"finalizing" figures

[teixeirak]

@ValentineHerr , I think the last "major" task involving you is to fix up the figures in the main manuscript:

schematic_figure

• [ ] Needs a bit of fixup, mainly by me. I will open a separate issue.

quilt_comparison

• [x] I think this is done.

multipanel figures with all sites (pre_temp_groups, DBH_responses, Year_responses)

Two main issues:

• The pre_temp_groups figure has such short panels that responses are hard to see
• The species legends don't currently fit on any of the 3

Some potential solutions/improvements:

• [ ] Reduce all font sizes to the minimum. I need to look at the journal guidelines to see what that is.
• [ ] Rather than listing species legends separately for each site, could we make one master list with even spacing? This would probably be ordered by site, or alphabetical by species with site listed in parentheses. This would require setting the color for each species independently ahead of plotting.
• [x] I think we only need a species legend on one of the 3 (either DBH or year), and the other two could refer to it.
• [x] If possible, it would be preferable to list species' latin names rather than codes.
• [x] If we're free of the legend in pre_temp_groups, we could change to a 4 col x 5 row matrix, which would allow much better visualization of the climate responses.
• [ ] I've currently included the version of Year_responses with all 3 growth metrics, as this illustrates the consistency of the response, but we could use the BAI-only version, particularly if there are space constraints.

[ValentineHerr]

If we're free of the legend in pre_temp_groups, we could change to a 4 col x 5 row matrix, which would allow much better visualization of the climate responses.

Do you mean a horizontal plot with 2 col by 5 row for Precipiation group then 2 col by 5 row for Temperature ? Could we split into 2 figures to have two 2x5 figures? (one for precip, the other for temp) Either way is easy for me.

[ValentineHerr]

if one figure, maybe best to alternate Precip and Temp so that 2 plots in a row are from the same site... right?

[teixeirak]

if one figure, maybe best to alternate Precip and Temp so that 2 plots in a row are from the same site... right?

That's what I originally had in mind, but splitting into two separate plots may be better, and GCB allows plenty of plots. I think that's a good idea; let's go with that. That will make it so the legend isn't a problem.

[ValentineHerr]

Actually keeping it in the same doesn't look too bad.

[ValentineHerr]

I fixed the x-axis in comment above

splitting into 2 figures, by group, would actually make legend tricky if there are several sites on the same row, and columns

[teixeirak]

Actually keeping it in the same doesn't look too bad.

Oh, beautiful!! What an improvement! Let's keep that.

[ValentineHerr]

What do you think of this for the DBH figure?

it is 3000px x 3000px

[teixeirak]

I think that works nicely!

[ValentineHerr]

except I need to find a way to remove the species that didn't make it in the analysis, like QURU in LD...

[teixeirak]

Do you mean those that didn't (1) make the analysis at all, (2) didn't make the year analysis, or (3) aren't plotted because they weren't significant? Category 3 should definitely be included, and maybe 2 (if you show a legend on the year plot).

[ValentineHerr]

A bit of everything.... For example, if I take only the species that appear in summary_core_analysed.csv I get this:

But, for example, for LD, QUVE is in the legend but it was not analyzed with DBH because there is not enough trees with DBH. So I guess it should technically not appear...

[ValentineHerr]

(note: I think I am still struggling with legend colors... I think it is still not consistent across plots because of these issues of species dropped etc... I thought I fixed it but I think I see an issue with PILO at CB... ...still learning ggplots!)

[ValentineHerr]

color issue might actually just be from this last thing I did, where it gets ordered by [Genus species] rather than species CODE. Will see if that is true

[teixeirak]

But, for example, for LD, QUVE is in the legend but it was not analyzed with DBH because there is not enough trees with DBH. So I guess it should technically not appear...

Of course, we need species without DBH to appear here for the climate legend, so I think we need the full set of species that appear anywhere in the analysis (dropping ones from Harvard where there's <7 of a species). This will mean that the absence of a line for a species doesn't necessarily indicate no significance--it could also be insufficient data.

[ValentineHerr]

Oh right, I forgot we were using the analysis without dbh for figure 3.

[ValentineHerr]

So final versions should be this:

(note: I fixed the color order at CB, it was not orrect because order of sp code is not the same as latin name. Doesn't make a nice looking color scale, but I think that is okay)

[ValentineHerr]

I pushed the new figures.

Figures S9-18 have the old version of the legend. Is that okay?

[teixeirak]

Thanks! Yes, the SI figures are fine. Although I wonder if we should add year to all of them.

[ValentineHerr]

Might be a lot of figures, those are often 4x4 figures.

[teixeirak]

Would it be easy to do 4 columns? If not, just leave it.

[ValentineHerr]

I pushed figures with Year and updated the legends. Let me know what you think.

[teixeirak]

Regarding the SI figures: Hmmm... Looks great, except I'm realizing that the species for which year effects can't be estimated are missing from those. Would it be tough to plot the models without year for those species? If not, maybe just save copies with and without CO2, as its good to have both on record, and I'll need to decide which to use.

[teixeirak]

Regarding Year_responses_BAI_only, I think I'll put this in the main document and Year_responses in the SI. One little change on this one: could you please put BAI as the y-axis label and site names as titles? on each plot? One of our coauthors was confused by the current setup with variables as column labels. It would be tricky to change that, so let's see if others have issues with it. But for this particular figure we can change it.

[teixeirak]

Oh, and we need y-axis labels on the climate responses figure.

[ValentineHerr]

Would it be tough to plot the models without year for those species?

See if you like what I pushed. Only the Year plot is from the Year analysis.

[ValentineHerr]

Regarding Year_responses_BAI_only

Is this good?

[teixeirak]

See if you like what I pushed. Only the Year plot is from the Year analysis.

Hmmm... That's misleading in that the other responses would change when year is included in the analysis. We'd need to have the year model for all terms of the species where its tested. If that's complicated, please just save separate versions with and without year. Maybe I'll stick both in that already-massive SI.

[teixeirak]

Is this good?

Yes, thanks.

[ValentineHerr]

That's misleading in that the other responses would change when year is included in the analys

agreed, I'll save both versions

[ValentineHerr]

we need y-axis labels on the climate responses figure.

[teixeirak]

That takes care of it, thanks.

[teixeirak]

would it be easy to make plots of the significant climate x DBH interactions? I'm thinking plots like the climate response plots, but with separate lines for min and max DBH.

[ValentineHerr]

I pushed the with Year and without Year figures. Do we use the "show case" ones (SCBI and New Mexico)? The one with Year is too crowded.

[ValentineHerr]

would it be easy to make plots of the significant climate x DBH interactions?

Might be a bit tricky. Will see now.

[teixeirak]

Do we use the "show case" ones (SCBI and New Mexico)? The one with Year is too crowded.

No, I dropped that figure.

[teixeirak]

I pushed the with Year and without Year figures.

Thanks!

[teixeirak]

@ValentineHerr , it would be helpful. to add the species legend to the year plot, space permitting/ if its easy enough. (I'm finding myself flipping back and forth a lot to see the species legend as I look at that figure.)

[ValentineHerr]

I added the legend. Do you also want it in the Year plot BAI only?

[teixeirak]

yes, just the BAI year plot. I'm not currently using the other (and it would be too crowded)

[ValentineHerr]

Ok this should be done

[teixeirak]

I think we can close this issue.