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
Package: cvasi 1.5.1
Nils Kehrein
cvasi: Calibration, Validation, and Simulation of TKTD Models
Eases the use of ecotoxicological effect models. Can simulate common toxicokinetic-toxicodynamic (TK/TD) models such as General Unified Threshold models of Survival (GUTS) and Lemna. It can derive effects and effect profiles (EPx) from scenarios. It supports the use of 'tidyr' workflows employing the pipe symbol. Time-consuming tasks can be parallelized.
Authors:
cvasi_1.5.1.tar.gz
cvasi_1.5.1.zip(r-4.7-x86_64)cvasi_1.5.1.zip(r-4.7-arm64)cvasi_1.5.1.zip(r-4.6-x86_64)cvasi_1.5.1.zip(r-4.6-arm64)cvasi_1.5.1.zip(r-4.5-x86_64)
cvasi_1.5.1.tgz(r-4.6-x86_64)cvasi_1.5.1.tgz(r-4.6-arm64)cvasi_1.5.1.tgz(r-4.5-x86_64)cvasi_1.5.1.tgz(r-4.5-arm64)
cvasi_1.5.1.tar.gz(r-4.7-arm64)cvasi_1.5.1.tar.gz(r-4.7-x86_64)cvasi_1.5.1.tar.gz(r-4.6-arm64)cvasi_1.5.1.tar.gz(r-4.6-x86_64)
cvasi_1.5.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
cvasi/json (API)
| # Install 'cvasi' in R: |
| install.packages('cvasi', repos = c('https://cvasi-tktd.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/cvasi-tktd/cvasi/issues
Datasets:
- americamysis - A DEB abj scenario of Americamysis bahia
- dmagna - A DEBtox scenario of Daphnia magna
- focusd1 - A Lemna_SETAC scenario with variable environment
- metsulfuron - Lemna model fitted to _metsulfuron_ effect data
- minnow_it - A fitted GUTS-RED-IT scenario of the fathead minnow
- minnow_sd - A fitted GUTS-RED-SD scenario of the fathead minnow
- ringtest_c - EFSA Ringtest Dataset C
- ringtest_it - EFSA Ringtest Dataset A SD
- ringtest_sd - EFSA Ringtest Dataset A SD
- rsubcapitata - A Weber scenario of algae exposed to isoproturon
- schmitt2013 - A Lemna effect study data set with multiple treatment levels
ecotoxicologymodelingsimulation
Last updated from:4f9cbd39fe. Checks:15 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-arm64 | OK | 209 | ||
| linux-devel-x86_64 | OK | 218 | ||
| source / vignettes | OK | 283 | ||
| linux-release-arm64 | OK | 167 | ||
| linux-release-x86_64 | OK | 184 | ||
| macos-release-arm64 | OK | 265 | ||
| macos-release-x86_64 | OK | 356 | ||
| macos-oldrel-arm64 | OK | 228 | ||
| macos-oldrel-x86_64 | OK | 458 | ||
| windows-devel-arm64 | OK | 419 | ||
| windows-devel-x86_64 | OK | 211 | ||
| windows-release-arm64 | OK | 425 | ||
| windows-release-x86_64 | OK | 156 | ||
| windows-oldrel-x86_64 | OK | 149 | ||
| wasm-release | OK | 108 |
Exports:%>%Algae_SimpleAlgae_TKTDAlgae_Weberbatchcache_controlscalibrateCalibrationSetcalisetci_from_hessianDEB_abjDEB_DaphniaDEBtoxdiagnosticsdose_responseeffectepxepx_mtwexplore_spaceExposureSeriesfit_growthfit_tktdfxget_modelget_model_nameget_paramget_tagget_timesGUTS_RED_ITGUTS_RED_SDGUTS_SDimport_morseimport_swashimport_toxswais_debis_DEBis_gutsis_GUTSis_guts_itis_GUTS_ITis_guts_sdis_GUTS_SDis_lemnais_Lemnais_LemnaThresholdis_scenarioLemna_SchmittLemna_SchmittTholdLemna_SETAClik_profilelog_disablelog_enablelog_envirlog_liklog_msglog_scenariosMagmamorseMyrioMyrio_logno_exposurenum_infoparameter_setpll_debugplot_epxplot_lik_profileplot_param_spaceplot_ppcplot_scenarioplot_sdpull_metadataSamXsequenceset_boundsset_endpointsset_exposureset_forcingsset_initset_moaset_mode_of_actionset_noexposureset_notransferset_nowindowset_paramset_tagset_timesset_transferset_windowsimulatesimulate_batchsolversurvivaltd2cstox_data
Dependencies:clicodetoolscpp11crayondeSolvedigestdplyrfarverforcatsfurrrfuturegenericsGGallyggplot2ggstatsglobalsgluegridExtragtablehmsisobandlabelinglifecyclelistenvlubridatemagrittrparallellypatchworkpillarpkgconfigprettyunitsprogresspurrrR6RColorBrewerRcpprlangS7scalesstringistringrtibbletidyrtidyselecttimechangeunitsutf8vctrsviridisLitewithr
