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Fetch BBS Occurrence Data by Species

Source: R/bbs_fetch.R
bbs_fetch.Rd

This function fetches occurrence data for specified target species, utilizing both the event and occurrence tables from GBIF. The fetched dataset undergoes the following processing steps:

  1. Join: Combines the event, occurrence, and measurementorfacts datasheets from GBIF into a single cohesive dataset.

  2. Filter: Retains only the observations for specified species using the target_species argument. The entered Chinese common name was linked to scientific name by bbs_translate.

  3. Zero Fill: Converts implicit missing values into explicit ones by filling in zeros for trips where the target species was not observed. Specifically, if a plot was visited during a particular year or trip but the target species was not observed, the species count will show a value of 0 for that row.

Usage

bbs_fetch(target_species)

Arguments

target_species

Character string specifying the Chinese common name of the species of interest. It can accept a single character string, such as target_species = "紅嘴黑鵯", or a vector, such as target_species = c("紅嘴黑鵯", "白耳畫眉").Use "全部" to return all species.

Value

A tibble containing the species occurrence data.

Examples

# For single species data fetch
bbs_fetch(target_species = "紅嘴黑鵯")
#> # A tibble: 42,203 × 16
#>     year month   day site   locationID decimalLatitude decimalLongitude weather
#>    <dbl> <dbl> <dbl> <chr>  <chr>                <dbl>            <dbl> <chr>  
#>  1  2009     4    26 A02-01 A02-01_01             25.1             122. NA     
#>  2  2009     3    10 A02-01 A02-01_01             25.1             122. NA     
#>  3  2009     4     5 A02-01 A02-01_01             25.1             122. NA     
#>  4  2009     3    10 A02-01 A02-01_01             25.1             122. NA     
#>  5  2009     4    26 A02-01 A02-01_01             25.1             122. NA     
#>  6  2009     4     5 A02-01 A02-01_01             25.1             122. NA     
#>  7  2009     4    26 A02-01 A02-01_02             25.1             122. NA     
#>  8  2009     3    10 A02-01 A02-01_02             25.1             122. NA     
#>  9  2009     4     5 A02-01 A02-01_02             25.1             122. NA     
#> 10  2009     4    26 A02-01 A02-01_02             25.1             122. NA     
#> # ℹ 42,193 more rows
#> # ℹ 8 more variables: wind <chr>, habitat <chr>, scientificName <chr>,
#> #   vernacularName <chr>, individualCount <dbl>, time_slot <chr>,
#> #   distance <chr>, flock <chr>

# For multiple species data fetch
bbs_fetch(target_species = c("紅嘴黑鵯", "白耳畫眉"))
#> # A tibble: 79,941 × 16
#>     year month   day site   locationID decimalLatitude decimalLongitude weather
#>    <dbl> <dbl> <dbl> <chr>  <chr>                <dbl>            <dbl> <chr>  
#>  1  2009     4    26 A02-01 A02-01_01             25.1             122. NA     
#>  2  2009     3    10 A02-01 A02-01_01             25.1             122. NA     
#>  3  2009     4     5 A02-01 A02-01_01             25.1             122. NA     
#>  4  2009     3    10 A02-01 A02-01_01             25.1             122. NA     
#>  5  2009     4    26 A02-01 A02-01_01             25.1             122. NA     
#>  6  2009     4     5 A02-01 A02-01_01             25.1             122. NA     
#>  7  2009     4    26 A02-01 A02-01_02             25.1             122. NA     
#>  8  2009     3    10 A02-01 A02-01_02             25.1             122. NA     
#>  9  2009     4     5 A02-01 A02-01_02             25.1             122. NA     
#> 10  2009     4    26 A02-01 A02-01_02             25.1             122. NA     
#> # ℹ 79,931 more rows
#> # ℹ 8 more variables: wind <chr>, habitat <chr>, scientificName <chr>,
#> #   vernacularName <chr>, individualCount <dbl>, time_slot <chr>,
#> #   distance <chr>, flock <chr>

# To return data for all species
bbs_fetch(target_species = "全部")
#> # A tibble: 373,786 × 16
#>     year month   day site   locationID decimalLatitude decimalLongitude weather
#>    <dbl> <dbl> <dbl> <chr>  <chr>                <dbl>            <dbl> <chr>  
#>  1  2009     3    10 A02-01 A02-01_01             25.1             122. NA     
#>  2  2009     4     5 A02-01 A02-01_01             25.1             122. NA     
#>  3  2009     4     5 A02-01 A02-01_01             25.1             122. NA     
#>  4  2009     4    26 A02-01 A02-01_01             25.1             122. NA     
#>  5  2009     3    10 A02-01 A02-01_01             25.1             122. NA     
#>  6  2009     3    10 A02-01 A02-01_01             25.1             122. NA     
#>  7  2009     4     5 A02-01 A02-01_01             25.1             122. NA     
#>  8  2009     4     5 A02-01 A02-01_01             25.1             122. NA     
#>  9  2009     3    10 A02-01 A02-01_01             25.1             122. NA     
#> 10  2009     4    26 A02-01 A02-01_01             25.1             122. NA     
#> # ℹ 373,776 more rows
#> # ℹ 8 more variables: wind <chr>, habitat <chr>, scientificName <chr>,
#> #   vernacularName <chr>, individualCount <dbl>, time_slot <chr>,
#> #   distance <chr>, flock <chr>

# The function will return NULL if the target species is not found in the
# BBS species list
bbs_fetch(target_species = "隨機鳥")
#> ! The bird is not in the BBS species list
#> ! 查無鳥名
#> NULL