ropensci/rredlist

IUCN Red List API Client

rredlist

rredlist is an R client for the IUCN Red List (https://apiv3.iucnredlist.org/api/v3/docs). The IUCN Red List is a global list of threatened and endangered species. IUCN Red List docs: https://apiv3.iucnredlist.org/api/v3/docs

Installation

CRAN

install.packages("rredlist")

Development version

remotes::install_github("ropensci/rredlist")
# OR
install.packages("rredlist", repos="https://dev.ropensci.org")

Meta

• Please report any issues or bugs.
• License: MIT
• Get citation information for rredlist in R doing citation(package = 'rredlist')
• Please note that this package is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.

rredlist's Issues

Package with a similar name

Maybe the README&vignette could include a small sentence about redlistr?

send user agent in requests

New Maintainer Wanted :-)

Or new maintainer team. 😸

If you're interested, please comment in the issue.
For more info, see

• our guidance on Changing package maintainers;
• our Package Curation Policy.

$result is list() and NULL

Session Info

> sessionInfo()
R version 3.4.3 (2017-11-30)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1

Matrix products: default

locale:
[1] LC_COLLATE=English_United Kingdom.1252  LC_CTYPE=English_United Kingdom.1252   
[3] LC_MONETARY=English_United Kingdom.1252 LC_NUMERIC=C                           
[5] LC_TIME=English_United Kingdom.1252    

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] rredlist_0.4.0 taxize_0.9.2   xlsx_0.5.7     xlsxjars_0.6.1 rJava_0.9-9   

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.15      xml2_1.1.1        magrittr_1.5      ape_5.0           lattice_0.20-35  
 [6] R6_2.2.2          rlang_0.2.0       foreach_1.4.3     stringr_1.2.0     httr_1.3.1       
[11] plyr_1.8.4        tools_3.4.3       parallel_3.4.3    bold_0.5.0        grid_3.4.3       
[16] data.table_1.10.4 nlme_3.1-131      iterators_1.0.8   yaml_2.1.14       httpcode_0.2.0   
[21] tibble_1.4.2      reshape2_1.4.2    codetools_0.2-15  triebeard_0.3.0   curl_2.8.1       
[26] crul_0.4.0        mime_0.5          stringi_1.1.5     pillar_1.2.1      compiler_3.4.3   
[31] urltools_1.6.0    jsonlite_1.5      reshape_0.8.7     zoo_1.8-0  

EDIT: Whoops, my fault - the test species I used happened to be synonyms that didn't return results from IUCN! Ignore the below!

Thanks for a great tool. Since I last used the package, something seems to have changed, as the $result element now returns NULL. See below.

> results<-rl_search(name = "Artocarpus rigidus", key = key, verbose = TRUE)
* Found bundle for host apiv3.iucnredlist.org: 0x46d9a620 [can pipeline]
* Re-using existing connection! (#17) with host apiv3.iucnredlist.org
* Connected to apiv3.iucnredlist.org (176.58.126.20) port 80 (#17)
> GET /api/v3/species/Artocarpus%20rigidus?token=HIDDEN HTTP/1.1
Host: apiv3.iucnredlist.org
User-Agent: libcurl/7.54.1 r-curl/2.8.1 crul/0.4.0
Accept-Encoding: gzip, deflate
Accept: application/json, text/xml, application/xml, */*

< HTTP/1.1 200 OK
< Server: nginx/1.1.19
< Date: Sun, 11 Mar 2018 08:32:26 GMT
< Content-Type: application/json; charset=utf-8
< Content-Length: 41
< Connection: keep-alive
< X-Powered-By: Sails <sailsjs.org>
* Added cookie sails.sid="s%3AHglE_b-TyiEDpz-H7hPxz_Xq.Ko3gdIu10LW2aI%2BOYLa1Tfa9ususo7d5WWDwOqGchw8" for domain apiv3.iucnredlist.org, path /, expire 0
< Set-Cookie: sails.sid=s%3AHglE_b-TyiEDpz-H7hPxz_Xq.Ko3gdIu10LW2aI%2BOYLa1Tfa9ususo7d5WWDwOqGchw8; Path=/; HttpOnly
< Vary: Accept-Encoding
< 
* Connection #17 to host apiv3.iucnredlist.org left intact
> results
$name
[1] "Artocarpus rigidus"

$result
list()

I have used two different API keys, one I know was working previously, and a new one (that has been idle for a few months). I did iterate through several hundred species on the first run (with an error in the code meaning I can see if the first few worked), but even several minutes to half an hour later I get the same result.

