Package: bbsBayes2 1.1.3.3

Brandon P.M. Edwards

bbsBayes2: Hierarchical Bayesian Analysis of North American BBS Data

The North American Breeding Bird Survey (BBS) is a long-running program that seeks to monitor the status and trends of the breeding birds in North America. Since its start in 1966, the BBS has accumulated over 50 years of data for over 500 species of North American Birds. Given the temporal and spatial structure of the data, hierarchical Bayesian models are used to assess the status and trends of these 500+ species of birds. 'bbsBayes2' allows you to perform hierarchical Bayesian analysis of BBS data. You can run a full model analysis for one or more species, or you can take greater more control and specify how the data should be stratified, prepared for 'Stan', or modelled.

Authors:Brandon P.M. Edwards [aut, cre], Adam C. Smith [aut], Steffi LaZerte [aut]

bbsBayes2_1.1.3.3.tar.gz
bbsBayes2_1.1.3.3.zip(r-4.7)bbsBayes2_1.1.3.3.zip(r-4.6)bbsBayes2_1.1.3.3.zip(r-4.5)
bbsBayes2_1.1.3.3.tgz(r-4.6-any)bbsBayes2_1.1.3.3.tgz(r-4.5-any)
bbsBayes2_1.1.3.3.tar.gz(r-4.7-any)bbsBayes2_1.1.3.3.tar.gz(r-4.6-any)
bbsBayes2_1.1.3.3.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
bbsBayes2/json (API)
NEWS

# Install 'bbsBayes2' in R:

install.packages('bbsBayes2', repos = c('https://bbsbayes.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/bbsbayes/bbsbayes2/issues

Pkgdown/docs site:https://bbsbayes.github.io

Datasets:

bbs_data_sample - Sample BBS data
bbs_models - Stan models included in bbsBayes2
bbs_strata - List of included strata
equal_area_crs - Equal_area_crs
pacific_wren_model - Example model output
species_forms - Species forms
species_notes - Species notes

On CRAN:

5.05 score 12 stars 157 scripts 24 exports 90 dependencies

Last updated from:70f32c2fbf. Checks:7 ERROR, 2 OK. Indexed: yes.

Target	Result	Time
linux-devel-x86_64	ERROR	543
source / vignettes	OK	269
linux-release-x86_64	ERROR	619
macos-release-arm64	ERROR	393
macos-oldrel-arm64	ERROR	714
windows-devel	ERROR	828
windows-release	ERROR	701
windows-oldrel	ERROR	775
wasm-release	OK	166

Exports:%>%assign_prov_state copy_model_file fetch_bbs_data generate_indices generate_trends get_convergence get_model_vars get_summary have_bbs_data have_cmdstan load_bbs_data load_map plot_geofacet plot_indices plot_map prepare_data prepare_model prepare_spatial remove_cache run_model save_model_run search_species stratify

Dependencies:abind askpass backports bit bit64 boot checkmate class classInt cli clipr cpp11 crayon curl DBI deldir distributional dplyr e1071 farver filelock generics geofacet geogrid ggplot2 ggrepel glue gridExtra gtable HDInterval hms httr httr2 isoband jsonlite KernSmooth keyring labeling lattice lifecycle magrittr MASS Matrix matrixStats mgcv mime nlme numDeriv openssl pillar pkgconfig posterior prettyunits progress proxy purrr R6 rappdirs RColorBrewer Rcpp RcppArmadillo readr rlang rnaturalearth s2 S7 sbtools scales sf snakecase sp spData spdep stringi stringr sys tensorA terra tibble tidyr tidyselect tzdb units utf8 vctrs viridisLite vroom withr wk yaml

Help page	Topics
Categorize polygon by Province/State	assign_prov_state
Sample BBS data	bbs_data_sample
Stan models included in bbsBayes2	bbs_models
List of included strata	bbs_strata
bbsBayes2 defunct functions	bbsBayes2-defunct
bbsBayes2 deprecated functions	bbsBayes2-deprecated
Copy model file	copy_model_file
equal_area_crs	equal_area_crs
Fetch Breeding Bird Survey dataset	fetch_bbs_data
Regional annual indices of abundance	generate_indices
Generate regional trends	generate_trends
Convergence metrics	get_convergence
Get model variables	get_model_vars
Return the 'cmdstanr' summary	get_summary
Check whether BBS data exists locally	have_bbs_data
Check if cmdstan is installed	have_cmdstan
Load Breeding Bird Survey data	load_bbs_data
Load a geographic strata map	load_map
Example model output	pacific_wren_model
Create geofacet plot of population trajectories by province/state	plot_geofacet
Generate plots of index trajectories by stratum	plot_indices
Generate a map of trends by strata	plot_map
Filter for data quality	prepare_data
Prepare model parameters	prepare_model
Define neighbouring strata for spatial analyses	prepare_spatial
Remove bbsBayes2 cache	remove_cache
Run Bayesian model	run_model
Save output of run_model()	save_model_run
Search for species	search_species
Species forms	species_forms
Species notes	species_notes
Stratify and filter Breeding Bird Survey data	stratify

Package: bbsBayes2 1.1.3.3

bbsBayes2: Hierarchical Bayesian Analysis of North American BBS Data

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Help Manual

Usage by other packages (reverse dependencies)