Modeling Howto
Last update: 2025-09-11
Started: 2024-05-03
User Manual
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
Last update: 2025-08-21
Started: 2024-05-03
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Simple algae model without environment (Rendal et al. 2023) | AlgaeSimple-class AlgaeSimpleScenario-class Algae_Simple |
| Algae model variant (Weber et al. 2012) with scaled damage | AlgaeTKTD-class AlgaeTKTDScenario-class Algae_TKTD |
| Algae model, _SAM-X_ (Weber et al. 2012) | AlgaeWeber-class AlgaeWeberScenario-class Algae_Weber SAM-X SamX |
| Algae models | Algae-class Algae-models |
| A DEB abj scenario of Americamysis bahia | americamysis |
| Batch simulation of multiple exposure levels | batch |
| Cache control simulations | cache_controls |
| Fit model parameters to experimental data | calibrate calibrate,CalibrationSet-method calibrate,EffectScenario-method calibrate,list-method calibrate,ScenarioSequence-method |
| Calibration set | CalibrationSet CalibrationSet-class caliset |
| Parameter confidence intervals from fit | ci_from_hessian |
| DEB_abj | DebAbj-class DEB_abj |
| Dynamic Energy Budget (DEB) models | Deb-class DEB-models |
| DEBtox model | DebDaphnia-class DEBtox DebTox-class DEBtox2019 DEB_Daphnia |
| Diagnostics of solvers | diagnostics diagnostics.cvasi_simulate diagnostics.default |
| A DEBtox scenario of Daphnia magna | dmagna |
| Calculate a dose response curve | dose_response |
| Effect level | effect effect,EffectScenario-method effect,ScenarioSequence-method |
| Effect profiles (EPx values) | epx |
| Calculate EPx values for a series of moving time window | epx_mtw |
| Explore parameter space | explore_space |
| Exposure time-series | ExposureSeries ExposureSeries-class NoExposureSeries-class |
| Fit growth parameters | 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 |
| Fit TK/TD parameters | 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 |
| A Lemna_SETAC scenario with variable environment | focusd1 |
| Generic to calculate effects for a particular scenario | 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 |
| Get model name | get_model get_model,ANY-method get_model,EffectScenario-method get_model,list-method get_model,ParameterSet-method get_model_name |
| Get scenario parameters | get_param get_param,ANY-method get_param,EffectScenario-method get_param,list-method get_param,ParameterSet-method get_param,ScenarioSequence-method |
| Get scenario tag | get_tag get_tag,ANY-method get_tag,EffectScenario-method get_tag,list-method get_tag,ParameterSet-method get_tag,ScenarioSequence-method |
| Get output times | get_times get_times,ANY-method get_times,EffectScenario-method get_times,list-method get_times,ScenarioSequence-method |
| GUTS-IT scenario | GUTS-IT GutsIt-class GUTS_IT |
| GUTS-RED-IT scenario | GUTS-RED-IT GutsRedIt-class GUTS_RED_IT |
| GUTS-RED-SD scenario | GUTS-RED-SD GutsRedSd-class GUTS_RED_SD |
| GUTS-SD scenario | Guts-class GUTS-SD GutsSd-class GUTS_SD |
| GUTS-RED models | GUTS-RED-models |
| Import 'morse' model parameters | import_morse morse |
| SWASH project exposure profile import | import_swash |
| Import _TOXSWA_ exposure series | import_toxswa |
| Test if argument is a DEB scenario | is_DEB is_deb |
| Test if argument is a GUTS scenario | is_GUTS is_guts is_GUTS_IT is_guts_it is_GUTS_SD is_guts_sd |
| Test if argument is a Lemna scenario | is_Lemna is_lemna |
| Test if argument is a LemnaThreshold scenario | is_LemnaThreshold |
| Test if argument is an effect scenario | is_scenario |
| Lemna model (Schmitt et al. 2013) | LemnaSchmitt-class LemnaSchmittScenario-class Lemna_Schmitt Lemna_SchmittThold |
| Lemna model v1.3 (Klein et al. 2021) | LemnaSetac-class LemnaSetacScenario-class Lemna_SETAC |
