R Observatory: Metrics for ssdtools version 2.7.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

ssdtools

2.7.0Package record

Species Sensitivity Distributions

1packages dependsuggested by 1

10.4Kdownloads / year

87.0%test coverage

13/13flavors OK

Overview

About

Maintained by Joe ThorleyCRAN page ↗GitHub ↗Website ↗Issues ↗Declared funders: Australian Government Department of Climate Change, Energy, the Environment and Water, Environment and Climate Change Canada and 1 more

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.

Changes in 2.7.0

Bug Fixes

AICc is now Inf (as undefined) when the number of observations is less than or equal to the number of parameters. Previously it was only Inf when equal to the number of parameters plus 1 (poissonconsulting/ssdtools#175).
Fixed distribution function lookup to the ssdtools namespace only so that attached packages exporting m* helpers (notably actuar) no longer break ssd_fit_dists() (#479).
Fixed starting values for weighted fits, which previously used the logical weight flag in place of the weight vector.
Removed a duplicate ssd_elgumbel() definition.
Fixed the function names in two ssd_hp() deprecation messages.
ssd_hc() and ssd_hp() now return one row per input value when values are duplicated (poissonconsulting/ssdtools#141).
ssd_label_comma_hc() now marks the hazard concentration when big.mark or decimal.mark change the formatting of the label (#482).

Additions

Added ssd_element_text_hc(), a theme element that draws multi-line axis labels in bold, which replaces ggtext::element_markdown() for the hazard concentration label (#482).

Modifications

ssd_label_comma_hc() now puts the hazard concentration label on its own line instead of marking it up as markdown (#482).

Show all changes in 2.7.0Hide the rest of the changes in 2.7.0

Replaced the deprecated ..density.. with after_stat(density) in StatSsdpoint.

Dependencies

Moved dplyr and VGAM from Suggests to Imports and dropped the unused plyr, abind, magrittr, reshape2 and tidyselect dependencies. Fitting the Gompertz distribution no longer prompts to install VGAM.
Removed the dependency on the ggtext package, which is scheduled for archival on CRAN (#482).

Error Checking

ssd_plot() now checks that hc is numeric and that decimal.mark is a string and ssd_plot_data() now checks that suffix is a string.

Documentation

Removed the small sample bias vignette (moved to ssdvignettes).
Updated the range_shape1 and range_shape2 parameter descriptions.
Updated the README with the consultation process.

From NEWS.md in the release

Install

R (CRAN)pak (dev)Ubuntu (r2u)Fedora (COPR)openSUSE (OBS)

install.packages("ssdtools", repos = "https://cloud.r-project.org/")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

if (!requireNamespace("pak", quietly = TRUE))
  install.packages("pak", repos = "https://cloud.r-project.org/")
pak::pak("bcgov/ssdtools")

Development version from bcgov/ssdtools. Installs pak first if it is not already available.

Release

# enable cranapt (r2u) if it is not already set up, then install
grep -rqs r2u.stat.illinois.edu /etc/apt/sources.list /etc/apt/sources.list.d/ \
  || curl -fsSL https://raw.githubusercontent.com/eddelbuettel/r2u/master/inst/scripts/add_cranapt_noble.sh | sudo bash
sudo apt install -y r-cran-ssdtools

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled. We list this channel from recorded r2u download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

bspm (used by r2u) also needs make: sudo apt install make

# enable the iucar/cran COPR if it is not already present, then install
ls /etc/yum.repos.d/*iucar*cran*.repo >/dev/null 2>&1 \
  || sudo dnf copr enable -y iucar/cran
sudo dnf install -y R-CRAN-ssdtools

RPMs from the iucar/cran COPR, rebuilt from CRAN.

