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Get Relative Abundance Index (RAI) based on the sum of individual counts

Source: R/get_rai.R
get_rai_individuals.Rd

[Deprecated]

Usage

get_rai_individuals(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: Deployment unique identifier.

  • scientificName: Scientific name.

  • rai: 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 sum of individual counts related to 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()

Examples

x <- example_dataset()

# Calculate RAI based on number of individuals
get_rai_individuals(x) # species = "all" by default, so equivalent of
#> Warning: `get_rai_individuals()` 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  71.3 
#>  2 00a2c20d     Ardea cinerea        3.10
#>  3 00a2c20d     Rattus norvegicus    6.20
#>  4 00a2c20d     NA                   0   
#>  5 29b7d356     Anas platyrhynchos 171.  
#>  6 29b7d356     Anas strepera       40.2 
#>  7 29b7d356     Aves                10.0 
#>  8 29b7d356     NA                   0   
#>  9 577b543a     Martes foina        11.0 
#> 10 577b543a     Mustela putorius    32.9 
#> 11 577b543a     Vulpes vulpes       11.0 
#> 12 577b543a     NA                   0   
#> 13 62c200a9     Ardea                9.08
#> 14 62c200a9     Aves                 4.54
#> 15 62c200a9     NA                   0   
get_rai_individuals(x, species = "all")
#> # A tibble: 15 × 3
#> # Groups:   deploymentID, scientificName [15]
#>    deploymentID scientificName        rai
#>    <chr>        <chr>               <dbl>
#>  1 00a2c20d     Anas platyrhynchos  71.3 
#>  2 00a2c20d     Ardea cinerea        3.10
#>  3 00a2c20d     Rattus norvegicus    6.20
#>  4 00a2c20d     NA                   0   
#>  5 29b7d356     Anas platyrhynchos 171.  
#>  6 29b7d356     Anas strepera       40.2 
#>  7 29b7d356     Aves                10.0 
#>  8 29b7d356     NA                   0   
#>  9 577b543a     Martes foina        11.0 
#> 10 577b543a     Mustela putorius    32.9 
#> 11 577b543a     Vulpes vulpes       11.0 
#> 12 577b543a     NA                   0   
#> 13 62c200a9     Ardea                9.08
#> 14 62c200a9     Aves                 4.54
#> 15 62c200a9     NA                   0   

# Selected species
get_rai_individuals(
  x,
  species = c("Anas platyrhynchos", "Martes foina")
)
#> Warning: The `species` argument of `get_rai_individuals()` 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  71.3
#> 2 29b7d356     Anas platyrhynchos 171. 
#> 3 577b543a     Martes foina        11.0