rotl
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ropensci
Interface to Open Tree of Life API
You have file 'rotl/man/rotl.Rd' with \docType{package}, likely intended as a package overview help file, but without the appropriate PKGNAME-package \alias as per "Documenting packages" in R-exts. This seems to be...
Hi! We wanted to let you know that we (@opentreeoflife) now have an, as yet undocumented, bulk node info call. ``` curl -X POST https://api.opentreeoflife.org/v3/tree_of_life/node_info -H "content-type:application/json" -d '{"node_ids":["mrcaott246ott3364","mrcaott22834ott532753","mrcaott252688ott489372"]} '...
Hi @fmichonneau! Thank you for your handy package! I am using it in mine (https://github.com/taxonomicallyinformedannotation/tima-r) and I saw it comes with quite heavy dependencies. I did a quick ``` library(pkgndep)...
Created function `get_citations()`, to obtain citations from supporting studies for a subtree or induced subtree. Added argument `file_citations` to function `tol_induced_subtree()`. It accepts a file name for citations to be...
In the spirit of open science: is there an option to download citations of supporting studies when getting and induced subtree with `tol_induced_subtree`? We can get the citation of a...
library(rotl) taxa
I obtained ott ids from the tip labels of a set of trees downloaded with `rotl::get_study_tree` using the option `tip_label = "ott_id"` When running: ``` tree
I'm putting a little note in each of the packages (readme and vignette) used in taxize, pointing back to the taxize book https://ropensci.github.io/taxize-book/ Are youokay with doing that here?
`tnrs_match_names` lowercases the string provided by the user in the results, do we need to do this?
The documentation says `study_doi` is supported, but this seems to have been changed to `studyPublication` by OT. `studies_find_studies(property="ot:study_doi", value="http://dx.doi.org/10.1600/036364411X605092")` leads to ``` Error: HTTP failure: 400 unrecognized property: ot:study_doiBadInputExceptionorg.neo4j.server.rest.repr.BadInputExceptionlist("org.opentree.oti.plugins.studies_v3.find_studies(studies_v3.java:100)", "java.lang.reflect.Method.invoke(Method.java:498)",...
