Showing 14 of total 14 results (show query)
bcgov
ssdtools:Species Sensitivity Distributions
Species sensitivity distributions are cumulative probability distributions which are fitted to toxicity concentrations for different species as described by Posthuma et al.(2001) <isbn:9781566705783>. The ssdtools package uses Maximum Likelihood to fit distributions such as the gamma, log-logistic, log-normal and log-normal log-normal mixture. Multiple distributions can be averaged using Akaike Information Criteria. Confidence intervals on hazard concentrations and proportions are produced by bootstrapping.
Maintained by Joe Thorley. Last updated 24 days ago.
ecotoxicologyenvspecies-sensitivity-distributioncpp
10.0 match 31 stars 10.23 score 111 scripts 4 dependents
cran
ecotoxicology:Methods for Ecotoxicology
Implementation of the EPA's Ecological Exposure Research Division (EERD) tools (discontinued in 1999) for Probit and Trimmed Spearman-Karber Analysis. Probit and Spearman-Karber methods from Finney's book "Probit analysis a statistical treatment of the sigmoid response curve" with options for most accurate results or identical results to the book. Probit and all the tables from Finney's book (code-generated, not copied) with the generating functions included. Control correction: Abbott, Schneider-Orelli, Henderson-Tilton, Sun-Shepard. Toxicity scales: Horsfall-Barratt, Archer, Gauhl-Stover, Fullerton-Olsen, etc.
Maintained by Jose Gama. Last updated 9 years ago.
53.8 match 3 stars 1.89 score 26 scripts
open-aims
bayesnec:A Bayesian No-Effect- Concentration (NEC) Algorithm
Implementation of No-Effect-Concentration estimation that uses 'brms' (see Burkner (2017)<doi:10.18637/jss.v080.i01>; Burkner (2018)<doi:10.32614/RJ-2018-017>; Carpenter 'et al.' (2017)<doi:10.18637/jss.v076.i01> to fit concentration(dose)-response data using Bayesian methods for the purpose of estimating 'ECx' values, but more particularly 'NEC' (see Fox (2010)<doi:10.1016/j.ecoenv.2009.09.012>), 'NSEC' (see Fisher and Fox (2023)<doi:10.1002/etc.5610>), and 'N(S)EC (see Fisher et al. 2023<doi:10.1002/ieam.4809>). A full description of this package can be found in Fisher 'et al.' (2024)<doi:10.18637/jss.v110.i05>. This package expands and supersedes an original version implemented in 'R2jags' (see Su and Yajima (2020)<https://CRAN.R-project.org/package=R2jags>; Fisher et al. (2020)<doi:10.5281/ZENODO.3966864>).
Maintained by Rebecca Fisher. Last updated 7 months ago.
bayesian-inferenceconcentration-responseecotoxicologyno-effect-concentrationnon-linear-decaythreshold-derivationtoxicology
10.0 match 12 stars 8.11 score 360 scripts
zsteinmetz
envalysis:Miscellaneous Functions for Environmental Analyses
Small toolbox for data analyses in environmental chemistry and ecotoxicology. Provides, for example, calibration() to calculate calibration curves and corresponding limits of detection (LODs) and limits of quantification (LOQs) according to German DIN 32645 (2008). texture() makes it easy to estimate soil particle size distributions from hydrometer measurements (ASTM D422-63, 2007).
Maintained by Zacharias Steinmetz. Last updated 5 months ago.
analyticschemistryecotoxicologyenvironmentsoil
10.5 match 8 stars 6.30 score 83 scripts
cvasi-tktd
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.
Maintained by Nils Kehrein. Last updated 4 days ago.
ecotoxicologymodelingsimulation
10.5 match 2 stars 6.26 score 12 scripts
andschar
standartox:Ecotoxicological Information from the Standartox Database
The <http://standartox.uni-landau.de> database offers cleaned, harmonized and aggregated ecotoxicological test data, which can be used for assessing effects and risks of chemical concentrations found in the environment.
Maintained by Andreas Scharmüller. Last updated 3 years ago.
