Closed jsoberon closed 8 years ago
Hi! thanks for letting me know of your unexpected result. Am currently traveling and hoping to have a look at it after the weekend. More soon!
Thanks a lot. Look forward to your ideas.
I was able to reproduce and fix the issue. The root cause was that a slightly different name matching method was used for get_interaction_matrix, leading to the observed unexpected results. The fix has been included in the development version of rglobi. Please see https://github.com/ropensci/rglobi for instructions on how to do so. Hoping to include this fix into the upcoming release (e.g. 0.2.9)
Please confirm that this fixed the issue . . . and let me know if there's anything else that caught your attention. . .
Ahhh!!! Thanks Jorrit. I am going to try it in a couple of hours and will let you know if it works.
Many many thanks JS
Dear Jorrit, I tested your code with my data and now I do get a matrix with ones in it. I still need to check a few things, but this seems to be working now.
Many thanks for your help.
JS
Thanks for checking! Let me know if you find any other issues. Happy to help.
@jsoberon the fix is now available through cran as part of version rglobi v0.2.9 thanks to the quick review of Uwe Ligges of the r-project (see attached).
Thanks, on CRAN now.
Best,
Uwe Ligges
On 08.03.2016 20:46, Jorrit Poelen wrote:
[This was generated from CRAN.R-project.org/submit.html]
The following package was uploaded to CRAN:
===========================================
Package Information:
Package: rglobi
Version: 0.2.9
Title: R Interface to Global Biotic Interactions
Author(s): Jorrit Poelen [aut, cre], Stephen Gosnell [aut], Sergey
Slyusarev [aut]
Maintainer: Jorrit Poelen <jhpoelen@xs4all.nl>
Depends: R (>= 3.0.1)
Suggests: testthat, knitr
Description: A programmatic interface to the web service methods provided
by Global Biotic Interactions (GloBI). GloBI provides access
to spatial-temporal species interaction records from sources
all over the world. rglobi provides methods to search
species interactions by location, interaction type, and
taxonomic name. In addition, it supports Cypher, a graph
query language, to allow for executing custom queries on the
GloBI aggregate species interaction data set.
License: MIT + file LICENSE
Imports: rjson (>= 0.2.13), RCurl
The maintainer confirms that he or she
has read and agrees to the CRAN policies.
Submitter's comment: Dear Reviewers:
I built this package using [R CMD
build .] and checked it with command [R CMD check
--as-cran rglobi_0.2.9.tar.gz] on my Mac OS X (v
10.11.3) machine running R 3.2.3 . Also, the checks
were executed on travis-ci.org (running Ubuntu) and
winbuilder (running windows).
Fixes:
* a rglobi
user notices a discrepancy in name matching between
get_interaction_matrix and get_interactions methods
(see
https://github.com/globalbioticinteractions/globalbioticinteractions.github.io/issues/63).
The fix included in this version now makes sure that
the get_interaction_matrix and get_interactions
method use the same name matching method.
The
remaining note for this version is:
* checking CRAN
incoming feasibility ... NOTE
Maintainer: ‘Jorrit
Poelen <jhpoelen@xs4all.nl>’
Components with
restrictions and base license permitting such:
MIT
+ file LICENSE
File 'LICENSE':
YEAR: 2016
COPYRIGHT HOLDER: Jorrit Poelen
Thank you for taking
the time to review my submission.
-jorrit
Many thanks to all of you in this project. I think globis has a transformative potential, and myself and my students are already beginning to play with it.
Great work folks!!
Jorge S.
From: Jorrit Poelen [mailto:notifications@github.com] Sent: Tuesday, March 08, 2016 6:30 PM To: globalbioticinteractions/globalbioticinteractions.github.io globalbioticinteractions.github.io@noreply.github.com Cc: Soberon, Jorge jsoberon@ku.edu Subject: Re: [globalbioticinteractions.github.io] Strange matrix of interactions (#63)
@jsoberonhttps://github.com/jsoberon the fix is now available through cran as part of version rglobi v0.2.9 thanks to the quick review of Uwe Ligges of the r-project (see attached).
Thanks, on CRAN now.
Best,
Uwe Ligges
On 08.03.2016 20:46, Jorrit Poelen wrote:
[This was generated from CRAN.R-project.org/submit.html]
The following package was uploaded to CRAN:
Package Information:
Package: rglobi
Version: 0.2.9
Title: R Interface to Global Biotic Interactions
Author(s): Jorrit Poelen [aut, cre], Stephen Gosnell [aut], Sergey
Slyusarev [aut]
Maintainer: Jorrit Poelen jhpoelen@xs4all.nl<mailto:jhpoelen@xs4all.nl>
Depends: R (>= 3.0.1)
Suggests: testthat, knitr
Description: A programmatic interface to the web service methods provided
by Global Biotic Interactions (GloBI). GloBI provides access
to spatial-temporal species interaction records from sources
all over the world. rglobi provides methods to search
species interactions by location, interaction type, and
taxonomic name. In addition, it supports Cypher, a graph
query language, to allow for executing custom queries on the
GloBI aggregate species interaction data set.
License: MIT + file LICENSE
Imports: rjson (>= 0.2.13), RCurl
The maintainer confirms that he or she
has read and agrees to the CRAN policies.
Submitter's comment: Dear Reviewers:
I built this package using [R CMD
build .] and checked it with command [R CMD check
--as-cran rglobi_0.2.9.tar.gz] on my Mac OS X (v
10.11.3) machine running R 3.2.3 . Also, the checks
were executed on travis-ci.org (running Ubuntu) and
winbuilder (running windows).
Fixes:
a rglobi
user notices a discrepancy in name matching between
get_interaction_matrix and get_interactions methods
(see
https://github.com/globalbioticinteractions/globalbioticinteractions.github.io/issues/63).
The fix included in this version now makes sure that
the get_interaction_matrix and get_interactions
method use the same name matching method.
The
remaining note for this version is:
checking CRAN
incoming feasibility ... NOTE
Maintainer: ‘Jorrit
Poelen jhpoelen@xs4all.nl<mailto:jhpoelen@xs4all.nl>’
Components with
restrictions and base license permitting such:
MIT
File 'LICENSE':
YEAR: 2016
COPYRIGHT HOLDER: Jorrit Poelen
Thank you for taking
the time to review my submission.
-jorrit
— Reply to this email directly or view it on GitHubhttps://github.com/globalbioticinteractions/globalbioticinteractions.github.io/issues/63#issuecomment-194036029.
I am trying to get a matrix of interactions between a list of hawkmoths and plants. I do the following: pam=get_interaction_matrix(lstA,int2) lstA is a list with the genera of hawkmoths. int2 is the result of taking the union of the target_taxon_name part in: get_interactions(taxon=lstA,interaction.type="interactsWith"), get_interactions(taxon=lstA,interaction.type="visitsFlowersOf"), and get_interactions(taxon=lstA,interaction.type="pollinates").
These three lists are NOT empty, and their union contains 183 names. When I run pam=get_interaction_matrix(lstA,int2)
I get a 79X184 matrix of zeros. There should be ones there!!!! What I am doing wrong? Any help will be greatly appreciated.