Package: ef2 2.0.0
Colin Millar
ef2: 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:
ef2_2.0.0.tar.gz
ef2_2.0.0.zip(r-4.7-any)ef2_2.0.0.zip(r-4.6-any)ef2_2.0.0.zip(r-4.5-any)
ef2_2.0.0.tgz(r-4.6-any)ef2_2.0.0.tgz(r-4.5-any)
ef2_2.0.0.tar.gz(r-4.7-any)ef2_2.0.0.tar.gz(r-4.6-any)
ef2_2.0.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
ef2/json (API)
| # Install 'ef2' in R: |
| install.packages('ef2', repos = c('https://faskally.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/faskally/ef2/issues
Pkgdown/docs site:https://faskally.github.io
- ef2_data - Counts of salmon fry and parr from electrofishing.
Last updated from:4c92a7bd61. Checks:9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel | OK | 133 | ||
| source / vignettes | OK | 452 | ||
| linux-release | OK | 317 | ||
| macos-release | OK | 129 | ||
| macos-oldrel | OK | 107 | ||
| windows-devel | OK | 82 | ||
| windows-release | OK | 327 | ||
| windows-oldrel | OK | 94 | ||
| wasm-release | OK | 293 |
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Modelling Framework for the Estimation of Salmonid Abundance | ef2-package ef2 |
| Estimate abundance and density from removal samples | abundance |
| Conversion of an efp2 fit to a gam fit for plotting | as.gam2 |
| Cumulative capture probability of each sample | capture_prob |
| Counts of salmon fry and parr from electrofishing. | ef2_data |
| Estimate capture probabilities from electrofishing data | efp2 |
| Methods for efp2 fits | anova.efp2 confint.efp2 efp2-methods fitted.efp2 formula.efp2 logLik.efp2 model.matrix.efp2 plot.efp2 print.efp2 print.summary.efp2 residuals.efp2 summary.efp2 vcov.efp2 |
| Predict capture probabilities from an efp2 fit | predict.efp2 |
| Random walk penalties for smooth terms | rw_penalty |