13.6 match 14 stars 3.85 score 1 scripts
marc-girondot
HelpersMG:Tools for Environmental Analyses, Ecotoxicology and Various R Functions
Contains miscellaneous functions useful for managing 'NetCDF' files (see <https://en.wikipedia.org/wiki/NetCDF>), get moon phase and time for sun rise and fall, tide level, analyse and reconstruct periodic time series of temperature with irregular sinusoidal pattern, show scales and wind rose in plot with change of color of text, Metropolis-Hastings algorithm for Bayesian MCMC analysis, plot graphs or boxplot with error bars, search files in disk by there names or their content, read the contents of all files from a folder at one time.
Maintained by Marc Girondot. Last updated 2 months ago.
4.6 match 4 stars 4.59 score 160 scripts 4 dependents
benjaminhlina
ecotox:Analysis of Ecotoxicology
A simple approach to using a probit or logit analysis to calculate lethal concentration (LC) or time (LT) and the appropriate fiducial confidence limits desired for selected LC or LT for ecotoxicology studies (Finney 1971; Wheeler et al. 2006; Robertson et al. 2007). The simplicity of 'ecotox' comes from the syntax it implies within its functions which are similar to functions like glm() and lm(). In addition to the simplicity of the syntax, a comprehensive data frame is produced which gives the user a predicted LC or LT value for the desired level and a suite of important parameters such as fiducial confidence limits and slope. Finney, D.J. (1971, ISBN: 052108041X); Wheeler, M.W., Park, R.M., and Bailer, A.J. (2006) <doi:10.1897/05-320R.1>; Robertson, J.L., Savin, N.E., Russell, R.M., and Preisler, H.K. (2007, ISBN: 0849323312).
Maintained by Benjamin L Hlina. Last updated 2 months ago.
biologydose-response-modelinglogitprobittoxicology
4.3 match 3 stars 4.50 score 10 scripts
lbbe-software
fitdistrplus:Help to Fit of a Parametric Distribution to Non-Censored or Censored Data
Extends the fitdistr() function (of the MASS package) with several functions to help the fit of a parametric distribution to non-censored or censored data. Censored data may contain left censored, right censored and interval censored values, with several lower and upper bounds. In addition to maximum likelihood estimation (MLE), the package provides moment matching (MME), quantile matching (QME), maximum goodness-of-fit estimation (MGE) and maximum spacing estimation (MSE) methods (available only for non-censored data). Weighted versions of MLE, MME, QME and MSE are available. See e.g. Casella & Berger (2002), Statistical inference, Pacific Grove, for a general introduction to parametric estimation.
Maintained by Aurélie Siberchicot. Last updated 12 days ago.
1.0 match 54 stars 16.15 score 4.5k scripts 153 dependents
virgile-baudrot
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>.
Maintained by Virgile Baudrot. Last updated 6 months ago.
4.8 match 3.26 score 60 scripts
pepijn-devries
ECOTOXr:Download and Extract Data from US EPA's ECOTOX Database
The US EPA ECOTOX database is a freely available database with a treasure of aquatic and terrestrial ecotoxicological data. As the online search interface doesn't come with an API, this package provides the means to easily access and search the database in R. To this end, all raw tables are downloaded from the EPA website and stored in a local SQLite database <doi:10.1016/j.chemosphere.2024.143078>.
Maintained by Pepijn de Vries. Last updated 5 days ago.
0.5 match 10 stars 6.20 score 6 scripts
poissonconsulting
shinywqbench:R Shiny App to Calculates Aquatic Life Benchmarks
This package is the user interface to the wqbench R package and allows users to easily access standardized ecotoxicology data for thousands of chemicals. Either a SSD or deterministic method is used to determine the critical toxicity value and assessment factors to compute the aquatic life water quality benchmark for a compound.
Maintained by Angeline Tillmanns. Last updated 2 months ago.
0.5 match 2.95 score 2 scriptsvirgile-baudrot
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>.
Maintained by Virgile Baudrot. Last updated 1 years ago.
0.5 match 2.70 score 3 scripts
aursiber
ssd4mosaic:Web Application for the SSD Module of the MOSAIC Platform
Web application using 'shiny' for the SSD (Species Sensitivity Distribution) module of the MOSAIC (MOdeling and StAtistical tools for ecotoxICology) platform. It estimates the Hazardous Concentration for x% of the species (HCx) from toxicity values that can be censored and provides various plotting options for a better understanding of the results. See our companion paper Kon Kam King et al. (2014) <doi:10.48550/arXiv.1311.5772>.
Maintained by Aurélie Siberchicot. Last updated 5 days ago.
0.5 match 2.60 score