Figures

[elmacartney]

@elmacartney to address objectives 1 and 2

• [x] make panels of barcharts
• [x] make heat maps for discipline patters
• [x] tidy up species tree (including disciplines)
• [x] tidy up objective 3 figures (when ready)

@itchyshin to address objective 3

• [x] make bibliometric figurse
• [x] chord diagram for discplines
• [x] map for 1st author
• [x] map for collaborations

@mlagisz

• [x] Make a species tree divided by discipline

[itchyshin]

@elmacartney

You can look at Patrice's code here

https://p-pottier.github.io/Dev_plasticity_thermal_tolerance/#figures-for-publication

There are a couple of nice phylogeny figs - which you can use to make your tree fancy. @mlagisz says she has done what she can do quickly so Erin you can take over from there.

I am nearly there with the chord diagram for different fields. For the country one, I do not think a chord diagram works well so I will try something else

[itchyshin]

@elmacartney

Here is the shared citation across different sets of papers (the numbers indicate the numbers of shared citations - coupling without coupling with itself).

As you can guess, "crossdisciplinary" has more shared citations followed by "eco evo".

[itchyshin]

@elmacartney - also, I managed to completely match two data sets using the first author's name and title. But I have realised that we should always collect "DOI" - it is our mistake that we did not collect this. If we have DOI - merging two data sets will be pretty easy but we now have an alternative way of combining datasets anyways.

I have not done maps etc yet but I may get to later today or by Monday (hopefully the above gives some ideas)

@elmacartney you may want to calculate WHAT % different group share citations - you can look at small_matrix in the code

Please pull (I have not really explored how we could change the look of this diagram - it seems a lot more difficult than ggplot)

[itchyshin]

@elmacartney - if you want to customise colours here is a great link

https://r-charts.com/flow/chord-diagram/#data

Also you can change labelling etc

https://stackoverflow.com/questions/31943102/rotate-labels-in-a-chorddiagram-r-circlize

[elmacartney]

Great, thanks Shinichi! This figure looks great!

I have also completed the Species tree, but will add silhouettes manually of the most common species

On Fri, May 27, 2022 at 7:36 AM Shinichi Nakagawa @.***> wrote:

@elmacartney https://github.com/elmacartney - if you want to customise colours here is a great link

https://r-charts.com/flow/chord-diagram/#data

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[itchyshin]

@elmacartney actually the chord plot looks fine for collaborations

@mlagisz will tidy things up and also do the geo-map and get to you - Losia said she could finish this by early next week (probably Monday)

Then, we have all figures and we can probably meet once we have the figures - but you will be quite busy next week but see how we go

[elmacartney]

Thanks @itchyshin.

I have set both diagrams to have the rainbow colour scheme. Neither plot is an object, so I'm wondering if you or @mlagisz can help make these into objects/create a panel figure so that they are both one figure (i.e., A and B)?

On Fri, May 27, 2022 at 2:05 PM Shinichi Nakagawa @.***> wrote:

@elmacartney https://github.com/elmacartney actually the chord plot looks fine for collaborations [image: plot_zoom_png] https://user-images.githubusercontent.com/12078523/170626631-b6d1e6aa-7852-4d22-8660-52d59854f242.png

@mlagisz https://github.com/mlagisz will tidy things up and also do the geo-map and get to you - Losia said she could finish this by early next week (probably Monday)

Then, we have all figures and we can probably meet once we have the figures - but you will be quite busy next week but see how we go

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[mlagisz]

@elmacartney I am a bit unwell today. I might be able to look at it tomorrow or day after, once I recover.

[mlagisz]

@elmacartney here is the map of first authors: I also added the code to Objectve3 for making a single plot with two chord diagrams - these get saved into a chord_diagrams.pdf file.

[itchyshin]

@elmacartney - I think for collaboration and authorship distributions, one can talk about the domination of English speaking countries. This may be more pronounced than in the primary literature. You probably need to find some references but I am sure this may be already known. Also, cross-country collobraiton is rather limited - I guess this may also be a known feature of the secondary literature (or maybe not). I think it would be good to look into some scientometrics and bibliometrics literature.

As said before, I will be happy to meet and discuss what kinds of things we can potentially put into the Discussion section. Let me know if you want to meet and chat. Or you can go ahead and write what you can and we can discuss after that as well.

[elmacartney]

Great thanks @mlagisz and @itchyshin.

I will add everything and work on getting a draft to you soon, then we can perhaps meet to discuss changes.

[itchyshin]

@elmacartney - an excellent plan - looking forward to it

[elmacartney]

@szymekdr could you please work on two figures for the manuscript when you get a chance?

• [ ] Fig. 1: Should we make adaptations to our schematic from the protocol?
• [ ] Fig. 4: Species tree with barchart for number of SRs including that species. Could you please make this figure prettier? The code for the figure is in the RMD file 'Main_Figures_2' under 'Figure 4'. Should add silhouettes for the most common species (i.e., rats and mice etc), I chouldn't get the ggplot function to show read values on the y axis, and could probably use a better colour scheme - I chose discrete colours that were easily differentiated from each other.

Thanks!