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Get Relative Abundance Index (RAI) based on number of individuals

Source: R/get_rai.R
get_rai_individuals.Rd

Function to get the RAI (Relative Abundance Index) per deployment based on number of detected individuals instead of the number of observations. The RAI is normalized using 100 days deployment activity. In other words: RAI = 100 * (n/effort) where n is the number of individuals as calculated via get_n_individuals() and effort is the effort in days as calculated via get_effort().

Usage

get_rai_individuals(
  package = NULL,
  ...,
  species = "all",
  sex = NULL,
  life_stage = NULL,
  datapkg = lifecycle::deprecated()
)

Arguments

package

Camera trap data package object, as returned by read_camtrap_dp().

...

Filter predicates for filtering on deployments.

species

Character with scientific names or common names (case insensitive). If "all" (default) all scientific names are automatically selected.

sex

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.

life_stage

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.

datapkg

Deprecated. Use package instead.

Value

A tibble data frame with the following columns:

  • deploymentID: Deployment unique identifier.

  • scientificName: Scientific name.

  • rai: Relative abundance index.

See also

Other exploration functions: get_cam_op(), get_custom_effort(), get_effort(), get_n_individuals(), get_n_obs(), get_n_species(), get_rai(), get_record_table(), get_scientific_name(), get_species()

Examples

# Calculate RAI based on number of individuals
get_rai_individuals(mica) # species = "all" by default, so equivalent of
#> # A tibble: 36 × 3
#>    deploymentID                         scientificName       rai
#>    <chr>                                <chr>              <dbl>
#>  1 29b7d356-4bb4-4ec4-b792-2af5cc32efa8 Anas platyrhynchos 131. 
#>  2 29b7d356-4bb4-4ec4-b792-2af5cc32efa8 Anas strepera       60.3
#>  3 29b7d356-4bb4-4ec4-b792-2af5cc32efa8 Ardea                0  
#>  4 29b7d356-4bb4-4ec4-b792-2af5cc32efa8 Ardea cinerea        0  
#>  5 29b7d356-4bb4-4ec4-b792-2af5cc32efa8 Castor fiber         0  
#>  6 29b7d356-4bb4-4ec4-b792-2af5cc32efa8 Homo sapiens         0  
#>  7 29b7d356-4bb4-4ec4-b792-2af5cc32efa8 Martes foina         0  
#>  8 29b7d356-4bb4-4ec4-b792-2af5cc32efa8 Mustela putorius     0  
#>  9 29b7d356-4bb4-4ec4-b792-2af5cc32efa8 Vulpes vulpes        0  
#> 10 577b543a-2cf1-4b23-b6d2-cda7e2eac372 Anas platyrhynchos   0  
#> # ℹ 26 more rows
get_rai_individuals(mica, species = "all")
#> # A tibble: 36 × 3
#>    deploymentID                         scientificName       rai
#>    <chr>                                <chr>              <dbl>
#>  1 29b7d356-4bb4-4ec4-b792-2af5cc32efa8 Anas platyrhynchos 131. 
#>  2 29b7d356-4bb4-4ec4-b792-2af5cc32efa8 Anas strepera       60.3
#>  3 29b7d356-4bb4-4ec4-b792-2af5cc32efa8 Ardea                0  
#>  4 29b7d356-4bb4-4ec4-b792-2af5cc32efa8 Ardea cinerea        0  
#>  5 29b7d356-4bb4-4ec4-b792-2af5cc32efa8 Castor fiber         0  
#>  6 29b7d356-4bb4-4ec4-b792-2af5cc32efa8 Homo sapiens         0  
#>  7 29b7d356-4bb4-4ec4-b792-2af5cc32efa8 Martes foina         0  
#>  8 29b7d356-4bb4-4ec4-b792-2af5cc32efa8 Mustela putorius     0  
#>  9 29b7d356-4bb4-4ec4-b792-2af5cc32efa8 Vulpes vulpes        0  
#> 10 577b543a-2cf1-4b23-b6d2-cda7e2eac372 Anas platyrhynchos   0  
#> # ℹ 26 more rows

