I just leave here a note that CITES has an API to retrieve information on distribution and regulation of of species with commercial interest: http://api.speciesplus.net/

Can be added at some point.

Since last update:

`eol(name=c("Carpobrotus edulis", "Rosmarinus officinalis"))

Error in verbose() : could not find function "verbose"`

After looking a bit I manually loaded library(httr) and it works, but then produce a ridiculous amount of verbose output.

I am in using devtools::install_github("ropensci/originr") not the CRAN version.

sessionInfo()
R version 3.4.1 (2017-06-30)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS High Sierra 10.13.3

Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

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

other attached packages:
[1] httr_1.3.1 reshape2_1.4.3 taxize_0.9.2 originr_0.2.1.9115

loaded via a namespace (and not attached):
[1] Rcpp_0.12.16 xml2_1.2.0 magrittr_1.5 devtools_1.13.3
[5] ape_5.0 lattice_0.20-35 R6_2.2.2 foreach_1.4.4
[9] stringr_1.3.0 plyr_1.8.4 tools_3.4.1 parallel_3.4.1
[13] bold_0.5.0 grid_3.4.1 data.table_1.10.4-3 nlme_3.1-131
[17] git2r_0.19.0 withr_1.0.2 iterators_1.0.9 digest_0.6.13
[21] codetools_0.2-15 rsconnect_0.8 curl_3.1 crul_0.5.2
[25] memoise_1.1.0 stringi_1.1.7 compiler_3.4.1 jsonlite_1.5
[29] reshape_0.8.7 zoo_1.8-1

changed param names ropensci/taxize#723

Using the example code provided in the help:

This finds 2 records

library(originr)
  eol(name=c('Lymantria dispar','Cygnus olor','Hydrilla verticillata','Pinus concolor'),
      dataset='gisd',count = T)
>2

However the same command using dataset ='all' finds none

  eol(name=c('Lymantria dispar','Cygnus olor','Hydrilla verticillata','Pinus concolor'),
      dataset='all',count = T)
>0

Given that the description says "all == All datasets", this appears weird to me ?

Access to the Flora Europaea homepage [http://rbg-web2.rbge.org.uk/FE/fe.html]
is now redirected to the Euro+Med homepage :-(

asked someone about it

Fishbase has data on fish introductions. We can use rfishbase and just call two functions from the package:

introductions("Alburnus alburnus")
faoareas("Alburnus alburnus")
#idem: distribution("Alburnus alburnus")

Two other functions would be nice, but would need a bit more of work:

1. Search origin by species country(fish) would need to translate the CountryRefNo or c_code to the actual country. I can't find where this is stored. Sorry. Maybe @cboettig can point me out where?

2. Search by country. Here I am even more lost. c_code(c_code = "724") returns the same list of species (SpecCode) regardless of the code passed (c_code(c_code = "Spain") or c_code(c_code = "France")).

What do you think?

moved from ropensci/traits#53

look into

nsr(c("Pinus ponderosa", "Poa annua"), "United States") #ok
nsr(c("Pinus ponderosa", "Poa annua"), "United State") #return blank dataframe

And I can't find a list of valid country names. A link to accepted country names in the help may be cool.

When a factor is provided in the species names, it need to be transformed to as.chracter() in order to work.

Easy fix. I'll fix that soon.

https://gist.github.com/sckott/0951ef11dc6d2e22744e6b030fded3dd

Which I think shouldn't happen as it can potentially introduce errors.

library(originr)
eol(name="",dataset='gisd')

Suggestion: Return NA on default for strings shorter than 1 character.

The griis() function currently covers 122 countries. However, the article "Introducing the Global Register of Introduced and Invasive Species" states that information is available for 198 countries. Missing are for example "Sweden". Looking forward to seeing this package grow! very useful for me :)

@ibartomeus moved fxns about whether species are native or invasive to a sep package, this one - added you as author. chime in if you have any thoughts

will close this soon, just letting you know

http://www.griis.org/search3.php

via https://twitter.com/frod_san/status/725951339264516097

from ropensci/traits#55

Example:

library(originr)
is_native("Bombus occidentalis",where = "Continental US",region = "america")

Error in data.frame(name = sp, origin = Out, stringsAsFactors = FALSE) :
arguments imply differing number of rows: 1, 0

Bombus occidentalis should be native in the US (or return not included in itis as they don't seem to capture invertebrates well).

👋 @sckott!

• The badge points to ropensci Appveyor account but builds are at https://ci.appveyor.com/project/sckott/originr

• Appveyor deliveries have been consistently failing for a while. 😭 You'll need to email Appveyor team 🎊 at [email protected] and mention this about the latest delivery
  X-GitHub-Delivery: e38d92bc-4d4e-11e8-9053-d7924decbf9b
  Time: 2018-05-01 16:49:45

Thank you!

https://www.nature.com/articles/sdata2017202

Would be also good to contact the authors and let them know about the R package.