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spacemodR - Wildlife Chemical Risk Mapping Through Food Webs

A workflow to map the risk of chemicals for wildlife: habitat, food web, dispersal, exposure and risk. Starting from a raster of chemical concentrations in the environment (e.g., metals in soil, pesticides in fields), the package builds habitat layers for a set of species, organises them in a directed acyclic graph representing a food web, and propagates the flow of elements (e.g., food, energy, chemicals) along its links. It also provides soil interpolation by kriging, dispersal by kernel convolution or by circuit theory (through the optional 'Julia' package 'Omniscape'), land cover retrieval for France ('OCS-GE') and Europe ('EUNIS'), and Bayesian calibration of transfer models with 'Stan'.

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ecotoxicologyfood-websrisk-assessmentspatial-modellingonetbbcpp

5.58 score 18 scripts 347 downloads

rbioacc - Inference and Prediction of ToxicoKinetic (TK) Models

The MOSAICbioacc application is a turnkey package providing bioaccumulation factors (BCF/BMF/BSAF) from a toxicokinetic (TK) model fitted to accumulation-depuration data. It is designed to fulfil the requirements of regulators when examining applications for market authorization of active substances. See Ratier et al. (2021) <doi:10.1101/2021.09.08.459421>.

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onetbbcpp

4.82 score 11 scripts 349 downloads

morse - Modelling Reproduction and Survival Data in Ecotoxicology

Advanced methods for a valuable quantitative environmental risk assessment using Bayesian inference of survival and reproduction Data. Among others, it facilitates Bayesian inference of the general unified threshold model of survival (GUTS). See our companion paper Baudrot and Charles (2021) <doi:10.21105/joss.03200>, as well as complementary details in Baudrot et al. (2018) <doi:10.1021/acs.est.7b05464> and Delignette-Muller et al. (2017) <doi:10.1021/acs.est.6b05326>.

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jagscpp

3.66 score 76 scripts 478 downloads

morseDR - Bayesian Inference of Binary, Count and Continuous Data in Toxicology

Advanced methods for a valuable quantitative environmental risk assessment using Bayesian inference of several type of toxicological data. 'binary' (e.g., survival, mobility), 'count' (e.g., reproduction) and 'continuous' (e.g., growth as length, weight). Estimation procedures can be used without a deep knowledge of their underlying probabilistic model or inference methods. Rather, they were designed to behave as well as possible without requiring a user to provide values for some obscure parameters. That said, models can also be used as a first step to tailor new models for more specific situations.

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jagscpp

3.00 score 4 scripts 435 downloads

morseTKTD - Bayesian Inference of TKTD Models

Advanced methods for a valuable quantitative environmental risk assessment using Bayesian inference of survival Data with toxicokinetics toxicodynamics (TKTD) models. Among others, it facilitates Bayesian inference of the general unified threshold model of survival (GUTS). See models description in Jager et al. (2011) <doi:10.1021/es103092a> and implementation using Bayesian inference in Baudrot and Charles (2019) <doi:10.1038/s41598-019-47698-0>.

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onetbbcpp

3.00 score 6 scripts 334 downloads

rPBK - Inference and Prediction of Generic Physiologically-Based Kinetic Models

Fit and simulate any kind of physiologically-based kinetic ('PBK') models whatever the number of compartments. Moreover, it allows to account for any link between pairs of compartments, as well as any link of each of the compartments with the external medium. Such generic PBK models have today applications in pharmacology (PBPK models) to describe drug effects, in toxicology and ecotoxicology (PBTK models) to describe chemical substance effects. In case of exposure to a parent compound (drug or chemical) the 'rPBK' package allows to consider metabolites, whatever their number and their phase (I, II, ...). Last but not least, package 'rPBK' can also be used for dynamic flux balance analysis (dFBA) to deal with metabolic networks. See also Charles et al. (2022) <doi:10.1101/2022.04.29.490045>.

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onetbbcpp

2.70 score 4 scripts 316 downloads