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Simulate individual measurements for many populations

Source: R/community_generate.R
community_generate.Rd

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)
#>   record_id   routedataid countrynum statenum route rpid year count10 count20
#> 1    900000 9009911011994        900       99     1  101 1994       8      12
#> 2    900000 9009911011994        900       99     1  101 1994       8      12
#> 3    900000 9009911011994        900       99     1  101 1994       8      12
#> 4    900000 9009911011994        900       99     1  101 1994       8      12
#> 5    900000 9009911011994        900       99     1  101 1994       8      12
#> 6    900000 9009911011994        900       99     1  101 1994       8      12
#>   count30 count40 count50 stoptotal speciestotal  AOU sim_species_id
#> 1      15      12      15         5           62 4730           4730
#> 2      15      12      15         5           62 4730           4730
#> 3      15      12      15         5           62 4730           4730
#> 4      15      12      15         5           62 4730           4730
#> 5      15      12      15         5           62 4730           4730
#> 6      15      12      15         5           62 4730           4730
#>   individual_mass individual_bmr mean_size  sd_size abundance  sd_method
#> 1        32.85400       126.6242    37.475 3.300613        62 AOU lookup
#> 2        38.31770       141.3036    37.475 3.300613        62 AOU lookup
#> 3        29.43054       117.0691    37.475 3.300613        62 AOU lookup
#> 4        37.45661       139.0321    37.475 3.300613        62 AOU lookup
#> 5        39.52651       144.4677    37.475 3.300613        62 AOU lookup
#> 6        41.26546       148.9713    37.475 3.300613        62 AOU lookup
#>   scientific_name
#> 1 Alauda arvensis
#> 2 Alauda arvensis
#> 3 Alauda arvensis
#> 4 Alauda arvensis
#> 5 Alauda arvensis
#> 6 Alauda arvensis