Introduction and discussion outline

[christophe-rd]

Just for me. Last commit before cutting most things in the intro Will probably go back for refs and stuff later

[christophe-rd]

@lizzieinvancouver I re-worked the introduction outline as we talked about and worked with Victor on a first draft for the discussion. I tried to make it much more concise. It has the results section in it though. Hope this is not a problem. On the PDF, the discussion starts at p.6:

https://github.com/christophe-rd/wildchrokie/blob/60a00cea7e53e567cad98bc0f6ca3c4648a5436a/docs/manuscript/manuscriptOutline.pdf

https://github.com/christophe-rd/wildchrokie/blob/60a00cea7e53e567cad98bc0f6ca3c4648a5436a/docs/manuscript/manuscriptOutline.Rnw

[lizzieinvancouver]

@christophe-rd Thanks for this! I worked on your methods and results yesterday and need to input the edits into the .Rnw. Remind me issue should I should use?

Some quick thoughts on this issue to keep us moving .... The intro is much better, bravo! For the intro:

1. I suspect 1. will need to be two paragraphs but see how it goes as you write it.
2. You probably need one or two more parts to 4a -- before 4a -- to explain what you mean by internal constraints -- or avoid the term altogether and say 'even with good conditions trees may not be able to respond' then think about what you need to explain (and what order) to get to 4a and 4b.
3. I would think carefully about what you are trying to say when you say that growth may be more constrained than leaf phenology ... it could easily confuse the reader! You might be better sticking with plasticity and local adaptation (which seems to be all you're talking about, no?) and then walk through leaf phenology as though it directly affects growth and THEN (after) if you want to say more about growth that is somehow totally separate than phenology, talk about that separately and be clear on what you're trying to say.

Discussion:

1. Can you please use enumerate and only enumerate here? Somehow you 1abc ... then A then 2 abc ... so I think you need another \enumerate in place of whatever you used for the A etc.
2. Side note: You'll need to cite Dan's paper for your point about EOS being warmer, that's the main finding of his paper.
3. You could probably think a little more on the order and message of 1 (and do you want to make ALL those points there? I might find one to skip).
4. I very much dislike a limitations paragraph or two, where you just list off everything wrong or less than ideal. It's especially bad to put it towards the end. Can you revisit this and think of where some of these points logically belong? For example, 6c seems to be a discussion about species ... and I imagine 6a could find another home; for 6b, be sure you think this is a problem before you suggest it -- do you have any reason to think a fully crossed (fully crossed how?) design would give a different answer?
5. I like 7! Can you add any more now that this paragraph may come after 5.... what do you results mean for species range shifts or whether models need to include population level effects? I also suggest you look deeply at papers that report population level effects and try to figure why they found them and you don't. You already have some citations and you could ask @DeirdreLoughnan for others she just got from a reviewer.

[christophe-rd]

@christophe-rd Thanks for this! I worked on your methods and results yesterday and need to input the edits into the .Rnw. Remind me issue should I should use?

@lizzieinvancouver, I edited the methods issue to include the results too. It's #37

Some quick thoughts on this issue to keep us moving .... The intro is much better, bravo! For the intro:

@lizzieinvancouver great thank you! These are really helpful. To confirm, I should work on another outline before writing these out?

Can you please use enumerate and only enumerate here? Somehow you 1abc ... then A then 2 abc ... so I think you need another \enumerate in place of whatever you used for the A etc.

Ok! Victor and I were talking about this and we thought it would be a good idea to add a section. But we can maybe add it later if it doesn't fit the enumerate.

I very much dislike a limitations paragraph or two, where you just list off everything wrong or less than ideal. It's especially bad to put it towards the end. Can you revisit this and think of where some of these points logically belong?

Will do!

For example, 6c seems to be a discussion about species ... and I imagine 6a could find another home; for 6b, be sure you think this is a problem before you suggest it -- do you have any reason to think a fully crossed (fully crossed how?) design would give a different answer?

I guess my point about this is that the strong answer from Bpap cold have been caused by this species having only 7 individuals vs 20-27 for the other species.

I like 7! Can you add any more now that this paragraph may come after 5.... what do you results mean for species range shifts or whether models need to include population level effects? I also suggest you look deeply at papers that report population level effects and try to figure why they found them and you don't. You already have some citations and you could ask @DeirdreLoughnan for others she just got from a reviewer.

Will do! Deirdre and I are meeting today for this. So we'll talk about it.

[lizzieinvancouver]

@christophe-rd

These are really helpful. To confirm, I should work on another outline before writing these out?

Yes! But I hope it should not take too long....

Ok! Victor and I were talking about this and we thought it would be a good idea to add a section. But we can maybe add it later if it doesn't fit the enumerate.