For install.packages() integration in R, also: sudo dnf install R-CoprManager

# add the autoCRAN OBS repo (Tumbleweed) if it is missing, then install
zypper -q lr | grep -qi autoCRAN \
  || sudo zypper addrepo https://download.opensuse.org/repositories/devel:/languages:/R:/autoCRAN/openSUSE_Tumbleweed/devel:languages:R:autoCRAN.repo
sudo zypper install -y R-ssdtools

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed). We list this channel from recorded autoCRAN download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

Health

CRAN checks

13OK

CRAN check page ↗

Slowest check: 13.8 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-09-05
NOTE11 OK, 2 NOTE2026-07-16
OK12 OK, 1 FAILURE2026-06-08
WARNING12 OK, 1 WARNING2026-06-07
OK12 OK2026-04-25

Show 3 earlier changesHide 3 earlier changes

NOTE11 OK, 3 NOTE2026-04-22
ERROR10 OK, 3 NOTE, 1 ERROR2026-04-18
NOTE11 OK, 3 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 2.7.0

READMEYes · 818 wordsVignettesYes · 2 · evaluation depends on the environmentNEWSYes · 100% structured · mentions 2.7.0Citation fileYes · cites a publicationWebsiteYes · pkgdown

The repository also keeps web-only articles.

Cites a JOSS paper

Help pages: 74 (23 internal)includes a package overview page
Examples that run: 91%52 run in a plain check · 5 never run
Exported functions with examples: 74%
Documented parameters: 99%
Return-value docs: 60%
Help pages citing references: 1%

Vignettes (2)

Getting Started with ssdtools HTML
Frequently Asked Questions HTML

How these are measured

Downloads

10.4K

CRAN downloads in the past year

Rank #4,369 · ~28/day · ~864/mo

Releases R versions

Daily download trend is not available in this view yet.

69830 days

1.9K90 days

10.4K1 year

Compare downloads with other packages →

Also on624 r2u13 autocran

How downloads are counted

Repository

bcgov/ssdtools ↗Organization: bcgov

40Stars

21Forks

30Open issues

0Open PRs

14Releases

2,499Commits

20Commit identities

rstatsecotoxicologyspecies-sensitivity-distributionenv

License file reads as Apache-2.0 · 2,499 commits · Last activity 2026-08-31 · +2.6% stars, 30d

Responsiveness

How these are sampled

PRs merged (all time): 85%
Median days to close, 50 most recently updated closed issues: 16
Median days to close, 50 most recently updated closed PRs: 1

Stars over time

2025-09-05 · 342026-09-20 · 40

How these are measured

PracticesBeta

19 development-tooling and community-health practices detected across 8 families in the upstream repository

Checks run against github.com/bcgov/ssdtools on 2026-10-11.

Continuous integration (2)

GitHub ActionsR CMD check workflow

The R CMD check workflow runs on Linux

Governance and community (5)

Code of conductContributing guidePR templateCODEOWNERSSupport guide

Docs source (3)

README.Rmdpkgdown

GitHub Pages site last deployed 2026-09-01

pkgdown site last built 2026-09-01

Coverage (2)

Coverage reporting (Codecov).covrignore

Show all practicesHide 4 practices

Reproducibility and dev environment (1)

data-raw/

CRAN release process (3)

cran-comments.mdrevdep/CRAN-SUBMISSION

Research and citation (1)

CITATION.cff

Lint, format, editor (2)

AirRStudio project

How this is detected·Detection ruleset v3 (2026-09-26)

AI coding toolsBeta

This repository shows signs of AI coding tools.

Claude Codefirst seen 2026-06-07
Named in .Rbuildignore: .claude
Commits: at least 29 crediting it in the message
Cursorfirst seen on or before 2026-08-04
Commits: at least 1 crediting it in the message

From outside contributors

Claude Code
Pull requests: 3 from outside contributors, first on 2026-06-10, 3 from forks

Models named in its commits

Claude Opus 511 commits · Aug 2026
Claude Opus 4.810 commits · Jun 2026
Claude Fable 58 commits · Jul 2026

Counts are commits, not lines of code. Commits by a tool's accounts count once across all of its accounts. Commits crediting it are the largest count among its credit lines, a minimum.How this is detected·Detection ruleset v4 (updated 2026-09-27)

Dependencies

Declared dependencies

35 external dependencies (excludes base and recommended)

Installing ssdtools adds 54 packages (27 with compiled code, 41 MB of source tarballs). Heaviest: stringi 11 MB, ggplot2 6.0 MB, Rcpp 1.8 MB.