# Selected species
get_rai_individuals(mica,
  species = c("Anas platyrhynchos", "Martes foina")
)
#> There are 2 deployments without observations: 62c200a9-0e03-4495-bcd8-032944f6f5a1 and 7ca633fa-64f8-4cfc-a628-6b0c419056d7
#> # A tibble: 8 × 3
#>   deploymentID                         scientificName       rai
#>   <chr>                                <chr>              <dbl>
#> 1 29b7d356-4bb4-4ec4-b792-2af5cc32efa8 Anas platyrhynchos 131. 
#> 2 29b7d356-4bb4-4ec4-b792-2af5cc32efa8 Martes foina         0  
#> 3 577b543a-2cf1-4b23-b6d2-cda7e2eac372 Anas platyrhynchos   0  
#> 4 577b543a-2cf1-4b23-b6d2-cda7e2eac372 Martes foina        11.0
#> 5 62c200a9-0e03-4495-bcd8-032944f6f5a1 Anas platyrhynchos   0  
#> 6 62c200a9-0e03-4495-bcd8-032944f6f5a1 Martes foina         0  
#> 7 7ca633fa-64f8-4cfc-a628-6b0c419056d7 Anas platyrhynchos   0  
#> 8 7ca633fa-64f8-4cfc-a628-6b0c419056d7 Martes foina         0  

# With common names, also mixing up languages
get_rai_individuals(mica, species = c("mallard", "steenmarter"))
#> Scientific name of mallard: Anas platyrhynchos
#> Scientific name of steenmarter: Martes foina
#> There are 2 deployments without observations: 62c200a9-0e03-4495-bcd8-032944f6f5a1 and 7ca633fa-64f8-4cfc-a628-6b0c419056d7
#> # A tibble: 8 × 3
#>   deploymentID                         scientificName       rai
#>   <chr>                                <chr>              <dbl>
#> 1 29b7d356-4bb4-4ec4-b792-2af5cc32efa8 Anas platyrhynchos 131. 
#> 2 29b7d356-4bb4-4ec4-b792-2af5cc32efa8 Martes foina         0  
#> 3 577b543a-2cf1-4b23-b6d2-cda7e2eac372 Anas platyrhynchos   0  
#> 4 577b543a-2cf1-4b23-b6d2-cda7e2eac372 Martes foina        11.0
#> 5 62c200a9-0e03-4495-bcd8-032944f6f5a1 Anas platyrhynchos   0  
#> 6 62c200a9-0e03-4495-bcd8-032944f6f5a1 Martes foina         0  
#> 7 7ca633fa-64f8-4cfc-a628-6b0c419056d7 Anas platyrhynchos   0  
#> 8 7ca633fa-64f8-4cfc-a628-6b0c419056d7 Martes foina         0  

# Mixed scientific and vernacular names
get_rai_individuals(mica, species = c("Anas platyrhynchos", "beech marten"))
#> Scientific name of beech marten: Martes foina
#> There are 2 deployments without observations: 62c200a9-0e03-4495-bcd8-032944f6f5a1 and 7ca633fa-64f8-4cfc-a628-6b0c419056d7
#> # A tibble: 8 × 3
#>   deploymentID                         scientificName       rai
#>   <chr>                                <chr>              <dbl>
#> 1 29b7d356-4bb4-4ec4-b792-2af5cc32efa8 Anas platyrhynchos 131. 
#> 2 29b7d356-4bb4-4ec4-b792-2af5cc32efa8 Martes foina         0  
#> 3 577b543a-2cf1-4b23-b6d2-cda7e2eac372 Anas platyrhynchos   0  
#> 4 577b543a-2cf1-4b23-b6d2-cda7e2eac372 Martes foina        11.0
#> 5 62c200a9-0e03-4495-bcd8-032944f6f5a1 Anas platyrhynchos   0  
#> 6 62c200a9-0e03-4495-bcd8-032944f6f5a1 Martes foina         0  
#> 7 7ca633fa-64f8-4cfc-a628-6b0c419056d7 Anas platyrhynchos   0  
#> 8 7ca633fa-64f8-4cfc-a628-6b0c419056d7 Martes foina         0  

# Species parameter is case insensitive
get_rai_individuals(mica, species = c("ANAS plAtyRhynChOS"))
#> There are 3 deployments without observations: 577b543a-2cf1-4b23-b6d2-cda7e2eac372, 62c200a9-0e03-4495-bcd8-032944f6f5a1 and 7ca633fa-64f8-4cfc-a628-6b0c419056d7
#> # A tibble: 4 × 3
#>   deploymentID                         scientificName       rai
#>   <chr>                                <chr>              <dbl>
#> 1 29b7d356-4bb4-4ec4-b792-2af5cc32efa8 Anas platyrhynchos  131.
#> 2 577b543a-2cf1-4b23-b6d2-cda7e2eac372 Anas platyrhynchos    0 
#> 3 62c200a9-0e03-4495-bcd8-032944f6f5a1 Anas platyrhynchos    0 
#> 4 7ca633fa-64f8-4cfc-a628-6b0c419056d7 Anas platyrhynchos    0 

