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Get number of individuals for each deployment

Source: R/get_n_individuals.R
get_n_individuals.Rd

Gets the number of individuals (of a subset of species) per deployment. The number of observed individuals is stored in field count of observations.

Usage

get_n_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. If NULL all observations of all species are taken into account.

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 of the species. This column is omitted if parameter species = NULL.

  • n: Number of individuals.

See also

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

Examples

# Get number of observations for each species
get_n_individuals(mica)
#> # A tibble: 36 × 3
#>    deploymentID                         scientificName         n
#>    <chr>                                <chr>              <int>
#>  1 29b7d356-4bb4-4ec4-b792-2af5cc32efa8 Anas strepera          6
#>  2 29b7d356-4bb4-4ec4-b792-2af5cc32efa8 Anas platyrhynchos    13
#>  3 29b7d356-4bb4-4ec4-b792-2af5cc32efa8 Castor fiber           0
#>  4 29b7d356-4bb4-4ec4-b792-2af5cc32efa8 Mustela putorius       0
#>  5 29b7d356-4bb4-4ec4-b792-2af5cc32efa8 Vulpes vulpes          0
#>  6 29b7d356-4bb4-4ec4-b792-2af5cc32efa8 Martes foina           0
#>  7 29b7d356-4bb4-4ec4-b792-2af5cc32efa8 Ardea cinerea          0
#>  8 29b7d356-4bb4-4ec4-b792-2af5cc32efa8 Ardea                  0
#>  9 29b7d356-4bb4-4ec4-b792-2af5cc32efa8 Homo sapiens           0
#> 10 577b543a-2cf1-4b23-b6d2-cda7e2eac372 Anas strepera          0
#> # ℹ 26 more rows

# Get number of obs of all species, not identified individuals as well
get_n_individuals(mica, species = NULL)
#> # A tibble: 4 × 2
#>   deploymentID                             n
#>   <chr>                                <int>
#> 1 29b7d356-4bb4-4ec4-b792-2af5cc32efa8    19
#> 2 577b543a-2cf1-4b23-b6d2-cda7e2eac372     6
#> 3 62c200a9-0e03-4495-bcd8-032944f6f5a1     3
#> 4 7ca633fa-64f8-4cfc-a628-6b0c419056d7     2

# Get number of observations of Anas platyrhynchos
get_n_individuals(mica, species = "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         n
#>   <chr>                                <chr>              <int>
#> 1 29b7d356-4bb4-4ec4-b792-2af5cc32efa8 Anas platyrhynchos    13
#> 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

# Get number of observations of eurasian beaver (vernacular name)
get_n_individuals(mica, species = "eurasian beaver")
#> Scientific name of eurasian beaver: Castor fiber
#> There are 3 deployments without observations: 29b7d356-4bb4-4ec4-b792-2af5cc32efa8, 62c200a9-0e03-4495-bcd8-032944f6f5a1 and 7ca633fa-64f8-4cfc-a628-6b0c419056d7
#> # A tibble: 4 × 3
#>   deploymentID                         scientificName     n
#>   <chr>                                <chr>          <int>
#> 1 29b7d356-4bb4-4ec4-b792-2af5cc32efa8 Castor fiber       0
#> 2 577b543a-2cf1-4b23-b6d2-cda7e2eac372 Castor fiber       1
#> 3 62c200a9-0e03-4495-bcd8-032944f6f5a1 Castor fiber       0
#> 4 7ca633fa-64f8-4cfc-a628-6b0c419056d7 Castor fiber       0

# Mix scientific and vernacular names
get_n_individuals(mica, species = c("Anas platyrhynchos", "eurasian beaver"))
#> Scientific name of eurasian beaver: Castor fiber
#> There are 2 deployments without observations: 62c200a9-0e03-4495-bcd8-032944f6f5a1 and 7ca633fa-64f8-4cfc-a628-6b0c419056d7
#> # A tibble: 8 × 3
#>   deploymentID                         scientificName         n
#>   <chr>                                <chr>              <int>
#> 1 29b7d356-4bb4-4ec4-b792-2af5cc32efa8 Anas platyrhynchos    13
#> 2 29b7d356-4bb4-4ec4-b792-2af5cc32efa8 Castor fiber           0
#> 3 577b543a-2cf1-4b23-b6d2-cda7e2eac372 Anas platyrhynchos     0
#> 4 577b543a-2cf1-4b23-b6d2-cda7e2eac372 Castor fiber           1
#> 5 62c200a9-0e03-4495-bcd8-032944f6f5a1 Anas platyrhynchos     0
#> 6 62c200a9-0e03-4495-bcd8-032944f6f5a1 Castor fiber           0
#> 7 7ca633fa-64f8-4cfc-a628-6b0c419056d7 Anas platyrhynchos     0
#> 8 7ca633fa-64f8-4cfc-a628-6b0c419056d7 Castor fiber           0

# Case insensitive
get_n_individuals(mica, species = "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         n
#>   <chr>                                <chr>              <int>
#> 1 29b7d356-4bb4-4ec4-b792-2af5cc32efa8 Anas platyrhynchos    13
#> 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
get_n_individuals(mica, species = "eurasian BEAVER")
#> Scientific name of eurasian BEAVER: Castor fiber
#> There are 3 deployments without observations: 29b7d356-4bb4-4ec4-b792-2af5cc32efa8, 62c200a9-0e03-4495-bcd8-032944f6f5a1 and 7ca633fa-64f8-4cfc-a628-6b0c419056d7
#> # A tibble: 4 × 3
#>   deploymentID                         scientificName     n
#>   <chr>                                <chr>          <int>
#> 1 29b7d356-4bb4-4ec4-b792-2af5cc32efa8 Castor fiber       0
#> 2 577b543a-2cf1-4b23-b6d2-cda7e2eac372 Castor fiber       1
#> 3 62c200a9-0e03-4495-bcd8-032944f6f5a1 Castor fiber       0
#> 4 7ca633fa-64f8-4cfc-a628-6b0c419056d7 Castor fiber       0

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

# Specify sex
get_n_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         n
#>    <chr>                                <chr>              <int>
#>  1 29b7d356-4bb4-4ec4-b792-2af5cc32efa8 Anas strepera          1
#>  2 29b7d356-4bb4-4ec4-b792-2af5cc32efa8 Anas platyrhynchos     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 strepera          0
#> # ℹ 26 more rows

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

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