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Get number of observations for each deployment

Source: R/get_n_obs.R
get_n_obs.Rd

[Deprecated]

This function is deprecated. Use summarize_observations() instead.

Gets the number of event-based observations per deployment.

Usage

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

  • n: Number of observations.

See also

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

Examples

x <- example_dataset()

# Get number of observations for each species
get_n_obs(x)
#> Warning: `get_n_obs()` 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         n
#>    <chr>        <chr>              <int>
#>  1 00a2c20d     Anas platyrhynchos     9
#>  2 00a2c20d     Ardea cinerea          1
#>  3 00a2c20d     Rattus norvegicus      2
#>  4 00a2c20d     NA                     2
#>  5 29b7d356     Anas platyrhynchos     6
#>  6 29b7d356     Anas strepera          2
#>  7 29b7d356     Aves                   1
#>  8 29b7d356     NA                     2
#>  9 577b543a     Martes foina           1
#> 10 577b543a     Mustela putorius       3
#> 11 577b543a     Vulpes vulpes          1
#> 12 577b543a     NA                     1
#> 13 62c200a9     Ardea                  2
#> 14 62c200a9     Aves                   1
#> 15 62c200a9     NA                     2

# Get number of obs of all species, not identified individuals as well
get_n_obs(x, species = NULL)
#> # A tibble: 4 × 2
#> # Groups:   deploymentID [4]
#>   deploymentID     n
#>   <chr>        <int>
#> 1 00a2c20d        14
#> 2 29b7d356        11
#> 3 577b543a         6
#> 4 62c200a9         5
 
# Get number of observations of Anas platyrhynchos
get_n_obs(x, species = "Anas platyrhynchos")
#> Warning: The `species` argument of `get_n_obs()` 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: 2 × 3
#> # Groups:   deploymentID, scientificName [2]
#>   deploymentID scientificName         n
#>   <chr>        <chr>              <int>
#> 1 00a2c20d     Anas platyrhynchos     9
#> 2 29b7d356     Anas platyrhynchos     6

# Specify sex
get_n_obs(x, sex = "female")
#> Warning: The `sex` argument of `get_n_obs()` is deprecated as of camtraptor 1.0.0.
#> ℹ Argument `sex` is deprecated as of camtraptor 1.0.0. Please, use
#>   `filter_observations()` to filter by `sex`.
#> ℹ The deprecated feature was likely used in the camtraptor package.
#>   Please report the issue at <https://github.com/inbo/camtraptor/issues>.
#> # A tibble: 2 × 3
#> # Groups:   deploymentID, scientificName [2]
#>   deploymentID scientificName         n
#>   <chr>        <chr>              <int>
#> 1 00a2c20d     Anas platyrhynchos     4
#> 2 29b7d356     Anas platyrhynchos     3

# Specify life stage
get_n_obs(x, life_stage = c("subadult", "adult"))
#> Warning: The `life_stage` argument of `get_n_obs()` is deprecated as of camtraptor
#> 1.0.0.
#> ℹ Argument `life_stage` is deprecated as of camtraptor 1.0.0. Please, use
#>   `filter_observations()` to filter by `lifeStage`.
#> ℹ The deprecated feature was likely used in the camtraptor package.
#>   Please report the issue at <https://github.com/inbo/camtraptor/issues>.
#> # A tibble: 7 × 3
#> # Groups:   deploymentID, scientificName [7]
#>   deploymentID scientificName         n
#>   <chr>        <chr>              <int>
#> 1 00a2c20d     Anas platyrhynchos     7
#> 2 00a2c20d     Ardea cinerea          1
#> 3 29b7d356     Anas platyrhynchos     6
#> 4 29b7d356     Anas strepera          2
#> 5 577b543a     Martes foina           1
#> 6 577b543a     Mustela putorius       3
#> 7 577b543a     Vulpes vulpes          1