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Deirdre edited this page Mar 16, 2022 · 246 revisions

Welcome to the ospree wiki!

16 March 2022: Almost St. Patrick's Day round-up!

Limiting cues

  • A manuscript from a long, long time ago, I can still remember how ... link to ms folder
  • Deadline for re-submission: 22 April 2022

Traitors

Rangers

Phylogeny

  • There’s been progress in the ms. writing (intro and methods mostly), which is moving slowly. I could use help with English refinement (Lizzie is doing a lot in this front) and with filling of missing refs in text.
  • Most of my work on the project over the last week/week and ½ has focused on re-running a new version of the model by Deirdre that includes a Cholesky decomposition and seems to speed the modelling procedure. While new muplots seem fine and closely match those of the previous approach, there are some strong departures for lambdas and sigmas estimations. Posteriors of lambda for forcing remain moderately high and informative, lambdas for chilling and photoperiod now seem to follow some sort of uniform distribution, which are pretty uninformative. I may need some feedback, discussion to better understand this, and to make sure we agree on how we interpret this new finding. Since priors do not seem to change in the code, this flat shapes for lambdas of chilling and photo should not have to do with that, but I wondered if the new code misses any specification of the VCV? I would be happy to meet whoever interested on the topic sometime next week? You can check this issue by comparing the new figures in analyses/phylogeny/figures (the new figures end with _deird).
  • Lizzie here -- oh no! What happened? Well, I chatted with Geoff and looked at some files. Specifically I compared uber_threeslopeintercept.stan -- what I am pretty sure is the old Stan code we were running before and uber_threeslopeintercept_modified_cholesky.stan, our new Stan code, and confirmed they're the same but with the cholesky added. When you add a Cholesky though you end up in a new numerical space for the things inside the matrix, so next I checked phylo_ospree_compact3.R, our old R code that set up the priors, and phylo_ospree_compact4.R, the new code that sets up the priors and the priors look the same to me. That means we're using wildly different priors now. Geoff said we probably can figure how to get our old priors in this new space -- but it would likely take work. And, given that we tested all the old code and priors a fair bit (including Lizzie's original priors versus Geoff's tweaked ones) we think we should jettison this speed-up idea for the old, tried and true Stan code. Cholesky be damned; if we have model working well in the natural units we should stick with it. I apologize for this diversion, but learned something.
  • Lizzie and I agreed that for this ms. to still be novel and interesting it should be submitted soon, which we’ll aim to do at some point in May. For that I’ll aim to circulate some rough version of the ms. by the end of March for comments, edits, etc.

23 September 2021

Traitors

  • Could we remove study? We ran the trait-only model (no joint model) and the model with study seemed to run a little better so we plan to move forward with study (though the answers are not that different for most species, so we could drop it).
  • Next up: Prior-predictive checks on the trait-only models and run the full model with real data.
  • End of next week: Clean up models folder for traits so people can jump in on models and help, see where we're at.
  • Work on mean trait models (same as joint model but using mean trait values ... no trait model). Faith will keep of this (no issue yet).

Phylogeny

  • Working on cool figures
  • Could use help once he has the draft code done: run through the code to make sure it looks good, help with figure suggestions and edits.

Rangers

  • Simulation code is started ... figure out why we're doing this; maybe also pull North American climate data? Let's see where we end up.
  • Where are we at with models? See issue here
  • Nacho will work on conceptual figure; Cat's figures here

Making progress!

  • Rangers: Deadline for outline, then get feedback in a week at a meeting in a week or two (lab meeting?)
  • Phylo: Meet with Will, JD, and decide on focus ... then schedule 1-2 follow-up 30 minute meetings with phylo-interested folks
  • Traitors: Meet next week; then meet every other week until the retreat ... aim to figure out how long things are taking (switch to mean trait values if taking forever)

22 September 2021 (Equinox)

Phylo

  • Nacho presented new results from our new PMM model (see docs folder)
  • lambda is weaker for chilling and photoperiod; forcing is highest lambda
  • sigma^2 should be interpreted alongside lambda and vice versa
  • Methods (Geoff wrote up new methods) ... Add refs: Freckleton 2002, Housworth 2004 and check on sigma versus sigma^2
  • Speaking of methods ... do we want this to be a hybrid methods/data paper or keep as empirical paper? (Lizzie says pure methods would be a nightmare, may get harsh reviews and may get people who want us to use different data, may be asked to make it a package or such). Pitching this to an editor -- we can say, 'here are the cool questions we're asking, but we're also providing an important new extension of a major method.'
  • Next steps: Nacho has some notes on what additional (and better plots to make), run external analysis of model fit etc. (set model to 0 suggest Geoff). Meet with Jonathan/Will/Geoff on how to pitch paper (Nacho prepares summary talk)?
  • Tomorrow: Review sigmas and lambda together, look at plots of cues on tree.