Depends (1)

R >= 4.1

Imports (24)

chk dplyr furrr generics ggplot2 glue goftestgraphicsgridlifecycleparallelpurrr Rcpp readr rlang scales ssddatastatsstringr tibble TMB universalsutilsVGAM

LinkingTo (3)

Rcpp RcppEigen TMB

Suggests (14)

actuar covr EnvStats extraDistr fitdistrplusgrDevicesknitr latex2exp patchwork rmarkdown testthat tidyr tinytex withr

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

1direct

0indirect

Imports 1

Suggested by 1

Depends, Imports or LinkingTo, most downloaded first

GenHMM1d

Suggests, most downloaded first

serocalculator

How these are counted

Code & Tests

Datasets

People & History

People (26)

Joe Thorley

Author, Maintainer since 0.0.2 (2018)

Rebecca Fisher

Author · added in 0.1.0

David Fox

Author · added in 0.1.0

Carl Schwarz

Author

Ali Azizishirazi

Contributor

Graham Batley

Contributor · added in 1.0.4

Florencia D'Andrea

Contributor · added in 2.2.0

Seb Dalgarno

Contributor · added in 1.0.2

Emilie Doussantousse

Contributor · added in 0.0.3

Stephanie Hazlitt

Contributor

Nan-Hung Hsieh

Contributor · added in 0.1.0

Nadine Hussein

Contributor · added in 0.3.3

Show 11 more contributorsHide 11 contributors

Sergio Ibarra Espinosa

Contributor · added in 0.1.0

Duncan Kennedy

Contributor · added in 2.2.0

Sarah Lyons

Contributor · added in 2.0.0

Kathleen McTavish

Contributor · added in 0.0.3

Doug Spry

Contributor · added in 1.0.4

Eduard Szöcs

Contributor · added in 2.4.0

Andy Teucher

Contributor · added in 0.0.3

Heather Thompson

Contributor · added in 0.0.3

Angeline Tillmanns

Contributor

Hadley Wickham

Contributor · added in 2.0.0

Rick van Dam

Contributor · added in 1.0.4

Australian Government Department of Climate Change, Energy, the Environment and Water

Funder, Copyright holder · added in 2.0.0

Environment and Climate Change Canada

Funder, Copyright holder · added in 1.0.0

Province of British Columbia

Funder, Copyright holder

Listed in earlier versions (1)

Tony Bigwood

no longer listed · 2.0.0 to 2.1.0

Releases (28)

Pick two releases to compare their code metrics.

2.7.0Latest
record
2026-08-31 · current release · diff ↗ ·
added 1 export
ssd_element_text_hc
R
R 4.6.0 released · 2026-04-24
2.6.0
record
2026-03-05 · diff ↗
2.5.0
record
2025-12-01 · diff ↗
2.4.0
record
2025-09-12 · diff ↗ ·
added 4 exports
ssd_at_boundary, ssd_ci_methods, ssd_computable, ssd_est_methods
R
R 4.5.0 released · 2025-04-11
2.3.0
record
2025-02-20 · diff ↗
2.2.0
record
2025-01-14 · diff ↗ ·
added 2 exports
ssd_dists_shiny, ssd_label_comma_hc
2.1.0
record
2024-10-21 · diff ↗ ·
added 3 exports
ssd_pmulti_fitdists, ssd_qmulti_fitdists, ssd_rmulti_fitdists
2.0.0
record
2024-10-09 · diff ↗ ·
removed 1 export
ssd_cfplot

added 21 exports
params, scale_fill_ssd, ssd_censor_data, ssd_eburrIII3, ssd_egamma, ssd_egompertz, ssd_einvpareto, ssd_elgumbel, ssd_ellogis, ssd_ellogis_llogis, ssd_elnorm, ssd_elnorm_lnorm, ssd_emulti, ssd_eweibull, ssd_hp_bcanz, ssd_label_comma, ssd_licensing_md, ssd_min_pmix, ssd_pmulti, ssd_qmulti, ssd_rmulti
R
R 4.4.0 released · 2024-04-24
1.0.6
record
2023-09-07 · diff ↗
1.0.5
record
2023-08-29 · diff ↗
1.0.4
record
2023-05-17 · diff ↗
R
R 4.3.0 released · 2023-04-21
1.0.3
record
2023-04-12 · diff ↗

