Package: ef 2.0.0
Colin Millar
ef: Modelling Framework for the Estimation of Salmonid Abundance
Estimates capture probabilities and densities from multipass removal (electrofishing) data, following Millar et al. (2016) <doi:10.1016/j.fishres.2016.01.001>. Capture probability is modelled on the logit scale using fixed effects, penalised smooth terms and random effects, for example for between visit and between sample variation. The likelihood is computed using 'RTMB', with random effects integrated out using the Laplace approximation.
Authors:
ef_2.0.0.tar.gz
ef_2.0.0.zip(r-4.7-any)ef_2.0.0.zip(r-4.6-any)ef_2.0.0.zip(r-4.5-any)
ef_2.0.0.tgz(r-4.6-any)ef_2.0.0.tgz(r-4.5-any)
ef_2.0.0.tar.gz(r-4.7-any)ef_2.0.0.tar.gz(r-4.6-any)
ef_2.0.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
ef/json (API)
| # Install 'ef' in R: |
| install.packages('ef', repos = c('https://faskally.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/faskally/ef/issues
Pkgdown/docs site:https://faskally.github.io
- ef_data - Counts of salmon fry and parr from electrofishing.
Last updated from:b15661594e. Checks:8 OK, 1 ERROR. Indexed: no.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel | OK | 126 | ||
| source / vignettes | OK | 171 | ||
| linux-release | OK | 125 | ||
| macos-release | OK | 147 | ||
| macos-oldrel | ERROR | 160 | ||
| windows-devel | OK | 103 | ||
| windows-release | OK | 98 | ||
| windows-oldrel | OK | 89 | ||
| wasm-release | OK | 82 |
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Modelling Framework for the Estimation of Salmonid Abundance | ef-package ef |
| Conversion of an efp fit to a gam fit for plotting | as.gam |
| Counts of salmon fry and parr from electrofishing. | ef_data |
| Estimate capture probabilities from electrofishing data | efp |
| Methods for efp fits | anova.efp confint.efp efp-methods fitted.efp formula.efp logLik.efp model.matrix.efp plot.efp print.efp print.summary.efp residuals.efp summary.efp vcov.efp |
| Inverse logistic transformation | invlogit |
| Logistic transformation | logit |
| Predict capture probabilities from an efp fit | predict.efp |
| Random walk penalties for smooth terms | rw_penalty |
| Utility function to convert parameters to probabilities | transpar |