Package: cvasi 1.1.3
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_1.1.3.tar.gz
cvasi_1.1.3.tar.gz(r-4.5-noble)cvasi_1.1.3.tar.gz(r-4.4-noble)
cvasi_1.1.3.tgz(r-4.4-emscripten)cvasi_1.1.3.tgz(r-4.3-emscripten)
cvasi.pdf |cvasi.html✨
cvasi/json (API)
NEWS
| # Install 'cvasi' in R: |
| install.packages('cvasi', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/cvasi-tktd/cvasi/issues
- Rsubcapitata - An algae scenario
- Schmitt2013 - A Lemna data set with multiple treatment levels
- americamysis - A DEB abj scenario of Americamysis bahia
- dmagna - A DEBtox Daphnia magna scenario
- focusd1 - A Lemna_SETAC scenario with variable environment
- metsulfuron - Lemna data published by Schmitt
- minnow_it - A GUTS-RED-IT scenario of the fathead minnow
- minnow_sd - A GUTS-RED-SD scenario of the fathead minnow
Last updated 1 months agofrom:02644262e6. Checks:OK: 2. Indexed: no.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Aug 25 2024 |
| R-4.5-linux-x86_64 | OK | Aug 25 2024 |
Exports:%>%Algae_SimpleAlgae_TKTDAlgae_Webercache_controlscalibrateCalibrationSetcalisetDEB_abjDEB_Daphniadose_responseeffectepxepx_mtwExposureSeriesfxget_modelget_model_nameget_tagGUTS_RED_ITGUTS_RED_SDimport_exposure_textimport_swashimport_toxswais_DEBis_GUTSis_GUTS_ITis_GUTS_SDis_Lemnais_LemnaThresholdis_scenarioLemna_SchmittLemna_SchmittTholdLemna_SETAClog_disablelog_enablelog_envirlog_msglog_scenariosmorseMyrioMyrio_logno_exposureparameter_setpll_debugplot_epxplot_ppcplot_scenarioplot_sdpull_metadatasequenceset_endpointsset_exposureset_forcingsset_initset_moaset_mode_of_actionset_noexposureset_paramset_tagset_timesset_transferset_windowsimulatesimulate_batchsolversurvival
Dependencies:attemptclicodetoolscolorspacecpp11deSolvedigestdplyrfansifarverfurrrfuturegenericsggplot2globalsgluegridExtragtableisobandlabelinglatticelemnalifecyclelistenvlubridatemagrittrMASSMatrixmgcvmunsellnlmeparallellypillarpkgconfigpurrrR6RColorBrewerRcpprlangscalesstringistringrtibbletidyrtidyselecttimechangeunitsutf8vctrsviridisLitewithr
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Algae model with exponential growth but without additional forcings | AlgaeSimpleScenario-class Algae_Simple |
| Algae model with exponential growth, forcings (P, I) and scaled damage | AlgaeTKTDScenario-class Algae_TKTD |
| Algae model with exponential growth and forcings (I, T) | AlgaeWeberScenario-class Algae_Weber |
| Algae models | Algae-class Algae-models |
| A DEB abj scenario of Americamysis bahia | americamysis |
| Cache control simulations | cache_controls |
| Fit model parameters to experimental data | calibrate calibrate,CalibrationSet-method calibrate,EffectScenario-method calibrate,list-method |
| Calibration set | CalibrationSet CalibrationSet-class caliset |
| DEB_abj | DebAbj-class DEB_abj |
| DEBtox Daphnia | DebDaphnia-class DEB_Daphnia |
| Dynamic Energy Budget (DEB) models | DEB-models DebScenario-class |
| A DEBtox Daphnia magna scenario | dmagna |
| Calculate a dose response curve | dose_response |
| Effect level | effect |
| Effect profiles (EPx values) | epx |
| Calculate EPx values for a series of moving time window | epx_mtw |
| Exposure time-series | ExposureSeries ExposureSeries-class |
| A Lemna_SETAC scenario with variable environment | focusd1 |
| Generic to calculate effects for a particular scenario | fx fx,Algae-method fx,ANY-method fx,GutsRedIt-method fx,GutsRedSd-method fx,Lemna-method fx,Myriophyllum-method |
| Get model name | get_model get_model,ANY-method get_model,EffectScenario-method get_model,list-method get_model,parameter_set-method get_model_name |
