Package 'birdsize'

Title: Estimate Avian Body Size Distributions
Description: 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: Renata Diaz [aut, cre] , John Dunning [dtc]
Maintainer: Renata Diaz <[email protected]>
License: MIT + file LICENSE
Version: 0.0.0.9000
Built: 2024-10-28 05:52:02 UTC
Source: https://github.com/ropensci/birdsize

Help Index

Simulate individual measurements for many populations

Description

For a community (i.e. a collection of populations of different species, or of the same species at different points in time or locations, etc), simulate individual-level size and metabolic rate measurements.

Usage

community_generate(
  community_data_table,
  abundance_column_name = "speciestotal"
)

Arguments

community_data_table

dataframe containing at least one of AOU, scientific_name, or mean_size and a column for species abundances
abundance_column_name

character, the name of the column with species abundances. Defaults to "speciestotal".

Value

a dataframe one row per individual, all columns from community_data_table, and additional columns for species attributes.

Specifically:

  • AOU: the AOU, if provided

  • sim_species_id: the sim_species_id if provided

  • genus: the genus associated with the AOU if provided, or the genus if provided

  • species: the species associated with the AOU if provided, or the species if provided

  • individual_mass: the simulated body mass (in grams) for this individual

  • individual_bmr: the simulated basal metabolic rate for this individual

  • mean_size: the mean body mass for this species (i.e. the parameter used for simulation)

  • sd_size: the standard deviation of body mass for this species (i.e. the parameter used for simulation)

  • abundance: the number of individuals simulated of this species (i.e. parameter used for simulation)

  • sd_method: the method for finding the standard deviation for body mass for this species

  • scientific_name: the scientific name

Examples

demo_community <- community_generate(demo_route_clean)
head(demo_community)

Cleaned data for a hypothetical Breeding Bird Survey route.

Description

This is the cleaned version of demo_route_raw, a toy dataset for use in vignettes and function testing. It contains all the same column names as would be expected for a Breeding Bird survey route dataset downloaded, e.g. from ScienceBase or the Data Retriever (Pardieck et al. 2019). However, the actual data values are simulated data.

Usage

demo_route_clean

Format

A data frame with 27 rows and 15 variables:

record_id

inherited from data downloaded through the Data Retriever

routedataid

inherited from Pardieck et al. 2018 (as are all following fields). Unique data identification number.

countrynum

inherited. Three-digit numerical code for country. In these data, the toy countrynum is 900.

statenum

inherited. Two-digit numerical code for state, province, or territory. For these data, the toy number is 99.

route

inherited. Three-digit code identifying the route, unique within states. For this dataset, 1.

rpid

inherited. Three-digit run protocol identifier. Here, set to 101.

year

inherited. Four-digit year of the survey.

AOU

inherited. Five-digit species identification number.

count10

inherited. Total individuals of the species recorded on stops 1-10.

count20

inherited. Total individuals of the species recorded on stops 11-20.

count30

inherited. Total individuals of the species recorded on stops 21-30.

count40

inherited. Total individuals of the species recorded on stops 31-40.

count50

inherited. Total individuals of the species recorded on stops 40-50.

stoptotal

inherited. Total number of stops (of 50), where the species was recorded.

speciestotal

inherited. Total individuals of the species recorded across the entire run of the route (sum of stops).

Details

Nearly all column names are inherited from Pardieck et al. (2019) and are further explained in the Files and Fields Definitions document included as part of the Breeding Bird Survey data release.

The cleaning process removes unidentified species and those poorly sampled by Breeding Bird Survey methods (using the filter_bbs_survey function) and, for these data, filters the year to 1994 for rapid testing.

References

  • Pardieck, K. L., Ziolkowski, D. J., Lutmerding, M., Aponte, V., & Hudson, M.-A. (2019). North American Breeding Bird Survey Dataset 1966—2018, version 2018.0. U.S. Geological Survey. https://doi.org/10.5066/P9HE8XYJ

Raw data for a hypothetical Breeding Bird Survey route.

