morse-package: MOdelling tools for Reproduction and Survival data in...

In morse: Modelling Reproduction and Survival Data in Ecotoxicology

MOdelling tools for Reproduction and Survival data in Ecotoxicology

Description

Provides tools for the analysis of survival/reproduction toxicity test data in quantitative environmental risk assessment. It can be used to explore/visualize experimental data, and to get estimates of LC_{x} (X% Lethal Concentration) or, EC_{x} (X% Effective Concentration) by fitting exposure-response curves. The LC_{x}, EC_{x} and parameters of the curve are provided along with an indication of the uncertainty of the estimation. morse can also be used to get an estimation of the NEC (No Effect Concentration) by fitting a Toxico-Kinetic Toxico-Dynamic (TKTD) model (GUTS: General Unified Threshold model of Survival). Within the TKTD-GUTS approach, LC(x,t), EC(x,t) and MF(x,t) (x% Multiplication Factors aka Lethal Profiles) can be explored in proportion x and time t.

Details

Estimation procedures in morse 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, morse models can also be used as a first step to tailor new models for more specific situations.

The package currently handles survival and reproduction data. Functions dedicated to survival (resp. reproduction) analysis start with a surv (resp. repro) prefix. morse provides a similar workflow in both cases:

1. create and validate a data set

2. explore a data set

3. plot a data set

4. fit a model on a data set and output the expected estimates

5. check goodness of fit with posterior preditive check plot (ppc)

More specifically, for survival data handles with TKTD 'GUTS' model, morse provides:

1. plot LC(x,t) and MF(x,t).

2. compute goodness-of-fit measures (PPC percent, NRMSE and SPPE)

Those steps are presented in more details in the "Tutorial" vignette, while a more formal description of the estimation procedures are provided in the vignette called "Models in morse package". Please refer to these documents for further introduction to the use of morse.

This reference manual is a detailed description of the functions exposed in the package.

Getting started The package uses the rjags package (Plummer, 2013), an R interface to the JAGS library for Bayesian model estimation. Note that the rjags package does not include a copy of the JAGS library: you need to install it separately. For instructions on downloading JAGS, see the home page at https://mcmc-jags.sourceforge.io. Once done, simply follow the steps described in the tutorial vignette.

Package:	morse
Type:	Package
Version:	3.2.0
Date:	2018-11-15
License:	GPL (>=2)

Author(s)

Virgile Baudrot <[e-mail]>, Sandrine Charles <[e-mail]>, Marie Laure Delignette-Muller <[e-mail]>, Wandrille Duchemin <[e-mail]>, Benoit Goussen <[e-mail]>, Guillaume Kon-Kam-king <[e-mail]>, Christelle Lopes <[e-mail]>, Philippe Ruiz <[e-mail]>, Alexander Singer, <[e-mail]> Philippe Veber <[e-mail]>

Maintainer: Philippe Veber <[e-mail]>

References

Delignette-Muller, M.L., Ruiz P. and Veber P. (2017) Robust fit of toxicokinetic-toxicodynamic models using prior knowledge contained in the design of survival toxicity tests.

Delignette-Muller, M.L., Lopes, C., Veber, P. and Charles, S. (2014) Statistical handling of reproduction data for exposure-response modelling.

Forfait-Dubuc, C., Charles, S., Billoir, E. and Delignette-Muller, M.L. (2012) Survival data analyses in ecotoxicology: critical effect concentrations, methods and models. What should we use?

Plummer, M. (2013) JAGS Version 4.0.0 user manual. https://sourceforge.net/projects/mcmc-jags/files/Manuals/4.x/jags_user_manual.pdf/download

Baudrot, V., Preux, S., Ducrot, V., Pavé, A. and Charles, S. (2018) New insights to compare and choose TKTD models for survival based on an inter-laboratory study for Lymnaea stagnalis exposed to Cd.

EFSA PPR Scientific Opinion (2018) Scientific Opinion on the state of the art of Toxicokinetic/Toxicodynamic (TKTD) effect models for regulatory risk assessment of pesticides for aquatic organisms https://www.efsa.europa.eu/en/efsajournal/pub/5377.

See Also

rjags, ggplot2

morse documentation built on Oct. 29, 2022, 1:14 a.m.