continue excellent efforts on species ranges in OSPREE

[lizzieinvancouver]

I suggest starting with fagsyl and betpen and try to calculate some of the metrics we're interested in:

• geographical position within (or beyond) range of each species in each study
• climatic position within (or beyond) range of each species in each study
• distance to coast

See how far you get ..

[lizzieinvancouver]

As discussed on 10 October 2018: First steps could be:

1. Get a list of all species in OSPREE that are in more than two papers
2. Also get a list of all species in OSPREE in any one paper that manipulates all three cues (I suspect this is not many)
3. Pull range maps for said species!

[lizzieinvancouver]

Update: Progress ongoing at the 2018 Dec Retreat!

[lizzieinvancouver]

We have worked on hypotheses ... here next steps are to understand which species is which number in csv @MoralesCastilla: can you let us know?

Next steps @dbuona will coordinate next steps with @cchambe12 @DeirdreLoughnan.

[MoralesCastilla]

Species correspondance for those in the .csv can be found in /data/distributiondata/EU trees/EUplants_dbase_names.correspondance.txt -- Please remind that the script to extract climate data in GDD or Utah units is almost done (in need to know which are the parameters to compute chilling units): analyses/ranges/extract_climate_inrange_shapes.R. I'm happy to work more in this.

[lizzieinvancouver]

@AileneKane Will send a couple lines of code for calculating chill portions using mean (and for min and max), then @MoralesCastilla will try to add.

[AileneKane]

@MoralesCastilla @cchambe12 Here is some code to calculate chilling with ChillR, starting with fake climate data that has a Tmin and Tmax (Step 2, using functions in ChillR to create hourly data specific to a latitude) and then with climate data that has just Tmean (not using the ChillR functions to create hourly data, but using ChillR to estimate chliling). For the values that i picked, the two approaches yield the same chilling estimates. Let me know if you have questions!

[lizzieinvancouver]

@MoralesCastilla work with @cchambe12 on wrapping up some basic estimates so we can get moving! Trying to get this done as we think it goes in budburst paper.

[cchambe12]

@MoralesCastilla See Chill portions code in ospree/analyses/bb_analysis/PEP_climate/fagsyl_climate_prep.R (you can change it from Chill_portions' toUtah_Model' to compare) starting at line 207

[lizzieinvancouver]

@MoralesCastilla Will update the posted data, then @dbuona will lead efforts on next steps.

[lizzieinvancouver]

@MoralesCastilla Will expand to 6 species we think we have decent data on...

[lizzieinvancouver]

Next steps are some simple models ... see here : Take species-level means from posterior for chill and forcing cues ... and then look for basic tests of relationship.... Should get a bigger team working on this at a retreat or such.

[dbuona]

for brms model: chilling effect size ~ (mean SD of GDD) + (mean SD of chill portions) Population-Level Effects: Estimate Est.Error l-95% CI u-95% CI Eff.Sample Rhat Intercept -9.39 9.28 -25.55 9.10 1523 1.00 meanSDchill 0.55 0.39 -0.12 1.34 1224 1.00 meanSDforce 0.00 0.07 -0.16 0.13 1097 1.00

Family Specific Parameters: Estimate Est.Error l-95% CI u-95% CI Eff.Sample Rhat sigma 1.81 1.58 0.62 5.49 672 1.00

[lizzieinvancouver]

@dbuona Will update notes and report back tomorrow (Friday).

[lizzieinvancouver]

Goal to have species list and all range climate info in hand for retreat @dbuona @MoralesCastilla

[lizzieinvancouver]

@MoralesCastilla Will send @dbuona some code that does a couple example species, then @dbuona will take over pulling ranges and related climate data. Please have update on progress towards this by 30 Oct. Thanks!

[dbuona]

@MoralesCastilla From the Caudullo 2017 paper I was guided to here (https://www.fs.fed.us/nrs/atlas/littlefia/#Introduction) and was able to find shape files for 13 of our ospree North America trees. Do you know of any other places we might be able to find good north American range maps?

[MoralesCastilla]

@dbuona Hi Dan, the best repository for shapefile maps of northamerican species (that I'm aware of) is: https://github.com/wpetry/USTreeAtlas I have not checked it much recently, but for NA species in ospree that are not there, I guess we would need to use GBIF?

[lizzieinvancouver]

Making a reference to this in our wiki pages and closing!