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SCBI-ForestGEO / McGregor_climate-sensitivity-variation

repository for linking the climate sensitity of tree growth (derived from cores) to functional traits
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misc small things #119

Closed teixeirak closed 4 years ago

teixeirak commented 4 years ago
mcgregorian1 commented 4 years ago
  • [ ] "These droughts were classified as severe (1977) or extreme (1966, 1999) according to the PDSI metric" - Is there a citation for the range of PDSI values associated with severe and extreme drought?

I found this paper - not sure it's the "original" PDSI paper but it's early enough that I think it's warranted? The severe and extreme labels are from the PDSI chart, which is shown on this website.

mcgregorian1 commented 4 years ago
  • [ ] from Valentine: "There is no R2 in GLMM, but if I remember well there is a marginal and conditional R2. You should specify which one you are using. Maybe you did and I missed it. sorry if that is the case."

I'm assuming Valentine meant LMM as we've now dropped GLMM? In any case she's right, and I thankfully noted this in the code as a way to help me understand it. I've been using the conditional R2, as conditional is the R2 for everything. Marginal is just for the fixed effects.

I went through the paper but I'm not quite sure where to put it. We currently don't have a specific section referring to Table 5 (the multivariable results with the coefficients). I think it would be best to go there? Or would it be better to go in the caption?

mcgregorian1 commented 4 years ago
  • [x] In the heading of table 2, specify when the DBH applies (DBH at time of coring? Or DBH in a certain census year?)

I've been using the DBH solely from the 2018 census as representative of the most recent, reliable estimate. I have updated this in the document

teixeirak commented 4 years ago

I've been using the DBH solely from the 2018 census as representative of the most recent, reliable estimate. I have updated this in the document

Okay, but what about trees cored dead in 2016 or 2017?

mcgregorian1 commented 4 years ago

The way that I thought we were doing this table was that this represented the status of our plot at this current moment in time in order to give a general overview of the environment in which we conducted our study. If I remember correctly, the DBH at time of coring is missing for some trees, so I'd be using a mix of 2013 DBH plus 2016/2017 DBH plus 2018 DBH to give a mean and range that represents...something? In my mind keeping it to 2018 was a simple solution in that it provides a snapshot. Do you think it should be different?

On Tue, Jul 21, 2020 at 7:09 AM Kristina Anderson-Teixeira < notifications@github.com> wrote:

I've been using the DBH solely from the 2018 census as representative of the most recent, reliable estimate. I have updated this in the document

Okay, but what about trees cored dead in 2016 or 2017?

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teixeirak commented 4 years ago

The way that I thought we were doing this table was that this represented the status of our plot at this current moment in time in order to give a general overview of the environment in which we conducted our study. If I remember correctly, the DBH at time of coring is missing for some trees, so I'd be using a mix of 2013 DBH plus 2016/2017 DBH plus 2018 DBH to give a mean and range that represents...something? In my mind keeping it to 2018 was a simple solution in that it provides a snapshot. Do you think it should be different?

This is fine. We just need to specify what we're showing in the table. I've changed the heading to say "contemporary DBH" and then specified in the header that this was measured in 2018 for live trees or 2016-2017 for dead trees. I don't think we need to get into the details on the small number of trees that were missing measurements in one of those years.

teixeirak commented 4 years ago

I'm assuming Valentine meant LMM as we've now dropped GLMM? In any case she's right, and I thankfully noted this in the code as a way to help me understand it. I've been using the conditional R2, as conditional is the R2 for everything. Marginal is just for the fixed effects.

I went through the paper but I'm not quite sure where to put it. We currently don't have a specific section referring to Table 5 (the multivariable results with the coefficients). I think it would be best to go there? Or would it be better to go in the caption?

I've added it to the footnotes of Tables S6-S7. ALso, note that former Table 5 is now S6. I changed the file names accordingly. This affects issue #98.

teixeirak commented 4 years ago
  • [ ] "These droughts were classified as severe (1977) or extreme (1966, 1999) according to the PDSI metric" - Is there a citation for the range of PDSI values associated with severe and extreme drought?

I found this paper - not sure it's the "original" PDSI paper but it's early enough that I think it's warranted? The severe and extreme labels are from the PDSI chart, which is shown on this website.

I changed this to give the thresholds: "These droughts were classified as severe ($PDSI$ < -3.0; 1977) or extreme ($PDSI$ < -4.0; 1966, 1999) at our site". I think the thresholds are established enough that we don't need to give a specific thresh hold.