birdsize for the Breeding Bird Survey | Obtaining data | Cleaning data | Simulating individual-level measurements | References
Package: birdsize 0.0.0.9000
Renata Diaz
birdsize: Estimate Avian Body Size Distributions
Generate estimated body size distributions for populations or communities of birds, given either species ID or species' mean body size. Designed to work naturally with the North American Breeding Bird Survey, or with any dataset of bird species, abundance, and/or mean size data.
Authors:
birdsize_0.0.0.9000.tar.gz
birdsize_0.0.0.9000.zip(r-4.7)birdsize_0.0.0.9000.zip(r-4.6)birdsize_0.0.0.9000.zip(r-4.5)
birdsize_0.0.0.9000.tgz(r-4.6-any)birdsize_0.0.0.9000.tgz(r-4.5-any)
birdsize_0.0.0.9000.tar.gz(r-4.7-any)birdsize_0.0.0.9000.tar.gz(r-4.6-any)
birdsize_0.0.0.9000.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
birdsize/json (API)
| # Install 'birdsize' in R: |
| install.packages('birdsize', repos = c('https://ropensci.r-universe.dev', 'https://cloud.r-project.org')) |
Reviews:rOpenSci Software Review #577
Bug tracker:https://github.com/diazrenata/birdsize/issues
Datasets:
- demo_route_clean - Cleaned data for a hypothetical Breeding Bird Survey route.
- demo_route_raw - Raw data for a hypothetical Breeding Bird Survey route.
- known_species - List of species known to 'birdsize'
- toy_aou_community - Toy data frame of abundances and AOUs
- toy_size_community - Toy data frame of abundances and species mean sizes
- toy_species_name_community - Toy data frame of abundances and species names
Last updated from:78d7840018 (on main). Checks:7 NOTE, 3 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-x86_64 | NOTE | 332 | ||
| pkgdown docs | OK | 189 | ||
| source / vignettes | OK | 160 | ||
| linux-release-x86_64 | NOTE | 282 | ||
| macos-release-arm64 | NOTE | 200 | ||
| macos-oldrel-arm64 | NOTE | 207 | ||
| windows-devel | NOTE | 207 | ||
| windows-release | NOTE | 209 | ||
| windows-oldrel | NOTE | 209 | ||
| wasm-release | OK | 104 |
Exports:community_generatefilter_bbs_surveyindividual_metabolic_ratepop_generatespecies_definespecies_lookup
Dependencies:truncnorm
bbs-data
Last update: 2023-11-20
Started: 2022-11-02
birdsize
Overview | Species-level parameters | Population (one species) simulations | Using species identity | Using a known mean and standard deviation | Using a known mean, but no standard deviation | Community (multiple populations) simulations | Simulations using AOU | Simulation given species' names | Simulation given mean size measurements | Community-wide summary statistics | Biomass total by species | Community total biomass
Last update: 2023-11-20
Started: 2022-11-02
scaling
References
Last update: 2023-11-20
Started: 2022-12-15
species
Species known to birdsize | AOU lookup | Scientific name lookup | Unknown species or AOUs | Species not known to birdsize | Manually supplying species parameters | Order of operations | References
Last update: 2023-11-20
Started: 2022-12-12
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Simulate individual measurements for many populations | community_generate |
| Cleaned data for a hypothetical Breeding Bird Survey route. | demo_route_clean |
| Raw data for a hypothetical Breeding Bird Survey route. | demo_route_raw |
| Clean raw Breeding Bird Survey survey data | filter_bbs_survey |
| Estimate individual-level BMR | individual_metabolic_rate |
| List of species known to 'birdsize' | known_species |
| Simulate body masses for a population | pop_generate |
| Define a species | species_define |
| Species lookup | species_lookup |
| Toy data frame of abundances and AOUs (for vignettes) | toy_aou_community |
| Toy data frame of abundances and species mean sizes (for vignettes) | toy_size_community |
| Toy data frame of abundances and species names (for vignettes) | toy_species_name_community |
