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) . The ssdtools package uses Maximum Likelihood to fit distributions such as the log-normal, gamma, log-logistic, log-Gumbel, Gompertz and Weibull. The user can provide custom distributions. Multiple distributions can be averaged using Information Criteria. Confidence intervals on hazard concentrations and proportions are produced by parametric bootstrapping.

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ssdtools is an R package to plot and fit Species Sensitivity Distributions (SSD).

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.

#> # 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 ssd_fit_dists()

boron_dists <- ssd_fit_dists(boron_data)

and plot using the ggplot2 generic autoplot


The goodness of fit can be assessed using ssd_gof

#> # 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 ssd_hc

boron_hc5 <- ssd_hc(boron_dists, nboot = 10000)
#> # 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 stats generic predict

boron_pred <- predict(boron_dists)

and plotted together with the original data using ssd_plot.

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. See the data-raw folder for more information.

Getting Help or Reporting an Issue

To report bugs/issues/feature requests, please file an issue.

How to Contribute

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 


Unless required by applicable law or agreed to in writing, software
distributed under the License is distributed on an "AS IS" BASIS,
See the License for the specific language governing permissions and
limitations under the License.


ssdtools 0.0.3

  • Added ssdtools-manual vignette
  • Changed predict() and ssd_hc() nboot argument from 1001 to 1000
  • Added hc5_boron data object
  • No longer export ssd_fit_dist() as ssd_fit_dists() renders redundant
  • geom_hcintersect() now takes multiple values
  • More information in DESCRIPTION
  • Added CRAN badge
  • Removed dependencies: dplyr, magrittr, plyr, purrr
  • Moved from depends to imports: VGAM, fitdistrplus, graphics, ggplot, stats
  • Moved from imports to suggests: tibble

ssdtools 0.0.2

  • Added contributors
  • Added hex

ssdtools 0.0.1

  • Initial Release

Reference manual

It appears you don't have a PDF plugin for this browser. You can click here to download the reference manual.


0.3.6 by Joe Thorley, a month ago


Report a bug at https://github.com/bcgov/ssdtools/issues

Browse source code at https://github.com/cran/ssdtools

Authors: Joe Thorley [aut, cre, ctr] , Carl Schwarz [aut, ctr] , Angeline Tillmanns [ctb] , Ali Azizishirazi [ctb] , Rebecca Fisher [ctb] , David Fox [ctb] , Kathleen McTavish [ctb] , Heather Thompson [ctb] , Andy Teucher [ctb] , Emilie Doussantousse [ctb] , Stephanie Hazlitt [ctb] , Nadine Hussein [ctb] , Nan-Hung Hsieh [ctb] , Sergio Ibarra Espinosa [ctb] , Province of British Columbia [cph]

Documentation:   PDF Manual  

Apache License (== 2.0) | file LICENSE license

Imports chk, fitdistrplus, abind, actuar, ggplot2, graphics, grid, lifecycle, tibble, utils, scales, stats, VGAM, Rcpp

Suggests covr, knitr, rmarkdown, testthat, readr, rlang, purrr, tidyr, dplyr, R.rsp, mle.tools, reshape2

Linking to Rcpp

Imported by GenHMM1d.

See at CRAN