Description

A toy dataset for use in vignettes and function testing. It contains all the same column names as would be expected for a Breeding Bird survey route dataset downloaded, e.g. from ScienceBase or the Data Retriever (Pardieck et al. 2019). However, the actual data values are simulated data.

Usage

demo_route_raw

Format

A data frame with 1160 rows and 15 variables:

record_id

inherited from data downloaded through the Data Retriever

routedataid

inherited from Pardieck et al. 2018 (as are all following fields). Unique data identification number.

countrynum

inherited. Three-digit numerical code for country. In these data, the toy countrynum is 900.

statenum

inherited. Two-digit numerical code for state, province, or territory. For these data, the toy number is 99.

route

inherited. Three-digit code identifying the route, unique within states. For this dataset, 1.

rpid

inherited. Three-digit run protocol identifier. Here, set to 101.

year

inherited. Four-digit year of the survey.

AOU

inherited. Five-digit species identification number.

count10

inherited. Total individuals of the species recorded on stops 1-10.

count20

inherited. Total individuals of the species recorded on stops 11-20.

count30

inherited. Total individuals of the species recorded on stops 21-30.

count40

inherited. Total individuals of the species recorded on stops 31-40.

count50

inherited. Total individuals of the species recorded on stops 40-50.

stoptotal

inherited. Total number of stops (of 50), where the species was recorded.

speciestotal

inherited. Total individuals of the species recorded across the entire run of the route (sum of stops).

Details

Nearly all column names are inherited from Pardieck et al. (2019) and are further explained in the Files and Fields Definitions document included as part of the Breeding Bird Survey data release.

References

  • Pardieck, K. L., Ziolkowski, D. J., Lutmerding, M., Aponte, V., & Hudson, M.-A. (2019). North American Breeding Bird Survey Dataset 1966—2018, version 2018.0. U.S. Geological Survey. https://doi.org/10.5066/P9HE8XYJ

Clean raw Breeding Bird Survey survey data

Description

The raw data for the Breeding Bird Survey includes unidentified species and some species that are not well-sampled by the BBS methods. This function filters a dataframe to remove those species.

Usage

filter_bbs_survey(bbs_survey_data)

Arguments

bbs_survey_data

data frame with columns for species and AOU

Value

bbs_survey_data with unidentified species, nightbirds, waterbirds, non-targets removed

Examples

head(filter_bbs_survey(demo_route_raw))

Estimate individual-level BMR

Description

Given an individual's body mass (in grams), use allometric scaling (Fristoe 2015) to estimate basal metabolic rate.

Usage

individual_metabolic_rate(mass)

Arguments

mass

mass in grams

Value

estimated basal metabolic rate

References

  • Fristoe, T. S. (2015). Energy use by migrants and residents in North American breeding bird communities. Global Ecology and Biogeography, 24(4), 406–415. https://doi.org/10.1111/geb.12262

Examples

individual_metabolic_rate(10)

List of species known to birdsize

Description

A table of the AOU (Pardieck et al 2019), genus, and species of the 443 species with species-specific data built in to birdsize.

Usage

known_species

Format

A data frame with 443 rows and 6 variables:

AOU

AOU used in Paradieck et al. (2019)

genus

genus, from Paradieck et al. (2019)

species

species, from Paradieck et al. (2019)

References

  • Pardieck, K.L., Ziolkowski Jr., D.J., Lutmerding, M., Aponte, V., and Hudson, M-A.R., 2019, North American Breeding Bird Survey Dataset 1966 - 2018 (ver. 2018.0): U.S. Geological Survey, Patuxent Wildlife Research Center, https://doi.org/10.5066/P9HE8XYJ.

Simulate body masses for a population

Description

Draws body mass measurements for a population of birds (of all the same species) given the population size and either (1) the species AOU or (2) the mean and potentially standard deviation of body mass for that species.