Rangers:

  • Methods write-ups!
  • Cat will check on her plots
  • North America versus Europe issues ... Cat will check on these.
  • Simulations -- new data on variance in Betula pendula sites... Lizzie will work on these. Geoff said unbalanced data does improve the model.

Traitors

8 September 2021

Phylo

  • left off working on simulations and models that are fitting for simulated data and OSPREE! Geoff's recent additions did not produce divergent transitions, but we need to ensure everyone's version is producing the same values.
  • Geoff's additions are relatively minor (1) easier to change the priors in the R code vs Stan (2) line 67 fixed issue with finding a place for model to start (3) set boundaries on the lambdas.

Rangers

  • unclear if the grid cell weighting was fixed, joint-ish models were fit and we started to extract output.
  • Simulations tasks
  • Population vs species plot to summarize Cat's models (may be already done)
  • next meeting ideally pick up making the concept figure and start thinking about the paper writing

Traitors

OSPREE tasks for early September mini-retreat:

  • Geoff - check what changes were made to the model recently
  • Geoff - write up clarifying statements for methods
  • Nacho - move the phylogenetic code into the OSPREE repo and re-run the model for the OSPREE data, creating plots for us to look at
  • Cat w/ help from Ailene - work on writing simulation code, and checking whether we already have plots summarizing Cat's model for Population vs species
  • Geoff - run the phenology only model with set values for the trait effects
  • Deirdre - work on the trait only model
  • Faith - test the test data

November 2020 retreat!

  • Traiters before the retreat! (1) combine BIEN and TRY, (2) all agree hypotheses, (3) subset to the species for analyses, (4) decide on a team name (‘traits are great’ the ‘great traits’)
  • Phylo -- need to decide on analyses, before retreat is the dream!
  • Rangers aim to ... have a paper outline started before (and done by the end)

29 April 2020

15 April 2020 lab meeting

  • Quick check in on cleaning: issue 322, issue 354, issues 358-364
  • Phylogenetic mixed models
  • A link that may or may not work here

8 April 2020 lab meeting

  • Ranges:Check in on issues: 330 and 346 and 197
  • Progress on issue 366
  • Phylogeny next week -- tasks!
  • Issues with papers

Mid-December goals

  • Ranges: get North American shape files and get started on extraction code and send around shape files plots for NA and Europe! Make sure all European species are done.
  • Phylogeny: re-run without gymnosperms
  • Limiting cues: send around draft to co-authors
  • Traits: finish cleaning TRY
  • Chilling code: Hopefully done

Lab meetings in Spring 2020

We will alternate across three formats: one week focused on one OSPREE project (e.g., phylogeny, traits, ranges, percent budburst), then one week with regular lab meetings, then one week focused on two OSPREE projects. Rinse and repeat. Read up on git milestones here. When it's your team's week you should arrive with an update, questions and a new set of issues and milestones you'll next be working on.

15 January 2020

  • Traits: present preliminary figure & agree on decisions made
  • Percent budburst
  • Ranges check-in: All North American & European data ready?

22 January 2020

  • Phylogeny: Give talk that could be an outline of paper

5 February 2020

  • Ranges: Preliminary models

Meeting on 4 December 2019

  • Finish chilling code (Cat, working on it, should be done before Christmas break, will email everyone when ready -- REMEMBER TO UPDATE YOUR MODEL RESULTS then!)
  • Try to finish cleaning TRY (TRY team, working on it, need to split across computers)
  • limiting cues sent around (Lizzie, no -- sorry -- next week!)
  • Phylogeny at species-level (Done!but need to update)
  • European ranges done (Nacho, close!)
  • Goal for NA ranges (Dan)
  • % budburst: Fitting to simulations (Geoff, no, but next goal is to solve scaling issue, see issue (#306)

Retreat 2019! (November 19-23)

  • Who attended? Dan B., Cat C., Mira G., Faith J., G. Legault, Deirdre L., Nacho M-C., Darwin S., Lizzie
  • What we worked on is reviewed here
  • Discussed authorship on 23 November 2019 on ferry (Dan and Cat not present):
  1. percent budburst: uses best data from OSPREE, lead by Geoff (authorship is hard to know as much as may be very conceptual paper; milestone; everyone here agreed they would be okay not on it, except Geoff)
  2. ranges: everyone at this retreat
  3. traits: everyone at this retreat
  4. phylogeny: everyone at this retreat
  5. performance -- set aside for now as not much OSPREE data (will probably advance outside of OSPREE framework, Lizzie will let everyone know)

Meeting (12 November 2019)

  • Any important updates/questions from last week (that are not covered in the list below)?
  • Thermal time (issue here)
  • Check papers issue: (issue 295)
  • BB perc issue: (issue 310)
  • Climate data: what should be done? (issue 311)
  • Budburst manuscript: sliding window (issue 317)
  • Budburst ms: new figure (see here)
  • Updates on range work (issue 197)
  • Retreat logistics and research goals update! Links in sidebar at right ...

