The species_define
function works mostly behind the scenes to set up the parameters needed
to simulate individual body size measurements. Given any of: (1) the AOU as used in the
North American Breeding Bird Survey (Pardieck et al. 2019), (2) the
scientific name, (3) the species’ mean body size, or (4) the species’
mean and standard deviation body size,
species_define
returns the parameters used by
pop_generate
and community_generate
to
simulate individual size measurements for individuals of that species,
or returns an error message asking for more or different information. In
most instances, species_define
is called under-the-hood by
the generate
functions, and users do not need to interact
with it directly.
birdsize
birdsize
includes species-level parameters for 443
species of birds common in the North American Breeding Bird Survey. To
view the list of species included, examine the
known_species
data table, included:
head(known_species)
#> # A tibble: 6 × 3
#> AOU genus species
#> <int> <chr> <chr>
#> 1 2881 Perdix perdix
#> 2 2882 Alectoris chukar
#> 3 2890 Colinus virginianus
#> 4 2920 Oreortyx pictus
#> 5 2930 Callipepla squamata
#> 6 2940 Callipepla californica
Species included in known_species
can be retrieved via
either their AOU or scientific name. For example, the hummingbird
Selasphorous calliope has an AOU of 4360
.
hummingbird_name_parameters <- species_define(scientific_name = "Selasphorus calliope")
hummingbird_name_parameters
#> $AOU
#> [1] 4360
#>
#> $scientific_name
#> [1] "Selasphorus calliope"
#>
#> $mean_size
#> [1] 2.65
#>
#> $sd_size
#> [1] 0.1818394
#>
#> $sd_method
#> [1] "Scientific name lookup"
#>
#> $sim_species_id
#> [1] 4360
Note that the sd_method
field tells us which method we
used to look up the parameters. This field propagates throughout the
pop_generate
and community_generate
functions
to keep track of the underlying methodology.
Attempting to use species_define
with an AOU or species
not known to birdsize
will return an error:
birdsize
Some users may want to use this methodology with species not included
in known_species
, or to use different species-level
parameters than those built-in to birdsize
(for example, to
explore intraspecific variation in body size over time or space). To do
this, supply species_define
with mean, or mean and standard
deviation, values for each species. To help keep track of
species-parameter matches, use the sim_species_id
field to
assign a species identifier to each novel species.
Suppose we want to work with a hypothetical species with a mean body
size of 40g and a standard deviation of 2.5. Because this species
doesn’t have a scientific name or AOU included in birdsize
,
we label it using the arbitrary sim_species_id
of 1.
hypothetical_species_parameters <- species_define(mean_size = 40, sd_size = 2.5, sim_species_id = 1)
hypothetical_species_parameters
#> $AOU
#> [1] NA
#>
#> $scientific_name
#> [1] NA
#>
#> $mean_size
#> [1] 40
#>
#> $sd_size
#> [1] 2.5
#>
#> $sd_method
#> [1] "Mean and SD provided"
#>
#> $sim_species_id
#> [1] 1
This can be particularly useful when working with multiple new
species. For example, if we have 3 new species, we can store their
information in a separate table and iterate over
sim_species_id
to generate parameters for each species.
This happens under the hood in community_generate
.
multiple_species_info <- data.frame(
mean_size = c(10, 40, 50),
sd_size = c(1, 2.5, 3),
sim_species_id = 1:3
)
pmap_df(multiple_species_info, species_define)
#> # A tibble: 3 × 6
#> AOU scientific_name mean_size sd_size sd_method sim_species_id
#> <int> <chr> <dbl> <dbl> <chr> <int>
#> 1 NA <NA> 10 1 Mean and SD provided 1
#> 2 NA <NA> 40 2.5 Mean and SD provided 2
#> 3 NA <NA> 50 3 Mean and SD provided 3
If the standard deviation is not provided,
species_define
will estimate it (see the
scaling
vignette):
multiple_species_info_no_sd <- data.frame(
mean_size = c(10, 40, 50),
sim_species_id = 1:3
)
pmap_df(multiple_species_info_no_sd, species_define)
#> # A tibble: 3 × 6
#> AOU scientific_name mean_size sd_size sd_method sim_species_id
#> <int> <chr> <dbl> <dbl> <chr> <int>
#> 1 NA <NA> 10 0.693 SD estimated from mean 1
#> 2 NA <NA> 40 2.80 SD estimated from mean 2
#> 3 NA <NA> 50 3.51 SD estimated from mean 3
If multiple sets of information are provided (e.g. both
AOU
and scientific_name
),
species_define
will use it in this order of preference:
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.