Usage

pop_generate(
  abundance = NA_integer_,
  AOU = NA_integer_,
  scientific_name = NA_character_,
  mean_size = NA_real_,
  sd_size = NA_real_,
  sim_species_id = 1
)

Arguments

abundance

integer number of individuals to draw. Required.
AOU

the numeric AOU code used for this species in the Breeding Bird Survey
scientific_name

as "Genus species"
mean_size

numeric, mean body mass (in grams) for this species.
sd_size

numeric, standard deviation of body mass for this species.
sim_species_id

defaults AOU or 1

Details

abundance is required, as well as one of: AOU, scientific_name, or mean_size.

Value

a dataframe with abundance rows - one record per individual - and columns for species attributes.

Specifically:

  • AOU: the AOU, if provided

  • sim_species_id: the sim_species_id if provided

  • scientific_name: the scientific name if provided

  • individual_mass: the simulated body mass (in grams) for this individual

  • individual_bmr: the simulated basal metabolic rate for this individual

  • mean_size: the mean body mass for this species (i.e. the parameter used for simulation)

  • sd_size: the standard deviation of body mass for this species (i.e. the parameter used for simulation)

  • abundance: the number of individuals simulated of this species (i.e. parameter used for simulation)

  • sd_method: the method for finding the standard deviation for body mass for this species

Examples

pop_generate(abundance = 5, AOU = 2881)
pop_generate(abundance = 5, scientific_name = "Selasphorus calliope")
pop_generate(abundance = 5, mean_size = 20, sd_size = 3)

Define a species

Description

Creates a list with taxonomic/identifying information and parameters for mean and standard deviation of body mass.

Usage

species_define(
  AOU = NA_integer_,
  scientific_name = NA_character_,
  mean_size = NA_real_,
  sd_size = NA_real_,
  sim_species_id = 1
)

Arguments

AOU

the numeric AOU code used for this species in the Breeding Bird Survey
scientific_name

the species' scientific name, as "Genus species"
mean_size

mean body size
sd_size

sd of body size
sim_species_id

identifier; if using taxonomic info, defaults to AOU. If not, defaults to 1. Supplying other values can be useful for simulation models.

Details

The identifying information used depends on which parameters are provided, with the following order of preference: AOU > scientific name > user provided mean and sd > user provided mean and estimated sd.

Value

list with species parameter information

Examples

species_define(AOU = 2881)
species_define(scientific_name = "Perdix perdix")
species_define(mean_size = 400, sd_size = 30)
species_define(mean_size = 400)

Species lookup

Description

Given either AOU or scientific name, looks up a species' taxonomic information and mean and standard deviation of body size in sd_table.

Usage

species_lookup(AOU = NA_integer_, scientific_name = NA_character_)

Arguments

AOU

the numeric AOU code used for this species in the Breeding Bird Survey
scientific_name

the species' scientific name, as "Genus species"

Value

data frame with columns AOU, genus, species, mean_mass, mean_sd, contains_estimates, scientific_name

Examples

species_lookup(AOU = 2881)
species_lookup(scientific_name = "Selasphorus calliope")

Toy data frame of abundances and AOUs (for vignettes)

Description

This data table is a toy data frame for the vignettes. It has abundances and AOU codes for 5 species to make up a hypothetical community.

Usage

toy_aou_community

Format

A data frame with 5 rows and 2 variables:

AOU

AOU

abundance

Number of individuals to simulate masses for

Toy data frame of abundances and species mean sizes (for vignettes)

Description

This data table is a toy data frame for the vignettes. It has abundances and mean body sizes for 5 species to make up a hypothetical community.

Usage

toy_size_community

Format

A data frame with 5 rows and 3 variables:

mean_size

Mean mass, in g

abundance

Number of individuals to simulate masses for

sim_species_id

ID

Toy data frame of abundances and species names (for vignettes)

Description

This data table is a toy data frame for the vignettes. It has abundances and scientific names for 5 species to make up a hypothetical community.

Usage

toy_species_name_community

Format

A data frame with 5 rows and 2 variables:

scientific_name

Scientific name

abundance

Number of individuals to simulate masses for