API tokens being blocked

at least mine is. while their example token works in their docs, emailed about this

fix docs for rl_search and other fxn in same man file

right now region param has Binomial taxonomic name

Increase test coverage?

It might be a good issue for a new contributor.

E.g. rl_sp.R has no test but tests could be added using other examples?

rl_habitats or rl_habitats_ ?

Hello,

Could I ask what is the difference between rl_habitats and rl_habitats_ ?
Is the logic similar to the wm_attr_data and the wm_attr_data_ of the worrms package?
I would like to search for multiple species at once. I have extracted the species names in a (character) list, but it doesn't seem to work.
I get the error

Error: name must be length 1

both when I run

species_IUCN <- rl_habitats(species_list)

as well as when I run

species_IUCN <- rl_habitats_(species_list)

Also, how can I get a Redlist API key? I saw this issue #52 but I don't think it has been solved by now.

I am using R 4.1.1. and rredlist 0.7.1

Best,

Christina

rl_common_names docs update

title/description not accurate

Use underscore methods in high level methods

How exactly were the vcr cassettes generated?

I think I'm looking for info about how to set up testing with vcr, do you create each cassette by hand etc.

Add function to get API version

history route now added

http://apiv3.iucnredlist.org/api/v3/docs#species-g1

missing species from rl_sp_country output

Why are certain species missing from this output of species list by country despite IUCN having maps that show presence? Using foxes in ukraine as an example:

ua_species <- rl_sp_country("ua", key = token)
"Vulpes vulpes" %in% ua_species$result$scientific_name

This yields false, but should be true based on viewing the IUCN spatial maps. https://www.iucnredlist.org/species/23062/46190249

This may be same issue as #39

link to taxize book in readme/vignette for taxonomic cenetered use cases

Function to retrieve all species list

A major use for me is creating species lists by their upper taxonomy. To that end, I use this function frequently to retrieve a full species list with taxonomic information that I can then filter to a certain taxa group. Not sure if this is possible elsewhere in the package? I'm sure there is a way to clean or simplify this function to accommodate if the database changes-- current count is at 93,872.

rl_sp_all <- function(k){
    pg0 <- rl_sp(page=0, key = k)
    pg1 <-  rl_sp(page=1, key = k)
    pg2 <-  rl_sp(page=2, key = k)
    pg3 <-  rl_sp(page=3, key = k)
    pg4 <-  rl_sp(page=4, key = k)
    pg5 <-  rl_sp(page=5, key = k)
    pg6 <-  rl_sp(page=6, key = k)
    pg7 <-  rl_sp(page=7, key = k)
    pg8 <-  rl_sp(page=8, key = k)
    pg9 <-  rl_sp(page=9, key = k)
    all_pages <- rbind(pg0$result,pg1$result, pg2$result, pg3$result,pg4$result, pg5$result, pg6$result, pg7$result,  pg8$result,pg9$result)
}

fxns should stop with useful message when NA's passed

via https://twitter.com/FisheriesRobert/status/1081480840893419521

user vcr for testing

API vs Website again

I see the previous discussion on the API vs Website issue. I am encountering that as well. For the order I am looking at, we pulled country level occurrence data from the website and from the API. API returns a lower species count in most cases.

For example: "Nyassunio nyassaensis" occurs in 3 countries according to the website while
rl_occ_country("Nyassunio nyassaensis",key=IUCN_REDLIST_KEY)
returns no occurrences.

I guess I just want to understand why the website and API differ?

API vs website

Probably a stupid question but why is there http://www.iucnredlist.org/details/22706233/0 while rredlist::rl_search("seleucidis melanoleuca") returns no result?

Add something about vcr to the contributing guide

Depending on ropensci/vcr#145

Metadata function

Would be extremely helpful if there was a searchable metadata file that gives all options of variables. These documents tend to be buried in the redlist API host website or in pdf format. For instance. For "threats" would be great to upload these documents as a reference table.
IUCN_threats-classification_2012.pdf
IUCN_dec_2012_guidance_on_threat_impact_scoring.pdf

Add to docs about 2 second delay for frequent calls in a row

DRY: simplify internals for set of functions that all use name/id/region params

Collate subheading information from Habitat & Ecology

I suspect that by Red List API, this does not currently seem possible. But there are several subheadings in the "Habitat and Ecology" section that do not appear accessible via the package, when downloading rl_narrative or rl_search. Particularly: SYSTEM, HABITAT TYPE, GENERATION LENGTH (YEARS), CONGREGATORY, MOVEMENT PATTERNS, CONTINUING DECLINE IN AREA, EXTENT AND/OR QUALITY OF HABITAT

Has this come up before?

