ssdtools

An R package to fit and plot Species Sensitivity Distributions, cumulative probability distributions which are fitted to toxicity concentrations for different species.
https://github.com/bcgov/ssdtools

Category: Biosphere
Sub Category: Species Distribution Modeling

Keywords

ecotoxicology env rstats species-sensitivity-distribution

Keywords from Contributors

ssd water-quality-guideline citz flnr shiny

Last synced: about 24 hours ago
JSON representation

Repository metadata

An R package to fit and plot Species Sensitivity Distributions (SSDs)

• Host: GitHub
• URL: https://github.com/bcgov/ssdtools
• Owner: bcgov
• License: apache-2.0
• Created: 2017-11-28T22:29:01.000Z (over 7 years ago)
• Default Branch: main
• Last Pushed: 2025-04-17T00:44:17.000Z (10 days ago)
• Last Synced: 2025-04-21T21:11:29.251Z (5 days ago)
• Topics: ecotoxicology, env, rstats, species-sensitivity-distribution
• Language: R
• Homepage: https://bcgov.github.io/ssdtools/
• Size: 94.2 MB
• Stars: 33
• Watchers: 9
• Forks: 18
• Open Issues: 20
• Releases: 12
• Metadata Files:
  • Readme: README.Rmd
  • Changelog: NEWS.md
  • Contributing: .github/CONTRIBUTING.md
  • License: LICENSE
  • Code of conduct: .github/CODE_OF_CONDUCT.md
  • Citation: CITATION.cff
  • Support: .github/SUPPORT.md

README.Rmd

          ---
output: github_document
---



```{r, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "man/figures/README-",
  out.width = "100%"
)
```

# ssdtools 


[![Lifecycle: stable](https://img.shields.io/badge/lifecycle-stable-brightgreen.svg)](https://lifecycle.r-lib.org/articles/stages.html#stable)
[![R-CMD-check](https://github.com/bcgov/ssdtools/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/bcgov/ssdtools/actions/workflows/R-CMD-check.yaml)
[![Codecov test coverage](https://codecov.io/gh/bcgov/ssdtools/graph/badge.svg)](https://app.codecov.io/gh/bcgov/ssdtools)
[![CRAN status](https://www.r-pkg.org/badges/version/ssdtools)](https://cran.r-project.org/package=ssdtools)
[![DOI](https://joss.theoj.org/papers/10.21105/joss.07492/status.svg)](https://doi.org/10.21105/joss.07492)


`ssdtools` is an R package to fit and plot 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, log-logistic, log-Gumbel (also known as the inverse Weibull), gamma, Weibull 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.

## Introduction

The dependency [`ssddata`](https://github.com/open-AIMS/ssddata) provides example data sets for several chemicals including Boron.
The [ECOTOX](https://cfpub.epa.gov/ecotox/) Knowledgebase is another source of toxicity concentrations for over 12,000 chemicals.

```{r, message=FALSE}
library(ssdtools)
ssddata::ccme_boron
```

The six default distributions are fit using `ssd_fit_dists()`

```{r}
fits <- ssd_fit_dists(ssddata::ccme_boron)
```

and can be quickly plotted using `autoplot`

```{r, warning = FALSE, message = FALSE, fig.alt="A plot of the data and fitted distributions"}
autoplot(fits)
```

The goodness of fit can be assessed using `ssd_gof`

```{r}
ssd_gof(fits)
```

and the model-averaged 5% hazard concentration estimated (with bootstrapping to get confidence intervals) using `ssd_hc`.

```{r}
set.seed(99)
hc5 <- ssd_hc(fits, ci = TRUE)
print(hc5)
```

Model-averaged predictions complete with confidence intervals can also be estimated by parametric bootstrapping using the `stats` generic `predict`.

```{r, eval=FALSE}
boron_pred <- predict(fits, ci = TRUE)
```

The predictions can be plotted together with the original data using `ssd_plot`.

```{r, fig.alt="A plot of the data and model-averaged prediction with confidence intervals"}
library(ggplot2)

theme_set(theme_bw())

ssd_plot(ssddata::ccme_boron, boron_pred,
  shape = "Group", color = "Group", label = "Species",
  xlab = "Concentration (mg/L)", ribbon = TRUE
) +
  expand_limits(x = 3000) +
  scale_colour_ssd()
```

## Information

Get started with ssdtools at .

A shiny app to allow non-R users to interface with ssdtools is available at .

For the latest changes to the development version see the [NEWS](https://bcgov.github.io/ssdtools/news/) file.

For recent developments in SSD modeling including a review of existing software see:

*Fox, D.R., et al. 2021. Recent Developments in Species Sensitivity Distribution Modeling. Environ Toxicol Chem 40(2): 293–308. .*

## Citation

```{r, comment = "", echo = FALSE}
citation("ssdtools")
```

## Installation

### Release

To install the latest release version from [CRAN](https://CRAN.R-project.org/package=ssdtools).
```r
install.packages("ssdtools")
```

The website for the release version is at .

