f2be3fdbbc5adcd38cab77a61075c173d0", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cvasi-tktd/actions/runs/25624868463" }, { "r": "4.6.0", "os": "mac", "version": "1.5.1", "date": "2026-05-10T09:28:31.000Z", "arch": "x86_64", "commit": "4f9cbd39fe98351d15b77a5d34e8b5025bf0d55e", "fileid": "f93beb8dbb3918bad8a3ee9549f0206eb9ce796b6f65252a55428c9ba979b4e1", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cvasi-tktd/actions/runs/25624868463" }, { "r": "4.7.0", "os": "win", "version": "1.5.1", "date": "2026-05-10T09:16:55.000Z", "arch": "x86_64", "commit": "4f9cbd39fe98351d15b77a5d34e8b5025bf0d55e", "fileid": "9192dae464c145f4cb141d2d4ebfb70740a4200dabb505466f25d76e9f173125", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cvasi-tktd/actions/runs/25624868463" }, { "r": "4.5.3", "os": "win", "version": "1.5.1", "date": "2026-05-10T09:16:58.000Z", "arch": "x86_64", "commit": "4f9cbd39fe98351d15b77a5d34e8b5025bf0d55e", "fileid": "d5688bec309c94a842c1ea0f98cc26916abb5d6221b06818a5c95e605f7f0f31", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cvasi-tktd/actions/runs/25624868463" }, { "r": "4.6.0", "os": "win", "version": "1.5.1", "date": "2026-05-10T09:16:39.000Z", "arch": "x86_64", "commit": "4f9cbd39fe98351d15b77a5d34e8b5025bf0d55e", "fileid": "1c14b7dcd750f45344e8aecd760841db02f684d669af510b678b07540d5cc430", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cvasi-tktd/actions/runs/25624868463" }, { "r": "4.6.0", "os": "wasm", "version": "1.5.1", "date": "2026-05-22T12:12:00.000Z", "arch": "emscripten", "commit": "4f9cbd39fe98351d15b77a5d34e8b5025bf0d55e", "fileid": "81714b4d9098190c6c37f1ab06e49839e941203cc1fd86522484dba6e82d900f", "status": "success", "buildurl": "https://github.com/r-universe/cvasi-tktd/actions/runs/25624868463" } ] }