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ubms

Fit models to data from unmarked animals using Stan. Uses a similar interface to the R package 'unmarked', while providing the advantages of Bayesian inference and allowing estimation of random effects.

https://github.com/ecoverseR/ubms

Science Score: 26.0%

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    Low similarity (11.4%) to scientific vocabulary

Keywords

distance-sampling hierarchical-models n-mixture-model occupancy r stan
Last synced: 6 months ago · JSON representation

Repository

Fit models to data from unmarked animals using Stan. Uses a similar interface to the R package 'unmarked', while providing the advantages of Bayesian inference and allowing estimation of random effects.

Basic Info
Statistics
  • Stars: 37
  • Watchers: 7
  • Forks: 8
  • Open Issues: 3
  • Releases: 8
Topics
distance-sampling hierarchical-models n-mixture-model occupancy r stan
Created almost 6 years ago · Last pushed 7 months ago
Metadata Files
Readme Changelog License

README.md

ubms: Unmarked Bayesian Models with Stan

R build status CRAN status <!-- badges: end -->

ubms is an R package for fitting Bayesian hierarchical models of animal occurrence and abundance. The package has a formula-based interface compatible with unmarked, but the model is fit using MCMC with Stan instead of using maximum likelihood. Currently there are Stan versions of unmarked functions occu, occuRN, colext, occuTTD, pcount, distsamp, and multinomPois. These functions follow the stan_ prefix naming format established by rstanarm. For example, the Stan version of the unmarked function occu is stan_occu.

Advantages compared to unmarked:

  1. Obtain posterior distributions of parameters and derived parameters
  2. Include random effects in parameter formulas (same syntax as lme4)
  3. Assess model fit using WAIC and LOO via the loo package

Disadvantages compared to unmarked:

  1. MCMC is slower than maximum likelihood
  2. Not all model types are supported
  3. Potential for convergence issues

Installation

ubms is on CRAN:

r install.packages("ubms")

Alternatively, the latest development version can be installed from Github:

``` r

install.packages("devtools")

devtools::install_github("biodiverse/ubms") ```

Package Overview

A detailed vignette for the package is available here.

Owner

  • Name: Ecoverse
  • Login: ecoverseR
  • Kind: organization

R packages for Modeling Species Diversity and Distributions

GitHub Events

Total
  • Issues event: 2
  • Issue comment event: 2
  • Push event: 1
Last Year
  • Issues event: 2
  • Issue comment event: 2
  • Push event: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 1
  • Total pull requests: 0
  • Average time to close issues: 2 days
  • Average time to close pull requests: N/A
  • Total issue authors: 1
  • Total pull request authors: 0
  • Average comments per issue: 1.0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 1
  • Pull requests: 0
  • Average time to close issues: 2 days
  • Average time to close pull requests: N/A
  • Issue authors: 1
  • Pull request authors: 0
  • Average comments per issue: 1.0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
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Top Authors
Issue Authors
  • jcarlis3 (1)
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Dependencies

DESCRIPTION cran
  • R >= 3.4.0 depends
  • unmarked * depends
  • Matrix * imports
  • RSpectra * imports
  • Rcpp >= 0.12.0 imports
  • ggplot2 >= 2.0.0 imports
  • gridExtra * imports
  • lme4 * imports
  • loo * imports
  • methods * imports
  • pbapply * imports
  • rstan >= 2.18.1 imports
  • rstantools >= 2.0.0 imports
  • stats * imports
  • covr * suggests
  • devtools * suggests
  • knitr * suggests
  • pkgdown * suggests
  • raster * suggests
  • rlang * suggests
  • rmarkdown * suggests
  • roxygen2 * suggests
  • testthat * suggests
.github/workflows/R-CMD-check.yaml actions
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  • actions/upload-artifact main composite
  • r-lib/actions/setup-pandoc v1 composite
  • r-lib/actions/setup-r v1 composite
.github/workflows/build-mac-binary.yaml actions
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  • r-lib/actions/setup-pandoc v1 composite
  • r-lib/actions/setup-r v1 composite
.github/workflows/build-windows-binary.yaml actions
  • actions/cache v2 composite
  • actions/checkout v2 composite
  • actions/upload-artifact v1 composite
  • r-lib/actions/setup-pandoc v1 composite
  • r-lib/actions/setup-r v1 composite
.github/workflows/test-coverage.yaml actions
  • actions/cache v2 composite
  • actions/checkout v2 composite
  • r-lib/actions/setup-pandoc v1 composite
  • r-lib/actions/setup-r v1 composite