Study case: the African bush elephant (Loxodonta africana)

rcites team

10-08-2018

Introduction and setup

In Get started with rcites, we explained how to get a token and set it up for general access to the CITES Species+ database. Also, we very briefly introduced to how to code the key features of rcites. With this article, we aim to further introduce to the functionality and workflows of rcites. For this, we use the African bush elephant (Loxodonta africana, hereafter “elephant”) as a case study. The elephant not only is a highly endangered species that is illegally traded globally but also a flagship species of nature conservation and the logo species of CITES.

We start with a basic set up: we load the package and set the token:

library(rcites)
set_token("8QW6Qgh57sBG2k0gtt")

Retrieve the taxon id

In order to access information about the elephant, we first need to retrieve its Species+ taxon identifier. For this, we use the spp_taxonconcept() function and the elephant’s scientific name, Loxodonta africana, as query_taxon argument.

elephant_taxonconcept <- spp_taxonconcept(query_taxon = "Loxodonta africana")
#>  → Retrieving info from page 1 ........................✔
elephant_taxonconcept
#>  
#>  ── General info - CITES ($general): ───────────────────────────────────────
#>      id          full_name        author_year    rank name_status
#>  1 4521 Loxodonta africana (Blumenbach, 1797) SPECIES           A
#>             updated_at active cites_listing
#>  1 2019-05-09 11:12:49   TRUE          I/II
#>  
#>  ── Classification ($higher_taxa): ─────────────────────────────────────────
#>      id  kingdom   phylum    class       order       family
#>  1 4521 Animalia Chordata Mammalia Proboscidea Elephantidae
#>  
#>  ── Synonyms ($synonyms): ──────────────────────────────────────────────────
#>      id apply.do.call.rbind..tmp.wch....2..unlist.
#>  1 4521                                      37069
#>  2 4521                         Loxodonta cyclotis
#>  3 4521                           (Matschie, 1900)
#>  4 4521                                    SPECIES
#>  
#>  ── Common names ($common_names): ──────────────────────────────────────────
#>       id               name language
#>  1  4521              Ndovo       SW
#>  2  4521              Tembo       SW
#>  3  4521             Haathi       UR
#>  4  4521           Elefante       PT
#>  5  4521               Slon       RU
#>  6  4521            Elefant       NO
#>  7  4521            Olifant       NL
#>  8  4521 Afrikaanse olifant       NL
#>  9  4521  Elefante africano       ES
#>  10 4521  afrikansk elefant       SV
#>  -------truncated-------
#>  
#>  Information available: $all_id, $general, $higher_taxa, $accepted_names, $common_names, $synonyms, $cites_listings

As the first column of the output shows, the taxon identifier of the elephant is 4521. This taxon_id will be used for all next function coding.

Beyond the taxon identifier, the output also provides information about the taxon classification and other names, both synonyms and common names if any, in different languages.

Map the elephant’s distribution

Before giving more insights into the legislation status of the elephant, we have a look at where the elephant actually occurs naturally. For this, we can access the elephant’s distribution information with the spp_distributions() function. Thereafter, we can map the distribution with the help of the rworldmap package.

#>  42 codes from your data successfully matched countries in the map
#>  0 codes from your data failed to match with a country code in the map
#>  201 codes from the map weren't represented in your data

Access the legislation status

The functions spp_cites_legislation() and spp_eu_legislation() provide access to the legislation status information of the elephant.

First, we have a look at the CITES legislation status:

