Simplify endogenous factors

[alanaroseo]

@rdmanzanedo @FrederikBaumgarten @lizzieinvancouver

okay, this is a mess of people not following directions, including me :(

here's what we have:

unique (d$ifyes_whichendogenous) [1] NA
[2] "no"
[3] "no, leaf phenology and thus GSL (but in fact any measure of GSL) is clearly missing although very easy and important for this deciduous species. Also important because ring-porous species have differ in wood phenology!" [4] "no, no link to leaf phenology and more climatic characterization of the GS"
[5] "maybe"
[6] "a nice variety of different measures, but not fully exploited"
[7] "differences in relationship between SOS and spring NEP due to species composition of the site"
[8] "differences in relationship between EOS and autumn NEP due to species composition of the site"
[9] "greater photosynthesis early in the growing season is associated with earlier senescence"
[10] "provenance. Specifically they found evidence that provenances differed in both growth and phenology, but they did not test the gsl x growth (table 3) at the provenace level"
[11] "functional types"
[12] "greater GPP early in the growing season is associated with earlier senescence"
[13] "provenance"
[14] "no for latitude and bud burst timing and lammas are not realted to growth allocation, early buds = height, late buds = more roots"
[15] "elevation"
[16] "daylength, species"

there shouldn't be "no" in here so those can be NA, other things like elevation are not endogenous factors so probably also NA. they maybe needs a decision or should be NA. Species composition can probably be lumped in with "species" because this was from multi-species stands. I am not sure if [9] counts

so far I see:

• species
• provenance
• functional type (need to clarify if this is just species)

What do you two think? Probably easier to fix in the spreadsheet than via code

[alanaroseo]

I meant not sure about [9] or [12] which are kind the same. Are we calling physiological differences endogenous? I don't think it's unreasonable to, but we don't know that they are

[lizzieinvancouver]

@alanaroseo Thanks! I think of elevation as a possible mix (could be climate, could be provenance ... right?) so I can see why someone put that. Also species sometimes means 'species identity' so I can see that as endogenous.... but species as 'tree density' seems like competition. If this is too much of a mess, we could leave it out from needing to be fully cleaned (and leave out of figures) and use this info more just to help with references in-text? Spit-balling here.

I'd rather fix in the code; I can do it or find someone to help do it so we have it recorded.

[lizzieinvancouver]

Update to my last point: Tree growth response along an elevational gradient: climate or genetics?

We found that low genetic differentiation among populations indicates gene flow is high, suggesting that migration rate is high enough to counteract the selective pressures of local environmental variation. We observed lower growth rates towards higher elevations and a transition from negative to positive correlations with growing season temperature upward along the elevational transect. With increasing elevation there was also a clear increase in the explained variance of growth due to summer temperatures.

[lizzieinvancouver]

Maybe (1) fundamental genetic/developmental; (2) provenance; (3) species.

[alanaroseo]

here's the latest: [1] NA "provenance" "respiration" "age"
[5] "source limitation (photosynthesis)" "taxanomic variation" "photosynthetic timing"

What do you guys think about the source limitation one, is there a broader photosynthesis umbrella we can use lump it in with the photosynthetic timing?

[lizzieinvancouver]

@alanaroseo This seems a pretty good minimal list for now! I am all for merging the two photosynthesis ones except ... how would respiration fit in? They all start to feel sort of related, no?

[lizzieinvancouver]

Done! Though I am still struggling some on related issue on issue #29 so leaving that one alive and kicking.