Show 21 earlier eventsHide 21 earlier events

1.0.2
record
2022-05-15 · diff ↗
R
R 4.2.0 released · 2022-04-22
1.0.1
record
2022-04-10 · diff ↗
1.0.0
record
2022-04-01 · diff ↗ ·
removed 48 exports
GeomSsd, GeomSsdcens, StatSsd, StatSsdcens, dburrIII2, dburrIII3, dgamma, dllog, dllogis, dlnorm, dpareto, dweibull, is.fitdist, is.fitdistcens, is.fitdistscens, pburrIII2, pburrIII3, pgamma, pllog, pllogis, plnorm, ppareto, pweibull, qburrIII2, qburrIII3, qgamma, qllog, qllogis, qlnorm, qpareto and 18 more

added 65 exports
GeomSsdpoint, GeomSsdsegment, StatSsdpoint, StatSsdsegment, augment, autoplot, coef, estimates, geom_ssdpoint, geom_ssdsegment, glance, is_censored, logLik, nobs, plot, predict, scale_color_ssd, scale_colour_ssd, ssd_data, ssd_dists, ssd_dists_all, ssd_dists_bcanz, ssd_ecd_data, ssd_fit_bcanz, ssd_fit_burrlioz, ssd_hc_bcanz, ssd_hc_burrlioz, ssd_is_censored, ssd_pal, ssd_pburrIII3 and 35 more
0.3.7
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2021-10-27 · diff ↗
0.3.6
record
2021-09-22 · diff ↗
0.3.5
record
2021-09-03 · diff ↗
R
R 4.1.0 released · 2021-05-18
0.3.4
record
2021-05-14 · diff ↗
0.3.3
record
2021-02-19 · diff ↗
0.3.2
record
2020-09-02 · diff ↗
0.3.1
record
2020-09-01 · diff ↗
0.3.0
record
2020-07-10 · diff ↗ ·
added 5 exports
dlnorm, plnorm, qlnorm, rlnorm, slnorm
R
R 4.0.0 released · 2020-04-24
0.2.0
record
2020-04-15 · diff ↗
0.1.1
record
2020-01-24 · diff ↗
0.1.0
record
2020-01-13 · diff ↗ ·
added 33 exports
dburrIII2, dburrIII3, dgamma, dllogis, dweibull, pburrIII2, pburrIII3, pgamma, pllogis, pweibull, qburrIII2, qburrIII3, qgamma, qllogis, qweibull, rburrIII2, rburrIII3, rgamma, rllogis, rweibull, sburrIII2, sburrIII3, sgamma, sgompertz, slgumbel, sllog, sllogis, spareto, ssd_exposure, ssd_hp and 3 more
R
R 3.6.0 released · 2019-04-26
0.0.3
record
2018-11-25 · diff ↗ ·
removed 1 export
ssd_fit_dist

added 8 exports
dgompertz, dpareto, pgompertz, ppareto, qgompertz, qpareto, rgompertz, rpareto
0.0.2
record
2018-10-14
R
R 3.5.0 released · 2018-04-23

Package metadata

First published: 2018-10-14
Total releases: 28 / 8 yrs
License: Apache License (== 2.0) | file LICENSE
Minimum R: ≥ 4.1
Bundled data: 4.8 KB / 2 files
Download size: 1.8 MB

Cite

Cite this package

Run in R for the authors' entry:

citation("ssdtools")

The package provides a citation file, so citation() returns the authors' own entry.

It points to 10.21105/joss.07492.

The repository also keeps a CITATION.cff.

Cite the R Observatory

For a number measured here: a download total, a coverage figure, an archival date.

Format

APA

Balamuta, J. J. (2026). R Observatory: Metrics for ssdtools version 2.7.0 [Data set]. HJJB, LLC. Data release v2026-10-18. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-18, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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