Fail well

testing

Can't generate API token

Hi there,

I'm trying to get the IUCN categories for some species. For that you need a key, which one should be able to generate here:
https://apiv3.iucnredlist.org/api/v3/token

Nonetheless, the link doesn't work, and therefore I cannot retrieve any kind of information form rredlist.

Cheers,
Marcel

new comprehensive groups routes

http://apiv3.iucnredlist.org/api/v3/docs#comp-groups

test suite

Bad Gateway (HTTP 502) error when trying to get country occurrence data

Session Info

R version 3.3.3 (2017-03-06)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1

locale:
[1] LC_COLLATE=English_United Kingdom.1252  LC_CTYPE=English_United Kingdom.1252    LC_MONETARY=English_United Kingdom.1252
[4] LC_NUMERIC=C                            LC_TIME=English_United Kingdom.1252    

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] rredlist_0.4.0    data.table_1.10.4 dplyr_0.5.0       rCAT_0.1.5        rgdal_1.2-7       jsonlite_1.5      rgbif_0.9.8       raster_2.5-8     
[9] sp_1.2-4         

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.10     xml2_1.1.1       whisker_0.3-2    magrittr_1.5     munsell_0.4.3    colorspace_1.3-2 lattice_0.20-34  R6_2.2.0         quadprog_1.5-5  
[10] rlang_0.1.2      stringr_1.2.0    httr_1.2.1       plyr_1.8.4       tools_3.3.3      parallel_3.3.3   grid_3.3.3       geoaxe_0.1.0     gtable_0.2.0    
[19] DBI_0.6-1        rgeos_0.3-22     assertthat_0.1   lazyeval_0.2.0   httpcode_0.2.0   tibble_1.3.3     ggplot2_2.2.1    triebeard_0.3.0  curl_2.6        
[28] crul_0.3.8       pracma_1.9.9     oai_0.2.2        stringi_1.1.3    urltools_1.6.0   scales_0.4.1    

Hi, thanks again for this package, which I'm using a lot.

I'm just trying to get country occurrence data for all plants on the Red List, but I keep hitting a Bad Gateway (HTTP 502) error. See below for the code I'm using. I already have a vector with all plant taxonid's (plant.id) and I'm trying lapply on a function rl.countries that should get the country occurrence for each taxonid. I usually get part of the way through before I get the 502 error.

I've been in touch with the Red List admin team and they say everything fine with the API, so I'm just trying to work out where the problem is.

Many thanks,
Steve Bachman

#get countries occurrence list based on taxon ID
rl.countries = function(x){
  cntry = rl_occ_country(id=x,key=rlkey)
  result = cntry$result
  taxonid = cntry$name
  results = cbind(name,result)
  colnames(results)[1] = 'taxonid'
  return(results)
}

#run lapply on rl.countries function
#plants.id is vector of taxonid's for all plants (total = 24,408) 
apply.countries = lapply(plants.id,rl.countries)
countries_df = as.data.frame(do.call(rbind,apply.countries))

Error: Bad Gateway (HTTP 502)

r1_comp_groups download for 'birds' does not work

I have been having some issues when trying to download the comprehensive list of species in the 'birds' group. The code I am using works for mammals, but for some reason, I am unable to do this for birds. 

This is the code that I am using in R:

all_mammals <-rl_comp_groups(group = c('mammals'), key = token) # token is my IUCN key. This code works and returns a list of all species in the group 'mammal'.
all_birds <-rl_comp_groups(group = c('birds'), key = token) # This does not work.

Is this an issue with the API? I have checked that the group name is correct. Any help would be appreciated.

new maintainer?

@arw36 @stevenpbachman Any interest in taking over as maintainer of this package? Or know anyone that might be interested?

changes from iucn

• use https
• cite terms of use https://www.iucnredlist.org/terms/terms-of-use
• instead of 2015-4 here

  rredlist/R/rredlist-package.R

  Line 37 in ec7e619

  #' `IUCN 2015. IUCN Red List of Threatened Species. Version 2015-4

  tell users to cite version they are using at the time of use, see endpoint https://apiv3.iucnredlist.org/api/v3/docs#version and about page https://apiv3.iucnredlist.org/about
• here https://github.com/ropensci/rredlist/blob/master/R/rredlist-package.R#L48 add "ask the user to contact the Red List directly" and that their website probably doesn't use their API

Collecting species by population trend?