#>  → Now processing taxon_id '4521'......................✔
#>  
#>  ── Cites listings ($cites_listings): ──────────────────────────────────────
#>      id taxon_concept_id is_current appendix change_type effective_at
#>  1 3666             4521       TRUE       II           +   2007-09-13
#>  2 3665             4521       TRUE        I           +   2007-09-13
#>  3 3645             4521       TRUE        I          R+   1990-01-18
#>  
#>  ── Cites quotas ($cites_quotas): ──────────────────────────────────────────
#>        id taxon_concept_id quota publication_date public_display is_current
#>  1  20604             4521     0       2017-03-06           TRUE       TRUE
#>  2  20586             4521     0       2017-03-06           TRUE       TRUE
#>  3  20695             4521     0       2017-03-06           TRUE       TRUE
#>  4  20696             4521     0       2017-03-06           TRUE       TRUE
#>  5  20697             4521     0       2017-03-06           TRUE       TRUE
#>  6  20698             4521     0       2017-03-06           TRUE       TRUE
#>  7  20699             4521     0       2017-03-06           TRUE       TRUE
#>  8  20700             4521     0       2017-03-06           TRUE       TRUE
#>  9  20701             4521     0       2017-03-06           TRUE       TRUE
#>  10 20703             4521     0       2017-03-06           TRUE       TRUE
#>     unit geo_entity.iso_code2          geo_entity.name geo_entity.type
#>  1  <NA>                   CG                    Congo         COUNTRY
#>  2  <NA>                   AO                   Angola         COUNTRY
#>  3  <NA>                   BW                 Botswana         COUNTRY
#>  4  <NA>                   BF             Burkina Faso         COUNTRY
#>  5  <NA>                   CF Central African Republic         COUNTRY
#>  6  <NA>                   CI            Côte d'Ivoire         COUNTRY
#>  7  <NA>                   GW            Guinea Bissau         COUNTRY
#>  8  <NA>                   LR                  Liberia         COUNTRY
#>  9  <NA>                   SL             Sierra Leone         COUNTRY
#>  10 <NA>                   GA                    Gabon         COUNTRY
#>  -------truncated-------
#>  Field(s) not printed:  notes, url 
#>  
#>  ── Cites suspensions ($cites_suspensions): ────────────────────────────────
#>        id taxon_concept_id start_date is_current applies_to_import
#>  1  15986             <NA> 2013-05-16       TRUE             FALSE
#>  2  17621             4521 2014-08-11       TRUE              TRUE
#>  3  17620             4521 2014-08-11       TRUE              TRUE
#>  4  17686             4521 2014-10-10       TRUE              TRUE
#>  5  18709             4521 2010-08-16       TRUE              TRUE
#>  6  15983             <NA> 2011-01-19       TRUE             FALSE
#>  7  15971             <NA> 2004-07-30       TRUE             FALSE
#>  8  18955             4521 2016-04-01       TRUE              TRUE
#>  9  22079             <NA> 2018-01-30       TRUE             FALSE
#>  10 22076             <NA> 2018-01-22       TRUE             FALSE
#>     geo_entity.iso_code2             geo_entity.name geo_entity.type
#>  1                    GN                      Guinea         COUNTRY
#>  2                    ZW                    Zimbabwe         COUNTRY
#>  3                    TZ United Republic of Tanzania         COUNTRY
#>  4                    US    United States of America         COUNTRY
#>  5                    ZW                    Zimbabwe         COUNTRY
#>  6                    DJ                    Djibouti         COUNTRY
#>  7                    SO                     Somalia         COUNTRY
#>  8                    CN                       China         COUNTRY
#>  9                    DJ                    Djibouti         COUNTRY
#>  10                   LR                     Liberia         COUNTRY
#>  -------truncated-------
#>  Field(s) not printed:  notes, start_notification.name, start_notification.date, start_notification.url

We can do the same for the elephant’s legislation status in the European Union:

