`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 different species as described by Posthuma et al. (2001). The ssdtools package uses Maximum Likelihood to fit distributions such as the log-normal, gamma, burr Type-III, log-logistic, log-Gumbel, Gompertz and Weibull. The user can also provide custom distributions. Multiple distributions can be averaged using Information Criteria. Confidence intervals on hazard concentrations and proportions are produced by parametric 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 `ssd_fit_dists()`

and plot using the `ggplot2`

generic `autoplot`

The goodness of fit can be assessed using `ssd_gof`

```
ssd_gof(boron_dists)
#> # A tibble: 3 x 9
#> dist ad ks cvm aic aicc bic delta weight
#> * <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
#> 1 burrIII2 0.500 0.108 0.0628 241. 242. 244. 3.74 0.093
#> 2 gamma 0.440 0.117 0.0554 238. 238. 240. 0 0.606
#> 3 lnorm 0.507 0.107 0.0703 239. 240. 242. 1.40 0.301
```

and the model-averaged 5% hazard concentration estimated using `ssd_hc`

```
print(boron_hc5)
#> # A tibble: 1 x 6
#> percent est se lcl ucl dist
#> <dbl> <dbl> <dbl> <dbl> <dbl> <chr>
#> 1 5 1.30 0.813 0.521 3.58 average
```

Model-averaged predictions complete with confidence intervals can be produced using the `stats`

generic `predict`

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)
```

Posthuma, L., Suter II, G.W., and Traas, T.P. 2001. Species Sensitivity Distributions in Ecotoxicology. CRC Press.

Get started with ssdtools at https://bcgov.github.io/ssdtools/articles/ssdtools.html.

A shiny webpage developed for non-R-users is available at https://bcgov-env.shinyapps.io/ssdtools/.

The ssdtools package was developed as a result of earlier drafts of:

Schwarz, C., and Tillmanns, A. 2019. Improving Statistical Methods for Modeling Species Sensitivity Distributions. Province of British Columbia, Victoria, BC. Available from http://a100.gov.bc.ca/appsdata/acat/documents/r57400/2_1568399094009_8398900200.pdf.

The CCME `data.csv`

data file is derived from a factsheet prepared by the Canadian Council of Ministers of the Environment. See the `data-raw`

folder for more information.

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

```
To cite ssdtools in publications use:
Thorley, J. and Schwarz C., (2018). ssdtools An R package to fit
Species Sensitivity Distributions. Journal of Open Source Software,
3(31), 1082. https://doi.org/10.21105/joss.01082
A BibTeX entry for LaTeX users is
@Article{,
title = {{ssdtools}: An R package to fit Species Sensitivity Distributions},
author = {Joe Thorley and Carl Schwarz},
journal = {Journal of Open Source Software},
year = {2018},
volume = {3},
number = {31},
pages = {1082},
doi = {10.21105/joss.01082},
}
```

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.
```

ssdtools by the Province of British Columbia is licensed under a Creative Commons Attribution 4.0 International License.