# Specify sex
get_rai_individuals(mica, sex = "female")
#> There are 3 deployments without observations: 577b543a-2cf1-4b23-b6d2-cda7e2eac372, 62c200a9-0e03-4495-bcd8-032944f6f5a1 and 7ca633fa-64f8-4cfc-a628-6b0c419056d7
#> # A tibble: 36 × 3
#>    deploymentID                         scientificName       rai
#>    <chr>                                <chr>              <dbl>
#>  1 29b7d356-4bb4-4ec4-b792-2af5cc32efa8 Anas platyrhynchos   0  
#>  2 29b7d356-4bb4-4ec4-b792-2af5cc32efa8 Anas strepera       10.0
#>  3 29b7d356-4bb4-4ec4-b792-2af5cc32efa8 Ardea                0  
#>  4 29b7d356-4bb4-4ec4-b792-2af5cc32efa8 Ardea cinerea        0  
#>  5 29b7d356-4bb4-4ec4-b792-2af5cc32efa8 Castor fiber         0  
#>  6 29b7d356-4bb4-4ec4-b792-2af5cc32efa8 Homo sapiens         0  
#>  7 29b7d356-4bb4-4ec4-b792-2af5cc32efa8 Martes foina         0  
#>  8 29b7d356-4bb4-4ec4-b792-2af5cc32efa8 Mustela putorius     0  
#>  9 29b7d356-4bb4-4ec4-b792-2af5cc32efa8 Vulpes vulpes        0  
#> 10 577b543a-2cf1-4b23-b6d2-cda7e2eac372 Anas platyrhynchos   0  
#> # ℹ 26 more rows
get_rai_individuals(mica, sex = c("female", "unknown"))
#> There are 1 deployments without observations: 7ca633fa-64f8-4cfc-a628-6b0c419056d7
#> # A tibble: 36 × 3
#>    deploymentID                         scientificName       rai
#>    <chr>                                <chr>              <dbl>
#>  1 29b7d356-4bb4-4ec4-b792-2af5cc32efa8 Anas platyrhynchos 131. 
#>  2 29b7d356-4bb4-4ec4-b792-2af5cc32efa8 Anas strepera       60.3
#>  3 29b7d356-4bb4-4ec4-b792-2af5cc32efa8 Ardea                0  
#>  4 29b7d356-4bb4-4ec4-b792-2af5cc32efa8 Ardea cinerea        0  
#>  5 29b7d356-4bb4-4ec4-b792-2af5cc32efa8 Castor fiber         0  
#>  6 29b7d356-4bb4-4ec4-b792-2af5cc32efa8 Homo sapiens         0  
#>  7 29b7d356-4bb4-4ec4-b792-2af5cc32efa8 Martes foina         0  
#>  8 29b7d356-4bb4-4ec4-b792-2af5cc32efa8 Mustela putorius     0  
#>  9 29b7d356-4bb4-4ec4-b792-2af5cc32efa8 Vulpes vulpes        0  
#> 10 577b543a-2cf1-4b23-b6d2-cda7e2eac372 Anas platyrhynchos   0  
#> # ℹ 26 more rows