| Lemna models | Lemna-class Lemna-models |
| Likelihood profiling | lik_profile |
| Start and stop logging | log_disable log_enable |
| Log R environment properties | log_envir |
| Calculate log likelihood | log_lik |
| Add a log message | log_msg |
| Log scenario properties | log_scenarios |
| Macrophyte models | Macrophyte-models |
| Magma model (Witt et al., submitted) | Magma Myrio Myrio_log |
| Magma scenario class | Magma-class |
| Lemna model fitted to _metsulfuron_ effect data | metsulfuron |
| A fitted GUTS-RED-IT scenario of the fathead minnow | minnow_it |
| A fitted GUTS-RED-SD scenario of the fathead minnow | minnow_sd |
| Zero exposure | no_exposure |
| Print information about numerical solver result | num_info num_info.cvasi_fit num_info.cvasi_simulate num_info.default |
| Set of model parameters | ParameterSet-class parameter_set parameter_set-class |
| Disable parallelization for debugging | pll_debug |
| S3 plotting functions | plot plot.cvasi_drc plot.cvasi_simulate plot.lik_profile plot_lik_profile |
| Plot EPx values | plot_epx |
| Creates a PPC plot for a single dataset | plot_ppc |
| Create PPC plot for one or more datasets | plot_ppc_combi |
| Creates a prediction plot for one effect scenario | plot_scenario |
| Creates plot of model results (uncertainties optional) | plot_sd |
| Plot profiled parameter space | plot.param_space plot_param_space |
| Pull metadata from scenarios | pull_metadata |
| EFSA Ringtest Dataset C | ringtest_c |
| EFSA Ringtest Dataset A SD | ringtest_it |
| EFSA Ringtest Dataset A SD | ringtest_sd |
| A Weber scenario of algae exposed to isoproturon | rsubcapitata |
| Effect scenario classes | EffectScenario-class scenario Scenarios scenarios |
| A Lemna effect study data set with multiple treatment levels | schmitt2013 |
| Sequence of scenarios | ScenarioSequence-class sequence |
| Extract and replace elements of a sequence | length,ScenarioSequence-method sequence.extract [,ScenarioSequence,numeric,missing,missing-method [[,ScenarioSequence,numeric-method [[<-,ScenarioSequence,numeric,ANY,ANY-method [[<-,ScenarioSequence,numeric,missing,EffectScenario-method |
| Set boundaries of model parameters | set_bounds set_bounds,CalibrationSet,list-method set_bounds,EffectScenario,list-method set_bounds,list,list-method set_bounds,ScenarioSequence,list-method |
| Set effect endpoints | set_endpoints |
| Set exposure time-series | 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 |
| Set time-dependent parameters | set_forcings set_forcings,EffectScenario-method set_forcings,list-method |
| Set initial state | set_init set_init,EffectScenario-method set_init,ScenarioSequence-method set_init,vector-method |
| Set mode of action | set_moa set_mode_of_action |
| Set zero exposure | set_noexposure |
| Set scenario parameters | 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 |
| Set a tag | set_tag |
| Set output times | set_times set_times,ANY-method set_times,EffectScenario-method set_times,list-method set_times,ScenarioSequence-method |
| Set transfer events | set_notransfer set_transfer set_transfer,ANY-method set_transfer,Transferable-method |
| Set window length | set_nowindow set_window |
| Simulate an effect scenario | simulate simulate,EffectScenario-method simulate,ScenarioSequence-method simulate,SimulationBatch-method simulate,Transferable-method |
| Batch simulation using multiple exposure series | simulate_batch |
| Calls ODE solver for a particular model | 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 |
| Survival rate | survival |
| Create _calisets_ from _tox_data_ | td2cs |
| Prepare ecotox study data for fitting | ToxData-class tox_data |
| Biomass transfer class | Biomass-transfer Transferable Transferable-class |