Hi,

I was wondering if it were possible to collect species by population trend? i.e. decreasing, increasing, stable or unknown?

on some OS'es url encoding isnt working, leading to failed queries

Problem to retrieve data of synonym

The function "rl_search" do not retrieve data of synonym, but in the website is possible search the data. There is information about it in the API too (http://apiv3.iucnredlist.org/api/v3/docs#species-synonym). How can I handling it?

#Example: Synonym of _Loxodonta africana_ do not retrieve data
rl_search("Loxodonta cyclotis", key = IUCN_REDLIST_KEY)

sessionInfo()
R version 3.4.1 (2017-06-30)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 15063)

Matrix products: default

locale:
[1] LC_COLLATE=Portuguese_Brazil.1252  LC_CTYPE=Portuguese_Brazil.1252   
[3] LC_MONETARY=Portuguese_Brazil.1252 LC_NUMERIC=C                      
[5] LC_TIME=Portuguese_Brazil.1252    

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] rredlist_0.4.0

loaded via a namespace (and not attached):
[1] compiler_3.4.1  R6_2.2.2        curl_2.8.1      Rcpp_0.12.12   
[5] urltools_1.6.0  triebeard_0.3.0 crul_0.3.8      jsonlite_1.5   

Issue with downloading updated IUCN data (2023-1)

Hello,
The rl_sp(all = TRUE) function returns the previous version’s data (153,732 species). But the total assessed IUCN species count in the recent update (2023-1; December 11 2023 release) appears to be 157,190 (according to rl_sp_count).

I am in need of habitat and threat data for the 2023-1 version, but without the IUCN species names, I could not use the rl_habitats function to retrieve the updated information.

Is there an alternative approach to access the updated 2023-1 version?

Thank you,
Gopal

move to using markdown docs

implement type checker internally

cause API can silently drop inputs that make no sense, and to fail early cause that's how we do

change maintainer on cran

@willgearty when you get a chance, could you submit a new version to cran changing the maintainer to you? not urgent, but any correspondence from cran will go to me right now, so it'd be good to have it go to you instead. thanks!

Please add Plant Growth Form to rredlist

Thanks for developing ‘rredlist’ - finding it such a useful package. The IUCN API has now been updated to include the Plant Growth Form field. Is it possible to include this in the next update of rredlist please?

http://apiv3.iucnredlist.org/api/v3/docs#growth-forms

Thanks

Steve

Give back taxon names for `Named Species` slots in /threats route

An rredlist user pointed out that in the /threats route, at least sometimes when the 'title' key gives back "Named species" it doesn't give the name of the taxon. However, the taxon name appears to be on the web page, e.g.

http://apiv3.iucnredlist.org/api/v3/threats/species/id/62290750?token=

vs.

http://www.iucnredlist.org/details/classify/62290750/0#threats

Emailed IUCN dev about this, they are looking into it

Add a vignette

This package needs more documentation! Help out the community by contributing a vignette. If you don't know what a vignette is, check out http://r-pkgs.had.co.nz/vignettes.html for an introduction.

If you aren't sure how to contribute on github checkout https://github.com/ropensci/rredlist/blob/master/.github/CONTRIBUTING.md

Keep in mind our code of conduct https://github.com/ropensci/rredlist/blob/master/CONDUCT.md

Elevation data in API

coming soon ...

Change to new cran checks badge URL

👋🏽 I maintain the cran checks badges. Please change to the new cran checks badge URL (e.g., https://badges.cranchecks.info/worst/dplyr.svg). Old badges at (e.g. https://cranchecks.info/badges/worst/dplyr) will be unavailable as of Jan 1st 2023.

• Blog post announcing the change: https://recology.info/2022/06/cran-checks-badges/
• New badges repo: https://github.com/r-hub/cchecksbadges
• Old badges repo: https://github.com/sckott/cchecksapi

get countries by species name/ID

• http://apiv3.iucnredlist.org/api/v3/docs#species-occurrence-name
• http://apiv3.iucnredlist.org/api/v3/docs#species-occurrence-id

Info on how to cite the API

IUCN 2015. IUCN Red List of Threatened Species. Version 2015-4 <www.iucnredlist.org>

replace httr with crul