| Get scenario tag | get_tag get_tag,ANY-method get_tag,EffectScenario-method get_tag,list-method get_tag,parameter_set-method |
| GUTS-RED-IT scenario | GutsRedIt-class GUTS_RED_IT |
| GUTS-RED-SD scenario | GutsRedSd-class GUTS_RED_SD |
| GUTS-RED models | GUTS-RED-models |
| Import exposure profiles from text files | import_exposure_text |
| SWASH project exposure profile import | import_swash |
| Read TOXSWA exposure profiles from out-files | import_toxswa |
| Test if argument is a DEB model | is_DEB |
| Test if argument is a GUTS model | is_GUTS is_GUTS_IT is_GUTS_SD |
| Test if argument is a Lemna model | is_Lemna |
| Test if argument is a LemnaThreshold model | is_LemnaThreshold |
| Test if argument is an effect scenario | is_scenario |
| Lemna model (Schmitt et al. 2013) | LemnaSchmittScenario-class Lemna_Schmitt Lemna_SchmittThold |
| Lemna model (Klein et al. 2021) | LemnaSetacScenario-class Lemna_SETAC |
| Lemna models | Lemna-class Lemna-models |
| Start and stop logging | log_disable log_enable |
| Log R environment properties | log_envir |
| Add a log message | log_msg |
| Log scenario properties | log_scenarios |
| Macrophyte models | Macrophyte-models |
| Lemna data published by Schmitt (2013) | metsulfuron |
| A GUTS-RED-IT scenario of the fathead minnow | minnow_it |
| A GUTS-RED-SD scenario of the fathead minnow | minnow_sd |
| Import 'morse' model parameters | morse |
| Myriophyllum model with exponential growth | Myrio MyrioExpScenario-class |
| Myriophyllum model with logistic growth | MyrioLogScenario-class Myrio_log |
| Myriophyllum models | Myriophyllum-class Myriophyllum-models |
| Zero exposure | no_exposure |
| Set of model parameters | parameter_set parameter_set-class |
| Disable parallelization for debugging | pll_debug |
| 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 |
| Pull metadata from scenarios | pull_metadata |
| An algae scenario | Rsubcapitata |
| Effect scenario classes | EffectScenario-class scenario Scenarios scenarios |
| A Lemna data set with multiple treatment levels | Schmitt2013 |
| Sequence of scenarios | ScenarioSequence-class sequence |
| 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,list,ANY-method set_exposure,list,list-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,vector-method |
| Set mode of action | set_moa set_mode_of_action |
| Set zero exposure | set_noexposure |
| Set model parameters | set_param set_param,EffectScenario,parameter_set-method set_param,EffectScenario,vector-method set_param,list,parameter_set-method set_param,list,vector-method set_param,ScenarioSequence,parameter_set-method set_param,ScenarioSequence,vector-method |
| Set a tag | set_tag |
| Set output times | set_times |
| Set transfer events | set_transfer set_transfer,ANY-method set_transfer,Transferable-method |
| Set window length | set_window |
| Simulate an effect scenario | simulate simulate,EffectScenario-method simulate,ScenarioSequence-method simulate,Transferable-method |
| Batch simulation of several effect scenarios | simulate_batch |
| Calls ODE solver for a particular model | solver solver,AlgaeSimpleScenario-method solver,AlgaeTKTDScenario-method solver,AlgaeWeberScenario-method solver,ANY-method solver,DebAbj-method solver,DebDaphnia-method solver,GutsRedIt-method solver,GutsRedSd-method solver,LemnaSchmittScenario-method solver,LemnaSetacScenario-method solver,MyrioExpScenario-method solver,MyrioLogScenario-method |
| Survival rate | survival |
| Biomass transfer class | Biomass-transfer Transferable Transferable-class |
