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Find species id codes by searching for scientific, English and French species names.

Usage

search_species(name = NULL, show = "names", authority = NULL)

Arguments

name

Character. The species name to search for

show

Character. Either "all" or "names" (default). Whether to return all taxonomic information or only a subset with species names

authority

Character. If not NULL (default), return the alphanumeric code associated with avian species for this taxonomic authority.

Value

Data frame of species ids and taxonomic information

Details

species_search() is deprecated in favour of search_species()

Examples


# Show all ids
search_species()
#> # A tibble: 37,701 × 5
#>    species_id scientific_name          english_name      french_name taxon_group
#>         <int> <chr>                    <chr>             <chr>       <chr>      
#>  1          0 N/A                      No observations   Aucune obs… BIRDS      
#>  2         10 Tinamus major            Great Tinamou     Grand Tina… BIRDS      
#>  3         20 Nothocercus bonapartei   Highland Tinamou  Tinamou de… BIRDS      
#>  4         30 Crypturellus soui        Little Tinamou    Tinamou so… BIRDS      
#>  5         40 Crypturellus cinnamomeus Thicket Tinamou   Tinamou ca… BIRDS      
#>  6         50 Crypturellus boucardi    Slaty-breasted T… Tinamou de… BIRDS      
#>  7         60 Crypturellus kerriae     Choco Tinamou     Tinamou de… BIRDS      
#>  8         70 Dendrocygna viduata      White-faced Whis… Dendrocygn… BIRDS      
#>  9         80 Dendrocygna autumnalis   Black-bellied Wh… Dendrocygn… BIRDS      
#> 10         90 Dendrocygna arborea      West Indian Whis… Dendrocygn… BIRDS      
#> # ℹ 37,691 more rows

search_species("chickadee")
#> # A tibble: 22 × 5
#>    species_id scientific_name               english_name french_name taxon_group
#>         <int> <chr>                         <chr>        <chr>       <chr>      
#>  1      14270 Poecile carolinensis          Carolina Ch… Mésange de… BIRDS      
#>  2      14280 Poecile atricapillus          Black-cappe… Mésange à … BIRDS      
#>  3      14290 Poecile gambeli               Mountain Ch… Mésange de… BIRDS      
#>  4      14300 Poecile sclateri              Mexican Chi… Mésange gr… BIRDS      
#>  5      14310 Poecile rufescens             Chestnut-ba… Mésange à … BIRDS      
#>  6      14320 Poecile hudsonicus            Boreal Chic… Mésange à … BIRDS      
#>  7      14330 Poecile cinctus               Gray-headed… Mésange la… BIRDS      
#>  8      14388 Paridae sp.                   Chickadee sp Mésange sp. BIRDS      
#>  9      40668 Poecile carolinensis x atric… Carolina x … Hybride Mé… BIRDS      
#> 10      40669 Poecile carolinensis/atricap… Carolina/Bl… Mésange de… BIRDS      
#> # ℹ 12 more rows
search_species("black-capped chickadee")
#> # A tibble: 4 × 5
#>   species_id scientific_name                english_name french_name taxon_group
#>        <int> <chr>                          <chr>        <chr>       <chr>      
#> 1      14280 Poecile atricapillus           Black-cappe… Mésange à … BIRDS      
#> 2      40668 Poecile carolinensis x atrica… Carolina x … Hybride Mé… BIRDS      
#> 3      40669 Poecile carolinensis/atricapi… Carolina/Bl… Mésange de… BIRDS      
#> 4      44466 Poecile atricapillus x Baeolo… Black-cappe… Hybride Mé… BIRDS      

# Add alphanumeric code for BSCDATA authority
search_species("black-capped chickadee", authority = "BSCDATA")
#> # A tibble: 4 × 6
#>   species_id scientific_name        english_name french_name taxon_group BSCDATA
#>        <int> <chr>                  <chr>        <chr>       <chr>       <chr>  
#> 1      14280 Poecile atricapillus   Black-cappe… Mésange à … BIRDS       BCCH   
#> 2      40668 Poecile carolinensis … Carolina x … Hybride Mé… BIRDS       NA     
#> 3      40669 Poecile carolinensis/… Carolina/Bl… Mésange de… BIRDS       NA     
#> 4      44466 Poecile atricapillus … Black-cappe… Hybride Mé… BIRDS       NA     

# Show all taxonomic information
search_species("black-capped chickadee", show = "all")
#> # A tibble: 4 × 17
#>   species_id concept_id     scientific_name species_status added_dt english_name
#>        <int> <chr>          <chr>                    <int> <chr>    <chr>       
#> 1      14280 avibase-B1F0C… Poecile atrica…              1 NA       Black-cappe…
#> 2      40668 avibase-1B9B3… Poecile caroli…              4 NA       Carolina x …
#> 3      40669 avibase-F648A… Poecile caroli…              2 NA       Carolina/Bl…
#> 4      44466 avibase-6D7E1… Poecile atrica…              4 NA       Black-cappe…
#> # ℹ 11 more variables: french_name <chr>, phylum <chr>,
#> #   family_french_name <chr>, group_id <dbl>, order_taxon <chr>,
#> #   taxon_group <chr>, sort_order <int>, class <chr>, family_name <chr>,
#> #   concept_source <chr>, family_english_name <chr>

# Using the codes
nc_count(species = 14280)
#> Without a username, using 'show = "all"'
#> Using filters: species (14280)
#> # A tibble: 260 × 4
#>    collection      akn_level access nrecords
#>    <chr>               <int> <chr>     <int>
#>  1 ABATLAS1                5 full       1314
#>  2 ABATLAS2                5 full       3772
#>  3 ABBIRDRECS              5 full       2931
#>  4 BBS                     5 full      39794
#>  5 BBS50-CAN               5 full      53086
#>  6 BBS50-US-EAST           5 full      62460
#>  7 BBS50-US-WEST           5 full      55936
#>  8 BCATLAS1BE_DO           5 full        447
#>  9 BCATLAS1BE_RAW          5 full       3616
#> 10 BCATLAS1BE_SUMM         5 full       1553
#> # ℹ 250 more rows