Skip to contents

Get Relative Abundance Index (RAI)

Source: R/get_rai.R
get_rai.Rd

[Deprecated]

Usage

get_rai(x, ..., species = "all", sex = NULL, life_stage = NULL)

Arguments

x

Camera trap data package object, as returned by camtrapdp::read_camtrapdp().

...

[Deprecated] filter predicates for filtering on deployments are not supported anymore and an error is returned. Anything else throws a deprecation warning and will be ignored. Please use filter_deployments() to filter on deployments.

species

[Deprecated] Character with scientific names. Common names are not supported anymore as of camtraptor 1.0.0. Please, check filter_observations() to know how to filter by scientificName. If "all" (default) all scientific names are automatically selected. If NULL all observations of all species are taken into account.

sex

[Deprecated] Character defining the sex class to filter on, e.g. "female" or c("male", "unknown"). If NULL (default) all observations of all sex classes are taken into account. Please, check filter_observations() to know how to filter by sex.

life_stage

[Deprecated] Character vector defining the life stage class to filter on, e.g. "adult" or c("subadult", "adult"). If NULL (default) all observations of all life stage classes are taken into account. Please, check filter_observations() to know how to filter by lifeStage.

Value

A tibble data frame with the following columns:

  • deploymentID: character vector with the deployment unique identifiers.

  • scientificName: character vector with the scientific name.

  • rai: numeric vector with the relative abundance index.

Details

Gets the RAI (Relative Abundance Index) per deployment. The RAI is normalized using 100 days deployment activity. In other words: RAI = 100 * (n/effort) where n is the number of event-based observations and effort is the effort duration in days.

It is deprecated as of camtraptor 1.0.0. Please use summarize_observations()instead.

See also

Other deprecated exploration functions: get_custom_effort(), get_effort(), get_n_individuals(), get_n_obs(), get_n_species(), get_rai_individuals()

Examples

x <- example_dataset()

# Calculate RAI for all species
get_rai(x) # species = "all" by default, so equivalent of
#> Warning: `get_rai()` was deprecated in camtraptor 1.0.0.
#> ℹ Please use `summarize_observations(x, group_by = c("deploymentID",
#>   "latitude"), "longitude"), "scientificName")` instead.
#> ℹ The deprecated feature was likely used in the camtraptor package.
#>   Please report the issue at <https://github.com/inbo/camtraptor/issues>.
#> # A tibble: 15 × 3
#> # Groups:   deploymentID, scientificName [15]
#>    deploymentID scientificName       rai
#>    <chr>        <chr>              <dbl>
#>  1 00a2c20d     Anas platyrhynchos 27.9 
#>  2 00a2c20d     Ardea cinerea       3.10
#>  3 00a2c20d     Rattus norvegicus   6.20
#>  4 00a2c20d     NA                  6.20
#>  5 29b7d356     Anas platyrhynchos 60.3 
#>  6 29b7d356     Anas strepera      20.1 
#>  7 29b7d356     Aves               10.0 
#>  8 29b7d356     NA                 20.1 
#>  9 577b543a     Martes foina       11.0 
#> 10 577b543a     Mustela putorius   32.9 
#> 11 577b543a     Vulpes vulpes      11.0 
#> 12 577b543a     NA                 11.0 
#> 13 62c200a9     Ardea               9.08
#> 14 62c200a9     Aves                4.54
#> 15 62c200a9     NA                  9.08
get_rai(x, species = "all")
#> # A tibble: 15 × 3
#> # Groups:   deploymentID, scientificName [15]
#>    deploymentID scientificName       rai
#>    <chr>        <chr>              <dbl>
#>  1 00a2c20d     Anas platyrhynchos 27.9 
#>  2 00a2c20d     Ardea cinerea       3.10
#>  3 00a2c20d     Rattus norvegicus   6.20
#>  4 00a2c20d     NA                  6.20
#>  5 29b7d356     Anas platyrhynchos 60.3 
#>  6 29b7d356     Anas strepera      20.1 
#>  7 29b7d356     Aves               10.0 
#>  8 29b7d356     NA                 20.1 
#>  9 577b543a     Martes foina       11.0 
#> 10 577b543a     Mustela putorius   32.9 
#> 11 577b543a     Vulpes vulpes      11.0 
#> 12 577b543a     NA                 11.0 
#> 13 62c200a9     Ardea               9.08
#> 14 62c200a9     Aves                4.54
#> 15 62c200a9     NA                  9.08

# Selected species
get_rai(x, species = c("Anas platyrhynchos", "Martes foina"))
#> Warning: The `species` argument of `get_rai()` is deprecated as of camtraptor 1.0.0.
#> ℹ Argument `species` is deprecated as of camtraptor 1.0.0. Please, use
#>   `filter_observations()` to filter by `scientificName`.
#> ℹ The deprecated feature was likely used in the camtraptor package.
#>   Please report the issue at <https://github.com/inbo/camtraptor/issues>.
#> # A tibble: 3 × 3
#> # Groups:   deploymentID, scientificName [3]
#>   deploymentID scientificName       rai
#>   <chr>        <chr>              <dbl>
#> 1 00a2c20d     Anas platyrhynchos  27.9
#> 2 29b7d356     Anas platyrhynchos  60.3
#> 3 577b543a     Martes foina        11.0