Package: ssdtools 2.6.0.9002

Joe Thorley

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.

Authors:Joe Thorley [aut, cre], Rebecca Fisher [aut], David Fox [aut], Carl Schwarz [aut], Angeline Tillmanns [ctb], Seb Dalgarno [ctb], Kathleen McTavish [ctb], Heather Thompson [ctb], Doug Spry [ctb], Rick van Dam [ctb], Graham Batley [ctb], Ali Azizishirazi [ctb], Nadine Hussein [ctb], Sarah Lyons [ctb], Duncan Kennedy [ctb], Stephanie Hazlitt [ctb], Hadley Wickham [ctb], Sergio Ibarra Espinosa [ctb], Andy Teucher [ctb], Emilie Doussantousse [ctb], Nan-Hung Hsieh [ctb], Florencia D'Andrea [ctb], Eduard Szöcs [ctb], Province of British Columbia [fnd, cph], Environment and Climate Change Canada [fnd, cph], Australian Government Department of Climate Change, Energy, the Environment and Water [fnd, cph]

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manual.pdf |manual.html✨
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ssdtools/json (API)
NEWS

# Install 'ssdtools' in R:
install.packages('ssdtools', repos = c('https://poissonconsulting.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/bcgov/ssdtools/issues

Pkgdown/docs site:https://bcgov.github.io

Uses libs:
  • c++– GNU Standard C++ Library v3

On CRAN:

Conda:

bccpp

7.35 score 1 stars 7 packages 126 scripts 919 downloads 122 exports 68 dependencies

Last updated from:d4865f65c7. Checks:12 OK, 1 FAIL. Indexed: no.

TargetResultTimeFilesSyslog
linux-devel-arm64OK335
linux-devel-x86_64OK308
source / vignettesOK339
linux-release-arm64OK311
linux-release-x86_64OK299
macos-release-arm64OK221
macos-release-x86_64OK426
macos-oldrel-arm64OK179
macos-oldrel-x86_64OK536
windows-develOK349
windows-releaseOK318
windows-oldrelOK349
wasm-releaseFAIL154

Exports:augmentautoplotcoefcomma_signifdgompertzdlgumbelestimatesgeom_hcintersectgeom_ssdgeom_ssdpointgeom_ssdsegmentgeom_xribbonGeomHcintersectGeomSsdpointGeomSsdsegmentGeomXribbonglanceis_censoredis.fitdistslogLiknobsnparsparamspgompertzplgumbelplotpredictqgompertzqlgumbelrgompertzrlgumbelscale_color_ssdscale_colour_ssdscale_fill_ssdssd_at_boundaryssd_censor_datassd_ci_methodsssd_computablessd_datassd_distsssd_dists_allssd_dists_bcanzssd_dists_shinyssd_eburrIII3ssd_ecdssd_ecd_datassd_egammassd_egompertzssd_einvparetossd_elgumbelssd_ellogisssd_ellogis_llogisssd_elnormssd_elnorm_lnormssd_emultissd_est_methodsssd_eweibullssd_exposuressd_fit_bcanzssd_fit_burrliozssd_fit_distsssd_gofssd_hcssd_hc_bcanzssd_hc_burrliozssd_hpssd_hp_bcanzssd_is_censoredssd_label_commassd_label_comma_hcssd_licensing_mdssd_match_momentsssd_min_pmixssd_palssd_pburrIII3ssd_pgammassd_pgompertzssd_pinvparetossd_plgumbelssd_pllogisssd_pllogis_llogisssd_plnormssd_plnorm_lnormssd_plotssd_plot_cdfssd_plot_cfssd_plot_datassd_pmultissd_pmulti_fitdistsssd_pweibullssd_qburrIII3ssd_qgammassd_qgompertzssd_qinvparetossd_qlgumbelssd_qllogisssd_qllogis_llogisssd_qlnormssd_qlnorm_lnormssd_qmultissd_qmulti_fitdistsssd_qweibullssd_rburrIII3ssd_rgammassd_rgompertzssd_rinvparetossd_rlgumbelssd_rllogisssd_rllogis_llogisssd_rlnormssd_rlnorm_lnormssd_rmultissd_rmulti_fitdistsssd_rweibullssd_sort_datassd_wqg_bcssd_wqg_burrliozstat_ssdStatSsdpointStatSsdsegmenttidywaiver

Dependencies:abindbitbit64chkclicliprcodetoolscommonmarkcpp11crayoncurldigestdplyrfarverfurrrfuturegenericsggplot2ggtextglobalsgluegoftestgridtextgtablehmsisobandjpeglabelinglatticelifecyclelistenvlitedownmagrittrmarkdownMatrixparallellypillarpkgconfigplyrpngprettyunitsprogresspurrrR6rbibutilsRColorBrewerRcppRcppEigenRdpackreadrrlangS7scalesssddatastringistringrtibbletidyselectTMBtzdbuniversalsutf8vctrsviridisLitevroomwithrxfunxml2

Frequently Asked Questions

ssdtools Team

Rendered fromfaqs.Rmdusingknitr::rmarkdownon Jun 01 2026.