Oooh, okay. I guess that is fine -- but perhaps just write "subheader: title" and whatever title you are thinking so I understand better.

I guess my point about this is that the strong answer from Bpap cold have been caused by this species having only 7 individuals vs 20-27 for the other species.

Okay, sure -- I would just say larger sample sizes that are more even across species .... though an even number is HARD with a common garden situation so maybe just more reps should be the goal (and if you think it's a problem you could actually check it -- sample in 7 individuals repeatedly of the other species and see if you can repeat this.... I don't think you need to do this, I just am pointing out that you can test for this versus just assuming this is happening. I fear people get so into limitation sections that they come up with limitations that they could deal with or test for in other ways), and why not also say across more geographical distance? More is always good so be sure you pick out what you think are the most important 'more.'

[christophe-rd]

Okay, sure -- I would just say larger sample sizes that are more even across species .... though an even number is HARD with a common garden situation so maybe just more reps should be the goal (and if you think it's a problem you could actually check it -- sample in 7 individuals repeatedly of the other species and see if you can repeat this.... I don't think you need to do this, I just am pointing out that you can test for this versus just assuming this is happening. I fear people get so into limitation sections that they come up with limitations that they could deal with or test for in other ways), and why not also say across more geographical distance? More is always good so be sure you pick out what you think are the most important 'more.'

@lizzieinvancouver I get your point and didn't think about it that way. I guess it's kind of the same for extreme temperatures... We found an effect when including the slope on extreme temperatures, but only when we didn't have ayear. I couldn't find another home for 6b, so I just ignored it for now. Perhaps I'll think of another way when writing these.

For:

I like 7! Can you add any more now that this paragraph may come after 5.... what do you results mean for species range shifts or whether models need to include population level effects? I also suggest you look deeply at papers that report population level effects and try to figure why they found them and you don't. You already have some citations and you could ask @DeirdreLoughnan for others she just got from a reviewer.

I added two points, though I just skimmed the abstract of the papers Deirdre sent me. Will read them more carefully in the next few days. For now, I just added points from what I've already read.

You can find the updated version of the intro and outline here:

https://github.com/christophe-rd/wildchrokie/blob/3cf54d03cf94d274d57ce32b28c4a217e07c9b8e/docs/manuscript/manuscriptOutline.Rnw

[lizzieinvancouver]

@christophe-rd Great. I suggest you (1) read it again today with fresh eyes, (2) ask a co-author to give it a quick skim and point out anything they see, then (3) pass back to me. I suspect/hope we'll be quite close then.

[vvandermeersch]

Hi @christophe-rd ! I quickly read your intro/discussion outline. Below you will find some comments ; I have probably missed some things, but I hope this can still be helpful. That's just my personal perspective, feel free to ignore some points!

For the intro:

• paragraph 2 could be the end of paragraph 1
• you could make the transitions between 1–2 and 3, and between 4 and 5, more explicit (as they are not totally obvious to me). More generally, I think it's good to think carefully about all the transitions
• 'Longer seasons are not necessarily warmer', maybe more explicitly: 'A longer growing season does not necessarily mean more favorable conditions for growth throughout the season' (including warm enough?)
• in 6.a., you just write 'Earlier SOS also means earlier EOS', maybe think about what it means for a tree? Is the tree missing good warmer days for growth if it shutdowns early?

For the discussion:

• your subheaders are not informtive ('Patterns across species and predictors', 'Species-specific patterns'), you want to carry a message in the titles!
• 'Stronger response to EOS than SOS, because temperature is warmer' : does this align with what we know about the intra-annual dynamics of growth? It might be worth looking at studies based on dendrometer data or microcores from the same region?
• some points lack discussion, for example: 'Contrary, X and Y driven by EOS: more reactive to warmer, late season temperature'... This sound like only 'Results' to me
• I also feel you could discuss a bit more somewhere what it could imply if EOS matters more with ACC... Like, EOS occurs during summer, a period that may become increasingly dry and therefore less favorable for growth?

[christophe-rd]

@vvandermeersch thank you very much for your comments on a very short notice! These are really helful.

I have two questions:

your subheaders are not informtive ('Patterns across species and predictors', 'Species-specific patterns'), you want to carry a message in the titles!

Would you just remove the subheaders or change them to something more informative?

'Stronger response to EOS than SOS, because temperature is warmer' : does this align with what we know about the intra-annual dynamics of growth? It might be worth looking at studies based on dendrometer data or microcores from the same region?

Good idea! If you any paper that come to mind, let me know!

[vvandermeersch]

Would you just remove the subheaders or change them to something more informative?

I think I would try first more informative ones, and maybe remove them later if they seem useless?
For example, if your 'Patterns across species and predictors' section is mostly about the coherent responses across species, you could have something like 'Growth increases with growing season length across species' or such