#>  → Now processing taxon_id '4521'......................✔
#>  
#>  ── EU listings ($eu_listings): ────────────────────────────────────────────
#>       id taxon_concept_id is_current annex change_type effective_at
#>  1 27868             4521       TRUE     B           +   2017-02-04
#>  2 27801             4521       TRUE     A           +   2017-02-04
#>  
#>  ── EU decisions ($eu_decisions): ──────────────────────────────────────────
#>        id taxon_concept_id start_date is_current eu_decision_type.name
#>  1  26285             4521 2015-04-09       TRUE              Positive
#>  2  25508             4521 2014-09-03       TRUE              Positive
#>  3   2765             4521 2011-12-02       TRUE                    i)
#>  4  11682             4521 2012-02-23       TRUE              Positive
#>  5  24825             4521 2014-05-28       TRUE              Positive
#>  6  27017             4521 2015-09-15       TRUE              Positive
#>  7  27360             4521 2016-06-27       TRUE              Negative
#>  8  30377             4521 2017-06-21       TRUE              Negative
#>  9  30553             4521 2017-06-21       TRUE              Positive
#>  10 30664             4521 2017-11-09       TRUE        Suspension (a)
#>     eu_decision_type.type geo_entity.iso_code2             geo_entity.name
#>  1       POSITIVE_OPINION                   ZW                    Zimbabwe
#>  2       POSITIVE_OPINION                   BW                    Botswana
#>  3             NO_OPINION                   ET                    Ethiopia
#>  4       POSITIVE_OPINION                   NA                     Namibia
#>  5       POSITIVE_OPINION                   ZA                South Africa
#>  6       POSITIVE_OPINION                   ZM                      Zambia
#>  7       NEGATIVE_OPINION                   MZ                  Mozambique
#>  8       NEGATIVE_OPINION                   TZ United Republic of Tanzania
#>  9       POSITIVE_OPINION                   TZ United Republic of Tanzania
#>  10            SUSPENSION                   CM                    Cameroon
#>     geo_entity.type start_event.name start_event.date source.code
#>  1          COUNTRY       SRG 71 Soc       2015-04-09           W
#>  2          COUNTRY       SRG 69 Soc       2014-09-03           W
#>  3          COUNTRY       SRG 58 Soc       2011-12-02           W
#>  4          COUNTRY       SRG 59 Soc       2012-02-23           W
#>  5          COUNTRY       SRG 68 Soc       2014-05-28           W
#>  6          COUNTRY       SRG 73 Soc       2015-09-15           W
#>  7          COUNTRY       SRG 76 Soc       2016-06-27           W
#>  8          COUNTRY       SRG 79 Soc       2017-06-21           W
#>  9          COUNTRY       SRG 79 Soc       2017-06-21           W
#>  10         COUNTRY     No 2017/1915       2017-11-09           W
#>     source.name term.code term.name
#>  1         Wild       TRO  trophies
#>  2         Wild      <NA>      <NA>
#>  3         Wild      <NA>      <NA>
#>  4         Wild      <NA>      <NA>
#>  5         Wild      <NA>      <NA>
#>  6         Wild       TRO  trophies
#>  7         Wild       TRO  trophies
#>  8         Wild      <NA>      <NA>
#>  9         Wild       TRO  trophies
#>  10        Wild       TRO  trophies
#>  Field(s) not printed:  notes, eu_decision_type.description, start_event.url

With the combination of map2 and the legislation data, one might be able to illustrate the elephant’s trade directions. This and other use examples of the rcites data output will be added bit by bit.

Access the elephant’s Species+ reference data

Last but not least, it is important to identify which references the Species+ information about the elephant is based on. For this, we can access the Species+ reference data with the spp_references() function.

#>  
#>  ── References ($references): ──────────────────────────────────────────────
#>        id                                             citation is_standard
#>  1  10265 Anon. 1978. Red data book: Mammalia. IUC [truncated]       FALSE
#>  2   6344 Barnes, R. F., Agnagna, M., Alers, M. P. [truncated]       FALSE
#>  3  17013 Blanc, J.J., Thouless, C.R., Hart, J.A., [truncated]       FALSE
#>  4   6371 Burton, M. P. 1994. Alternative projecti [truncated]       FALSE
#>  5   6532 Douglas-Hamilton, I. 1987. African Eleph [truncated]       FALSE
#>  6   6534 Douglas-Hamilton, I. 1987. African Eleph [truncated]       FALSE
#>  7   6825 Jackson, P. 1982. Elephants and rhinos i [truncated]       FALSE
#>  8   7224 Meester, J. and Setzer, H. W (eds.) 1974 [truncated]       FALSE
#>  9   7609 Parker, I. and Amin, M. 1983. Ivory cris [truncated]       FALSE
#>  10 19397 Parker, I.S.C. and Martin, E.B. 1982. Ho [truncated]       FALSE
#>  -------truncated-------
#>  [1] 15  3