### Development

To install the development version from [GitHub](https://github.com/bcgov/ssdtools)
```r
# install.packages("remotes")
remotes::install_github("bcgov/ssdtools")
```

or from [r-universe](https://bcgov.r-universe.dev/ssdtools).
```r
install.packages("ssdtools", repos = c("https://bcgov.r-universe.dev", "https://cloud.r-project.org"))
```

The website for the development version is at .

### Getting Help or Reporting an Issue

To report bugs/issues/feature requests, please file an [issue](https://github.com/bcgov/ssdtools/issues/).

### Contribution

If you would like to contribute to the package, please see our 
[CONTRIBUTING](https://github.com/bcgov/ssdtools/blob/master/.github/CONTRIBUTING.md) guidelines.

### Code of Conduct

Please note that the ssdtools project is released with a [Contributor Code of Conduct](https://contributor-covenant.org/version/2/1/CODE_OF_CONDUCT.html). 
By contributing to this project, you agree to abide by its terms.

## References

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



```{r, results = "asis", echo = FALSE}
cat(ssdtools::ssd_licensing_md())
```

        

Citation (CITATION.cff)

cff-version: "1.2.0"
authors:
- family-names: Thorley
  given-names: Joe
  orcid: "https://orcid.org/0000-0002-7683-4592"
- family-names: Fisher
  given-names: Rebecca
  orcid: "https://orcid.org/0000-0001-5148-6731"
- family-names: Fox
  given-names: David
  orcid: "https://orcid.org/0000-0002-3178-7243"
- family-names: Schwarz
  given-names: Carl
  orcid: "https://orcid.org/0000-0002-8525-862X"
contact:
- family-names: Thorley
  given-names: Joe
  orcid: "https://orcid.org/0000-0002-7683-4592"
doi: 10.5281/zenodo.14609128
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Thorley
    given-names: Joe
    orcid: "https://orcid.org/0000-0002-7683-4592"
  - family-names: Fisher
    given-names: Rebecca
    orcid: "https://orcid.org/0000-0001-5148-6731"
  - family-names: Fox
    given-names: David
    orcid: "https://orcid.org/0000-0002-3178-7243"
  - family-names: Schwarz
    given-names: Carl
    orcid: "https://orcid.org/0000-0002-8525-862X"
  date-published: 2025-01-28
  doi: 10.21105/joss.07492
  issn: 2475-9066
  issue: 105
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 7492
  title: "ssdtools v2: An R package to fit Species Sensitivity
    Distributions"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.07492"
  volume: 10
title: "ssdtools v2: An R package to fit Species Sensitivity
  Distributions"

---

Owner metadata

• Name: bcgov
• Login: bcgov
• Email: [email protected]
• Kind: organization
• Description: This is the home for code that is open
• Website: https://github.com/bcgov/BC-Policy-Framework-For-GitHub
• Location: Canada
• Twitter:
• Company:
• Icon url: https://avatars.githubusercontent.com/u/916280?v=4
• Repositories: 2150
• Last ynced at: 2024-12-16T17:13:08.511Z
• Profile URL: https://github.com/bcgov

---

GitHub Events

Total

• Create event: 12
• Issues event: 17
• Release event: 4
• Watch event: 3
• Delete event: 5
• Issue comment event: 43
• Push event: 93
• Pull request review comment event: 2
• Pull request review event: 18
• Pull request event: 44
• Fork event: 3

Last Year

• Create event: 12
• Issues event: 17
• Release event: 4
• Watch event: 3
• Delete event: 5
• Issue comment event: 43
• Push event: 93
• Pull request review comment event: 2
• Pull request review event: 18
• Pull request event: 44
• Fork event: 3

---

Committers metadata

Last synced: 5 days ago

Name	Email	Commits
Joe Thorley	j****e@p****a	1801
Seb Dalgarno	s****b@p****a	18
Duncan Kennedy	d****n@p****a	14
Nadine Hussein	n****3@g****m	13
Rebecca Fisher	R****r@a****u	10
atillmanns	a****s@g****a	8
Eduard Szöcs	e****s@b****m	8
Sarah Lyons	s****h@p****a	7
stephhazlitt	s****t@g****a	6
Nan-Hung Hsieh	n****h@c****u	4
cschwarz-stat-sfu-ca	c****z@s****a	3
Nan-Hung Hsieh	n****3@h****m	2
Hadley Wickham	h****m@g****m	1
Sergio Ibarra Espinosa	z****a@g****m	1
repo-mountie[bot]	4****]	1
Rebecca Fisher	r****r@A****u	1

Committer domains:

• poissonconsulting.ca: 4
• gov.bc.ca: 2
• aims-7bqq564.aims.gov.au: 1
• stat.sfu.ca: 1
• cvm.tamu.edu: 1
• basf.com: 1
• aims.gov.au: 1

---

Issue and Pull Request metadata

Last synced: 2 days ago

More stats: https://issues.ecosyste.ms/repositories/lookup?url=https://github.com/bcgov/ssdtools

---

---

---

Package metadata

• Total packages: 1
• Total downloads:
  • cran: 1,022 last-month
• Total dependent packages: 1
• Total dependent repositories: 4
• Total versions: 24
• Total maintainers: 1

---

Dependencies

Score: 13.678251081807012