Author: rcites team

# Bulk analysis with rcites

#### rcites team

#### 15-08-2018

## Broad taxon concept queries

If you want to query all taxa, you can use `spp_taxonconcept()` with `query_taxon = ""` (assuming your token is already set up):

    res_cms <- spp_taxonconcept("", taxonomy = "CMS") #slow

    #>  ℹ Retrieving info from page 1 ........................ ✔
    #>  ℹ 10 pages available, retrieving info from 9 more
    #>  ℹ Retrieving info from page 2 ........................ ✔
    #>  ℹ Retrieving info from page 3 ........................ ✔
    #>  ℹ Retrieving info from page 4 ........................ ✔
    #>  ℹ Retrieving info from page 5 ........................ ✔
    #>  ℹ Retrieving info from page 6 ........................ ✔
    #>  ℹ Retrieving info from page 7 ........................ ✔
    #>  ℹ Retrieving info from page 8 ........................ ✔
    #>  ℹ Retrieving info from page 9 ........................ ✔
    #>  ℹ Retrieving info from page 10 ....................... ✔

    dim(res_cms$general)

    #>  [1] 2541    7

Alternatively, you can retrieve, for example, the first three pages of results returned by the API.

    res_cites <- spp_taxonconcept("", page = 1:2)

    #>  ℹ Retrieving info from page 1 ........................ ✔
    #>  ℹ 167 pages available, retrieving info from 1 more
    #>  ℹ Retrieving info from page 2 ........................ ✔

    dim(res_cites$general)

    #>  [1] 1000    8

## Retrieving information for a set of taxon_concept ID

All `spp_` functions (i.e. `spp_distributions()`, `spp_eu_legislation()`, `spp_cites_legislation()` and `spp_references()`) can handle a vector of taxon_id which allows bulk analysis. Below we exemplify this feature for the four functions.

### spp_distributions()

    vc_txn <- c('4521', '3210', '10255')
    res1 <- spp_distributions(taxon_id = vc_txn, verbose = FALSE)
    ## Number of countries concerned per taxon ID
    table(res1$distributions$taxon_id)

    #>
    #>  10255  3210  4521
    #>     15     8    42

### spp_cites_legislation()

    res2 <- spp_cites_legislation(taxon_id = vc_txn, verbose = FALSE)
    res2$cites_listings

    #>  # A tibble: 12 × 7
    #>     taxon_id id    taxon_concept_id is_current appendix change_type effective_at
    #>     <chr>    <chr> <chr>            <lgl>      <chr>    <chr>       <chr>
    #>   1 4521     30344 4521             TRUE       I        +           2017-01-02
    #>   2 4521     30115 4521             TRUE       II       +           2019-11-26
    #>   3 4521     32160 4521             TRUE       II       R+          2019-11-26
    #>   4 4521     32161 4521             TRUE       II       R+          2019-11-26
    #>   5 4521     32156 4521             TRUE       II       R+          2019-11-26
    #>   6 4521     32158 4521             TRUE       II       R+          2019-11-26
    #>   7 4521     32154 4521             TRUE       II       R+          2019-11-26
    #>   8 4521     32159 4521             TRUE       II       R+          2019-11-26
    #>   9 4521     32157 4521             TRUE       II       R+          2019-11-26
    #>  10 4521     32155 4521             TRUE       II       R+          2019-11-26
    #>  11 3210     4661  3210             TRUE       II       +           1987-10-22
    #>  12 10255    4645  10255            TRUE       I        +           2005-01-12

### spp_eu_legislation()

    res3 <- spp_eu_legislation(taxon_id = vc_txn, verbose = FALSE)
    res3$eu_listings

    #>  # A tibble: 4 × 7
    #>    taxon_id id    taxon_concept_id is_current annex change_type effective_at
    #>    <chr>    <chr> <chr>            <lgl>      <chr> <chr>       <chr>
    #>  1 4521     31788 4521             TRUE       A     +           2019-12-14
    #>  2 4521     31876 4521             TRUE       B     +           2019-12-14
    #>  3 3210     30578 3210             TRUE       B     +           2019-12-14
    #>  4 10255    30516 10255            TRUE       A     +           2019-12-14

### spp_references()

    res4 <- spp_references(taxon_id = vc_txn, verbose = FALSE)
    ## Number of references per taxon ID
    table(res4$references$taxon_id)

    #>
    #>  10255  3210  4521
    #>      1     3    15