Pollinators-bees system data

[SteveViss]

Hi @ibartomeus,

It will be nice to include your data as part of the package (data folder).
Hence, I can use them to do do some unit testing on package functionalities.

Let me know what do you think,
Cheers.

[ibartomeus]

Yes, I'll upload a template with a few rows this coming week and updated it when perfectly clean. (still travelling, this is never ending!)

On Sun, Dec 4, 2016 at 5:45 PM Steve Vissault ***@***.***> wrote: Assigned #12 <#12> to @ibartomeus <https://github.com/ibartomeus>. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#12 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AB8IgmI6W8ZksbQ91XqAcDxq053-xRDRks5rEu4vgaJpZM4LDoPd> .

-- -- Ignasi Bartomeus PhD www.bartomeuslab.com @ibartomeus Skype: nachobartomeus Dpto. Ecología Integrativa Estación Biológica de Doñana (EBD-CSIC) Avda. Américo Vespucio s/n Isla de la Cartuja 41092, Sevilla (Spain)

[SteveViss]

Perfect, let me know if you need help (by writing on this issue). That was nice to meet you! Have a good trip!

[ibartomeus]

Data available at : https://github.com/bw4sz/Montreal_Workshop/tree/master/Data
Before pushing it to this repo I have a few questions:

Interactions, plant and pollinator datasets can be merged, should I upload just one unique dataset? Or the three tables separately?

Other issues:
-I still need to fetch some more pollinator traits, as there are too many NA's for now.

• Phylogeny: Plant data can be obtained from phylomatic, but any idea about pollinator data? I have a dated bee tree (in nexus) for bee genera, but I wouldn't want to exclude flies, vespids, beetles,... Maybe we can build an undated taxonomic tree depicting the relationships among genara, families, orders?

[SteveViss]

Hi @ibartomeus,

I started to work on your issue before leaving for vacation. I'm still working on it. What I'm doing is this: I'm writing an update to your markdown document (montreal_workshop repo) to add a new section which reshape your data in order to get the data input format needed by the function as.alienData(). The idea is to use a standard format (which is the output of the as.alienData() function) and store the output in /data/.

[ibartomeus]

Great, I'll have updated and hopefully final data (same format) next week. Happy to help!

[ibartomeus]

@SteveViss I don't see any update in the M_w repo. If you tell me the data format needed I can try to do it this week and get data part done!

[SteveViss]

@ibartomeus, sorry for the delay. I restart to work on this today, I'll push before the end of the day. Can you tell me what means IT in the pol_tr data.frame?

[ibartomeus]

Intertegular distance. A proxy of body size.

Just let me know what do you need next.

[SteveViss]

library(devtools)
install_github("TheoreticalEcosystemEcology/alienR", ref = "alienData")
library("alienR")
load("data/argsAlienData.RData") # How I created this file is explained in the explnation.Rmd. File is in attachment
dataBartomeus <- as.alienData(idObs=idObs,interactPair=interactPair,traitInd=traitInd,traitSp=traitSp)
str(dataBartomeus)

head(dataBartomeus$idObs)
head(dataBartomeus$interactSp) #being this a bipartite netw, you don't want to have a square matrix here
dim(dataBartomeus$interactSp)
head(dataBartomeus$interactInd)
dim(dataBartomeus$interactInd) #same here, this is quite a waste of space, because most indiv won't interact with others, and certainly not with themselves
head(dataBartomeus$coOcc) #this I think is not well calculated. SHould be from idObs
head(dataBartomeus$traitSp)
head(dataBartomeus$traitInd)

[SteveViss]

@ibartomeus, you're the specialist. So I'll include of these comments.
Thanks !

[ibartomeus]

Sorry I should have used the issue and not the mail. some details:

I don't get how cOcc is created from the interaction matrix (interactPair) as this do not has any information on where and when. I expect co-ocurrence ignores real interactions and only uses if two species are present at the same time (Round in my case) and place (site in my case). Right? This would need to be amended if I am right.

as.alienData also create potential interaction matrices that are squared. This lead to a lot of structural NA's in bipartite networks, which IMO are suboptimal.