Last update: 2025-04-17
Started: 2019-12-04

Getting Started with ssdtools

ssdtools Team

Rendered fromssdtools.Rmdusingknitr::rmarkdownon Jun 01 2026.

Last update: 2025-12-15
Started: 2018-11-15

Readme and manuals

Help Manual

Help pageTopics
Augmented Data from fitdists Objectaugment.fitdists
Plot a fitdists Objectautoplot.fitdists
Turn a fitdists Object into a Tidy Tibblecoef.fitdists
Estimates for fitdists Objectestimates.fitdists
Species Sensitivity Hazard Concentration Intersectiongeom_hcintersect
Species Sensitivity Data Pointsgeom_ssdpoint
Species Sensitivity Censored Segmentsgeom_ssdsegment
Ribbon on X-Axisgeom_xribbon
Get a tibble summarizing each distributionglance.fitdists
Is fitdists Objectis.fitdists
Predict Hazard Concentrations of fitburrlioz Objectpredict.fitburrlioz
Predict Hazard Concentrations of fitdists Objectpredict.fitdists
Discrete color-blind scale for SSD Plotsscale_color_ssd scale_colour_ssd scale_fill_ssd
Is At Boundaryssd_at_boundary ssd_at_boundary.fitdists ssd_at_boundary.tmbfit
Censor Datassd_censor_data
Is Computable Standard Errorsssd_computable ssd_computable.fitdists ssd_computable.tmbfit
Data from fitdists Objectssd_data
Species Sensitivity Distributionsssd_dists
All Species Sensitivity Distributionsssd_dists_all
BCANZ Distributionsssd_dists_bcanz
All Shiny Species Sensitivity Distributionsssd_dists_shiny
Default Parameter Estimatesssd_e ssd_eburrIII3 ssd_egamma ssd_egompertz ssd_einvpareto ssd_elgumbel ssd_ellogis ssd_ellogis_llogis ssd_elnorm ssd_elnorm_lnorm ssd_emulti ssd_eweibull
Empirical Cumulative Densityssd_ecd
Empirical Cumulative Density for Species Sensitivity Datassd_ecd_data
Proportion Exposuressd_exposure
Fit BCANZ Distributionsssd_fit_bcanz
Fit Burrlioz Distributionsssd_fit_burrlioz
Fit Distributionsssd_fit_dists
Goodness of Fitssd_gof ssd_gof.fitdists
Hazard Concentrations for Species Sensitivity Distributionsssd_hc ssd_hc.fitburrlioz ssd_hc.fitdists ssd_hc.list
BCANZ Hazard Concentrationsssd_hc_bcanz
Hazard Proportionssd_hp ssd_hp.fitburrlioz ssd_hp.fitdists
BCANZ Hazard Proportionssd_hp_bcanz
Is Censoredssd_is_censored ssd_is_censored.data.frame ssd_is_censored.fitdists
Label numbers with significant digits and commassd_label_comma
Label numbers with significant digits and comma. If 'hc_value' is present in breaks, put on new line and make bold.ssd_label_comma_hc
Licensing Markdownssd_licensing_md
Match Momentsssd_match_moments
Calculate Minimum Proportion in Mixture Modelsssd_min_pmix
Color-blind Palette for SSD Plotsssd_pal
Cumulative Distribution Functionssd_p ssd_pburrIII3 ssd_pgamma ssd_pgompertz ssd_pinvpareto ssd_plgumbel ssd_pllogis ssd_pllogis_llogis ssd_plnorm ssd_plnorm_lnorm ssd_pmulti ssd_pmulti_fitdists ssd_pweibull
Plot Species Sensitivity Data and Distributionsssd_plot
Plot Cumulative Distribution Function (CDF)ssd_plot_cdf ssd_plot_cdf.fitdists ssd_plot_cdf.list
Plot Species Sensitivity Datassd_plot_data
Quantile Functionssd_q ssd_qburrIII3 ssd_qgamma ssd_qgompertz ssd_qinvpareto ssd_qlgumbel ssd_qllogis ssd_qllogis_llogis ssd_qlnorm ssd_qlnorm_lnorm ssd_qmulti ssd_qmulti_fitdists ssd_qweibull
Random Number Generationssd_r ssd_rburrIII3 ssd_rgamma ssd_rgompertz ssd_rinvpareto ssd_rlgumbel ssd_rllogis ssd_rllogis_llogis ssd_rlnorm ssd_rlnorm_lnorm ssd_rmulti ssd_rmulti_fitdists ssd_rweibull
Sort Species Sensitivity Datassd_sort_data
ggproto Classes for Plotting Species Sensitivity Data and DistributionsGeomHcintersect GeomSsdpoint GeomSsdsegment GeomXribbon ssdtools-ggproto StatSsdpoint StatSsdsegment
Subset fitdists Objectsubset.fitdists
Turn a fitdists Object into a Tibbletidy.fitdists