Species sensitivity distributions are cumulative probability distributions which are fitted to toxicity concentrations for multiple species. The ssdtools package uses Maximum Likelihood to fit log-normal, log-logistic, log-Gumbel, Gompertz, gamma or Weibull distributions. Multiple distributions can be averaged using Information Criteria. Confidence intervals can be calculated for the fitted cumulative distribution function or specific hazard concentrations (percentiles). Confidence intervals are currently produced by bootstrapping.
ssdtools is an R package to plot and fit Species Sensitivity
SSDs are cumulative probability distributions which are fitted to toxicity concentrations for multiple species. The ssdtools package uses Maximum Likelihood to fit log-normal, log-logistic, log-Gumbel, Gompertz, gamma or Weibull distributions. Multiple distributions can be averaged using Information Criteria. Confidence intervals on fits and hazard concentrations are produced by bootstrapping.
To install the latest version from CRAN
To install the latest development version:
ssdtools provides a data set for several chemicals including Boron.
library(ssdtools)boron_data#> # A tibble: 28 x 5#> Chemical Species Conc Group Units#> <chr> <chr> <dbl> <fct> <chr>#> 1 Boron Oncorhynchus mykiss 2.1 Fish mg/L#> 2 Boron Ictalurus punctatus 2.4 Fish mg/L#> 3 Boron Micropterus salmoides 4.1 Fish mg/L#> 4 Boron Brachydanio rerio 10 Fish mg/L#> 5 Boron Carassius auratus 15.6 Fish mg/L#> 6 Boron Pimephales promelas 18.3 Fish mg/L#> 7 Boron Daphnia magna 6 Invertebrate mg/L#> 8 Boron Opercularia bimarginata 10 Invertebrate mg/L#> 9 Boron Ceriodaphnia dubia 13.4 Invertebrate mg/L#> 10 Boron Entosiphon sulcatum 15 Invertebrate mg/L#> # ... with 18 more rows
Multiple distributions can be fit using
boron_dists <- ssd_fit_dists(boron_data)
and plot using the
The goodness of fit can be assessed using
ssd_gof(boron_dists)#> # A tibble: 6 x 9#> dist ad ks cvm aic aicc bic delta weight#> * <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>#> 1 lnorm 0.507 0.107 0.0703 239. 240. 242. 1.42 0.133#> 2 llog 0.487 0.0993 0.0595 241. 241. 244. 3.40 0.049#> 3 gompertz 0.602 0.120 0.0822 238. 238. 240. 0 0.271#> 4 lgumbel 0.829 0.158 0.134 244. 245. 247. 6.58 0.01#> 5 gamma 0.441 0.117 0.0555 238. 238. 240. 0.019 0.268#> 6 weibull 0.435 0.117 0.0543 238. 238. 240. 0.014 0.269
and the model-averaged 5% hazard concentration estimated using
boron_hc5 <- ssd_hc(boron_dists, nboot = 10000)
print(boron_hc5)#> # A tibble: 1 x 5#> percent est se lcl ucl#> * <int> <dbl> <dbl> <dbl> <dbl>#> 1 5 1.25 0.736 0.602 3.22
Model-averaged predictions complete with confidence intervals can be
produced using the
boron_pred <- predict(boron_dists)
and plotted together with the original data using
ssd_plot(boron_data, boron_pred, shape = "Group", color = "Group", label = "Species",xlab = "Concentration (mg/L)", ribbon = TRUE) + expand_limits(x = 3000)
The ssdtools manual is available at https://bcgov.github.io/ssdtools/articles/ssdtools-manual.html.
A shiny webpage developed for non-R-users is available at https://poissonconsulting.shinyapps.io/ssdtools/.
The data included in
ssdtools are sourced from the Canadian
environmental quality guidelines published by the Canadian Council of
Ministers of the Environment.
folder for more information.
To report bugs/issues/feature requests, please file an issue.
If you would like to contribute to the package, please see our CONTRIBUTING guidelines.
Please note that this project is released with a Contributor Code of Conduct. By participating in this project you agree to abide by its terms.
The code is released under the Apache License 2.0
Copyright 2015 Province of British Columbia Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at http://www.apache.org/licenses/LICENSE-2.0 Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.