half cover date for greenup needs updating

[plzmsu]

@dobsonk2 @moriahy

Currently the half cover date is computed across all % cover, over the entire year. This doesn't capture greenup. I am working on editing this today.

I'm also going to end the "plant_comp_clean_L0.R" script at creating the full L1 cover data.

A new script will include the phenology L1 data.

[dobsonk2]

Phoebe -

I'm a bit confused on this - I think we decided to do half cover of the max percent cover for each year to account for differences in the amount of litter between the chambers and the ambient plots early in the growing season, which might hide the actual first date of greenup (and the original code for half cover greenup was from this script https://github.com/SpaCE-Lab-MSU/warmXtrophic/blob/master/archived_scripts/archived/2016_Emergence_finaldata_by_site.R)

Maybe greenup could be better reflected by calculating half cover date relative to some other date in the year, besides the max date?

Also sounds good for the cleaning script!

[plzmsu]

@dobsonk2 There are multiple ways of computing greenup. The half cover option is ok, but the year-to-year variability in how many times we measured % cover may be influencing the result. In some instances, the % cover of the same species declines in a plot through time, at least over a week or so - this is in the margin of observation error.

Another approach is to rely more on the earlier measures (just the "greenup" % cover data - the data taken every ~ 3 days or so until all species in all plots greened), and exclude the later measures. I started on that in the new phenology_date.sR script which is in the phenology_scripts folder.

I think some work with the greenup variable might help explain why we see an increase in half cover date over time, for both warmed & ambient plots.

When I re-ran some of the lmer models just now (without 2015), they still show that increase.

For now, I removed 2015 and did some other script cleaning and got up through re-running the lmer models.

[dobsonk2]

@plzmsu Sounds good! Also, we talked before about moving the greenup data into the phenology folder - can I go ahead and do this now? I wanted to double check before I did so. At some point I'll also re-make the file path figure in the readme to show where everything can be found

[plzmsu]

@dobsonk2 Yes go ahead and move greenup stuff to phenology. phenology_dates.R is in there and that file should eventually incorporate all date-related phenology prep work (so, adding in flower, seed date-related code to that script: @moriahy ). Right now it is just greenup work.

Note that % cover work should remain in plant_comp_scripts.