Extract the count series corresponding to a location and/or a species

This function identifies the count series relative to a species and/or a location in a named list like the output of function format_data(). If both species and location are provided, the series of counts of the species at the specified location is extracted. Otherwise, all series corresponding to the specified criterion (species or location) are extracted.

Usage

filter_series(data, species = NULL, location = NULL)

Arguments

data: a named list. The output of function format_data().
species: a character string. A species name.
location: a character string. A site name.

Value

A subset of data, i.e. a named list.

Examples

## Load Garamba raw dataset ----
file_path <- system.file("extdata", "garamba_survey.csv", 
                         package = "popbayes")
                         
garamba <- read.csv(file = file_path)

## Create temporary folder ----
temp_path <- tempdir()

## Format dataset ----
garamba_formatted <- popbayes::format_data(
  data              = garamba, 
  path              = temp_path,
  field_method      = "field_method",
  pref_field_method = "pref_field_method",
  conversion_A2G    = "conversion_A2G",
  rmax              = "rmax")
#> ✔ Detecting 10 count series.

## Number of count series ----
length(garamba_formatted)
#> [1] 10

## Retrieve count series names ----
popbayes::list_series(path = temp_path)
#>  [1] "garamba__alcelaphus_buselaphus"  "garamba__giraffa_camelopardalis"
#>  [3] "garamba__hippotragus_equinus"    "garamba__kobus_ellipsiprymnus"  
#>  [5] "garamba__kobus_kob"              "garamba__loxodonta_africana"    
#>  [7] "garamba__ourebia_ourebi"         "garamba__redunca_redunca"       
#>  [9] "garamba__syncerus_caffer"        "garamba__tragelaphus_scriptus"  

## Get data for Alcelaphus buselaphus (at all sites) ----
x <- popbayes::filter_series(garamba_formatted, 
                             species = "Alcelaphus buselaphus")
#> ✔ Found 1 series with "Alcelaphus buselaphus".

## Get data at Garamba (for all species) ----
x <- popbayes::filter_series(garamba_formatted, 
                             location = "Garamba")
#> ✔ Found 10 series with "Garamba".

## Get data for Alcelaphus buselaphus at Garamba only ----
x <- popbayes::filter_series(garamba_formatted, 
                             location = "Garamba",
                             species  = "Alcelaphus buselaphus")
#> ✔ Found 1 series with "Alcelaphus buselaphus" and "Garamba".