# Specify life stage
get_rai_individuals(mica, life_stage = "adult")
#> There are 1 deployments without observations: 62c200a9-0e03-4495-bcd8-032944f6f5a1
#> # A tibble: 36 × 3
#>    deploymentID                         scientificName       rai
#>    <chr>                                <chr>              <dbl>
#>  1 29b7d356-4bb4-4ec4-b792-2af5cc32efa8 Anas platyrhynchos   0  
#>  2 29b7d356-4bb4-4ec4-b792-2af5cc32efa8 Anas strepera       10.0
#>  3 29b7d356-4bb4-4ec4-b792-2af5cc32efa8 Ardea                0  
#>  4 29b7d356-4bb4-4ec4-b792-2af5cc32efa8 Ardea cinerea        0  
#>  5 29b7d356-4bb4-4ec4-b792-2af5cc32efa8 Castor fiber         0  
#>  6 29b7d356-4bb4-4ec4-b792-2af5cc32efa8 Homo sapiens         0  
#>  7 29b7d356-4bb4-4ec4-b792-2af5cc32efa8 Martes foina         0  
#>  8 29b7d356-4bb4-4ec4-b792-2af5cc32efa8 Mustela putorius     0  
#>  9 29b7d356-4bb4-4ec4-b792-2af5cc32efa8 Vulpes vulpes        0  
#> 10 577b543a-2cf1-4b23-b6d2-cda7e2eac372 Anas platyrhynchos   0  
#> # ℹ 26 more rows
get_rai_individuals(mica, life_stage = c("adult", "subadult"))
#> There are 1 deployments without observations: 62c200a9-0e03-4495-bcd8-032944f6f5a1
#> # A tibble: 36 × 3
#>    deploymentID                         scientificName       rai
#>    <chr>                                <chr>              <dbl>
#>  1 29b7d356-4bb4-4ec4-b792-2af5cc32efa8 Anas platyrhynchos 111. 
#>  2 29b7d356-4bb4-4ec4-b792-2af5cc32efa8 Anas strepera       60.3
#>  3 29b7d356-4bb4-4ec4-b792-2af5cc32efa8 Ardea                0  
#>  4 29b7d356-4bb4-4ec4-b792-2af5cc32efa8 Ardea cinerea        0  
#>  5 29b7d356-4bb4-4ec4-b792-2af5cc32efa8 Castor fiber         0  
#>  6 29b7d356-4bb4-4ec4-b792-2af5cc32efa8 Homo sapiens         0  
#>  7 29b7d356-4bb4-4ec4-b792-2af5cc32efa8 Martes foina         0  
#>  8 29b7d356-4bb4-4ec4-b792-2af5cc32efa8 Mustela putorius     0  
#>  9 29b7d356-4bb4-4ec4-b792-2af5cc32efa8 Vulpes vulpes        0  
#> 10 577b543a-2cf1-4b23-b6d2-cda7e2eac372 Anas platyrhynchos   0  
#> # ℹ 26 more rows

# Apply filter(s): deployments with latitude >= 51.18
get_rai_individuals(mica, pred_gte("latitude", 51.18))
#> df %>% dplyr::filter((latitude >= 51.18))
#> df %>% dplyr::filter((latitude >= 51.18))
#> # A tibble: 18 × 3
#>    deploymentID                         scientificName       rai
#>    <chr>                                <chr>              <dbl>
#>  1 29b7d356-4bb4-4ec4-b792-2af5cc32efa8 Anas platyrhynchos 131. 
#>  2 29b7d356-4bb4-4ec4-b792-2af5cc32efa8 Anas strepera       60.3
#>  3 29b7d356-4bb4-4ec4-b792-2af5cc32efa8 Ardea                0  
#>  4 29b7d356-4bb4-4ec4-b792-2af5cc32efa8 Ardea cinerea        0  
#>  5 29b7d356-4bb4-4ec4-b792-2af5cc32efa8 Castor fiber         0  
#>  6 29b7d356-4bb4-4ec4-b792-2af5cc32efa8 Homo sapiens         0  
#>  7 29b7d356-4bb4-4ec4-b792-2af5cc32efa8 Martes foina         0  
#>  8 29b7d356-4bb4-4ec4-b792-2af5cc32efa8 Mustela putorius     0  
#>  9 29b7d356-4bb4-4ec4-b792-2af5cc32efa8 Vulpes vulpes        0  
#> 10 577b543a-2cf1-4b23-b6d2-cda7e2eac372 Anas platyrhynchos   0  
#> 11 577b543a-2cf1-4b23-b6d2-cda7e2eac372 Anas strepera        0  
#> 12 577b543a-2cf1-4b23-b6d2-cda7e2eac372 Ardea                0  
#> 13 577b543a-2cf1-4b23-b6d2-cda7e2eac372 Ardea cinerea        0  
#> 14 577b543a-2cf1-4b23-b6d2-cda7e2eac372 Castor fiber        11.0
#> 15 577b543a-2cf1-4b23-b6d2-cda7e2eac372 Homo sapiens         0  
#> 16 577b543a-2cf1-4b23-b6d2-cda7e2eac372 Martes foina        11.0
#> 17 577b543a-2cf1-4b23-b6d2-cda7e2eac372 Mustela putorius    32.9
#> 18 577b543a-2cf1-4b23-b6d2-cda7e2eac372 Vulpes vulpes       11.0