Package: ssdtools 2.1.0.9001

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 parametric 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], Tony Bigwood [ctb], Ali Azizishirazi [ctb], Nadine Hussein [ctb], Sarah Lyons [ctb], Stephanie Hazlitt [ctb], Hadley Wickham [ctb], Sergio Ibarra Espinosa [ctb], Andy Teucher [ctb], Emilie Doussantousse [ctb], Nan-Hung Hsieh [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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NEWS

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

Peer review:

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

Pkgdown:https://bcgov.github.io

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

On CRAN:

bccpp

8.03 score 4 packages 113 scripts 506 downloads 117 exports 61 dependencies

Last updated 11 days agofrom:757573fa2a. Checks:OK: 9. Indexed: no.

TargetResultDate
Doc / VignettesOKDec 10 2024
R-4.5-win-x86_64OKDec 10 2024
R-4.5-linux-x86_64OKDec 10 2024
R-4.4-win-x86_64OKDec 10 2024
R-4.4-mac-x86_64OKDec 10 2024
R-4.4-mac-aarch64OKDec 10 2024
R-4.3-win-x86_64OKDec 10 2024
R-4.3-mac-x86_64OKDec 10 2024
R-4.3-mac-aarch64OKDec 10 2024

Exports:augmentautoplotcoefcomma_signifdgompertzdlgumbelestimatesgeom_hcintersectgeom_ssdgeom_ssdpointgeom_ssdsegmentgeom_xribbonGeomHcintersectGeomSsdpointGeomSsdsegmentGeomXribbonglanceis_censoredis.fitdistslogLiknobsnparsparamspgompertzplgumbelplotpredictqgompertzqlgumbelrgompertzrlgumbelscale_color_ssdscale_colour_ssdscale_fill_ssdssd_censor_datassd_datassd_distsssd_dists_allssd_dists_bcanzssd_eburrIII3ssd_ecdssd_ecd_datassd_egammassd_egompertzssd_einvparetossd_elgumbelssd_ellogisssd_ellogis_llogisssd_elnormssd_elnorm_lnormssd_emultissd_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:abindchkclicodetoolscolorspacecommonmarkcurldigestdplyrfansifarverfurrrfuturegenericsggplot2ggtextglobalsgluegoftestgridtextgtableisobandjpeglabelinglatticelifecyclelistenvmagrittrmarkdownMASSMatrixmgcvmunsellnlmeparallellypillarpkgconfigplyrpngpurrrR6rbibutilsRColorBrewerRcppRcppEigenRdpackrlangscalesssddatastringistringrtibbletidyselectTMBuniversalsutf8vctrsviridisLitewithrxfunxml2

Additional Technical Details

ssdtools Team

Rendered fromadditional-technical-details.Rmdusingknitr::rmarkdownon Dec 10 2024.

Last update: 2024-12-03
Started: 2024-05-02

Customising Plots

ssdtools Team

Rendered fromcustomising-plots.Rmdusingknitr::rmarkdownon Dec 10 2024.

Last update: 2024-10-02
Started: 2024-05-16

Distributions in ssdtools

ssdtools Team

Rendered fromdistributions.Rmdusingknitr::rmarkdownon Dec 10 2024.

Last update: 2024-12-03
Started: 2019-12-05

Getting Started with ssdtools

ssdtools Team

Rendered fromssdtools.Rmdusingknitr::rmarkdownon Dec 10 2024.

Last update: 2024-10-02
Started: 2018-11-15

Model Averaging SSDs

ssdtools Team

Rendered frommodel-averaging.Rmdusingknitr::rmarkdownon Dec 10 2024.

Last update: 2024-12-03
Started: 2024-05-02

Small sample bias in estimates

Rendered fromsmall-sample-bias.pdf.asisusingR.rsp::asison Dec 10 2024.

Last update: 2024-12-03
Started: 2019-12-05

Readme and manuals

Help Manual

Help pageTopics
Augmented Data from fitdists Objectaugment.fitdists
Plot a fitdists Objectautoplot.fitdists
Model Averaged Predictions for CCME Boron Databoron_pred
Turn a fitdists Object into a Tidy Tibblecoef.fitdists
Comma and Significance Formattercomma_signif
Gompertz Probability Density *[Deprecated]*dgompertz
Distribution Datadist_data
Log-Gumbel (Inverse Weibull) Probability Density *[Deprecated]*dlgumbel
Estimates for fitdists Objectestimates.fitdists
Species Sensitivity Hazard Concentration Intersectiongeom_hcintersect
Species Sensitivity Data Points *[Deprecated]*geom_ssd
Species Sensitivity Data Pointsgeom_ssdpoint
Species Sensitivity Censored Segmentsgeom_ssdsegment
Ribbon on X-Axisgeom_xribbon
Get a tibble summarizing each distributionglance.fitdists
Is Censored *[Deprecated]*is_censored
Is fitdists Objectis.fitdists
Parameter Descriptions for ssdtools Functionsargs arguments parameters params
Cumulative Distribution Function for Gompertz Distribution *[Deprecated]*pgompertz
Cumulative Distribution Function for Log-Gumbel Distribution *[Deprecated]*plgumbel
Predict Hazard Concentrations of fitburrlioz Objectpredict.fitburrlioz
Predict Hazard Concentrations of fitdists Objectpredict.fitdists
Quantile Function for Gompertz Distribution *[Deprecated]*qgompertz
Quantile Function for Log-Gumbel Distribution *[Deprecated]*qlgumbel
Random Generation for Gompertz Distribution *[Deprecated]*rgompertz
Random Generation for log-Gumbel Distribution *[Deprecated]*rlgumbel
Discrete color-blind scale for SSD Plotsscale_color_ssd scale_colour_ssd scale_fill_ssd
Censor Datassd_censor_data
Data from fitdists Objectssd_data
Species Sensitivity Distributionsssd_dists
All Species Sensitivity Distributionsssd_dists_all
BCANZ Distributionsssd_dists_bcanz
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 Concentrations for Burrlioz Fit *[Deprecated]*ssd_hc_burrlioz
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 and offset hazard concentration value if present in breaks.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
Cullen and Frey Plot *[Deprecated]*ssd_plot_cf
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
Water Quality Guideline for British Columbiassd_wqg_bc
Water Quality Guideline for Burrliozssd_wqg_burrlioz
ggproto Classes for Plotting Species Sensitivity Data and DistributionsGeomHcintersect GeomSsdpoint GeomSsdsegment GeomXribbon ssdtools-ggproto StatSsdpoint StatSsdsegment
Plot Species Sensitivity Data *[Deprecated]*stat_ssd
Subset fitdists Objectsubset.fitdists
Turn a fitdists Object into a Tibbletidy.fitdists