Meeting (30 October 2019)

Review: These issues should be done by now (hopefully):

  • Thermal time (issue here), but may need someone to check work.
  • Species complex update (issue 308)
  • Cleaning update (issue 304)
  • Percent budburst to days (issue 310)
  • Entered data was checked and fixed (issue 295)
  • New chilling issue (issue 311)

Updates, discussion topics

  • Please check out the two wiki pages on the retreat: research goals and logistics
  • Phylogeny update
  • Ranges update
  • Traits update

Meeting (16 October 2019)

  • Update on cleaning (issue 301) -- Lizzie will add a new issue to double-check cleaning code
  • Update on species complex (issue 308) -- Dan and Lizzie will check
  • Any other cleaning updates?
  • Update on phylogeny progress
  • Update on traits.
  • Update on ranges work
  • Update on beta distribution

Meeting (30 September 2019)

  • We aim to have a new species complex out by Friday!
  • Chilling code ... did we add ambient temperatures? Can we review the problem papers and make sure we have them correct and have made good notes? (Side note: I also asked Ben Cook if he thought our correlations between Livneh and Princeton were okay)
  • Update on cleaning (issues 301 and 304) ... waiting on info for fu18, prevey18 and vitra17 (Dan and Deirdre) ... also, cleaning updates from Cat and Nacho in files sourced in bb_cleanmergeall.R
  • Limiting cues co-authors: Report back on interactions (see issue here)

Meeting (18 September 2019, led by Cat and Dan ... thanks Cat & Dan)

  • Nacho gives phylogeny update
  • Maybe ... Ailene updates on photoperiod paper?
  • Update on cleaning (issues 301 and 304)
  • For those in need of a species list, temporary one may be ready soon -- see issue 308
  • Please do! Limiting cues co-authors: Report back on interactions (see issue here) ... at next OSPREE meeting (30 September)

Meeting (4 Sept 2019)

  • Traits! Discuss decisions on what data is reliable enough to include in our analysis

  • Manuscript updates

  • Cleaning 2019 data update updates

  • Issue reviews

  • Goals before the retreat!

  1. Have trait data for all species in hand and clean
  2. Goal to have analyses well underway by retreat ... Update on this from Nacho at next OSPREE weekly meeting.
  3. Goal to have species list and all range climate info in hand for retreat
  4. Goal to have new species list well before retreat and have these data super clean (including to budburst date).
  5. Beta distribution model for % budburst

5 August check-in

  • Journals quick-check in
  • Manuscripts check-in (Lizzie and Ailene)
  • New data check-in
  • When to meet next -- September! But keep working on your OSPREE tasks in August
  • Aim to wrap up early so chilling sub-group can meet

Big news -- we are adding a branch!

  • The new branch (tentatively named bbculdesac) will be for work on the non-updated OSPREE database
  • The master branch will continue forward with updated data, code etc.
  • What does this mean? If you are working on the non-updated OSPREE database (that is all current manuscripts) you need to git checkout bbculdesac and do all your work there (all edits, commits etc.) then be sure to switch back to master when working on updated data and all related projects (traits, phylogeny etc.) git checkout master
  • If you ever use the branch then keep track of where you are and be careful!
  • Check out some resources here

It once was July, the time of the second mini-retreat!

Lizzie put some notes here!

Stuff to discuss on Friday call (please add to this list):

  • Quick review of finding old files (at least on github)
  • Kick off with journals
  • Paper entry!
  • Dan checked in on ranges, and found ...?
  • Trait cleaning ... what can we do to help?
  • Perpheclim updates
  • Phylogeny update
  • Cue correlation figure updates (if done)
  • Should we analyze the performance data (some notes here)?

It once was late June and it's the first mini-meeting! See notes here for the Seattle meeting wiki

At our last meeting (5 June 2019)

  • Photoperiod ms- Question about figures (Ailene)
  • BB ms- New issues for everyone!

Here's a review of the meeting ...

No more git Desktop! Please use git in Terminal (or in Rstudio, if you use RStudio please be sure it is set up so you have to click/choose to add each file).

OSPREE new data task ... Who does what, see issues # 234 and 268

Mini-meeting... I will send out times! Please suggest preferred times for the Skype meeting! (Dan requests after 11am PDTon the 27th; Best times for Nacho ... ideally before MADRID 8pm, up to 10pm is reasonable)

Budburst MS notes and deadlines!:

  • Issue #259 -- come up with better title ideas and email to Ailene, do not be limited by what is there now ... go wherever you want based on what you think the MS is about.
  • Various issues assigned to Cat, Dan, Dan F., Tim
  • Nacho Can you help with some maps and figures? See issues #261 and #262
  • PEP data issues (Cat and Ailene have a meeting setup tomorrow but please keep Lizzie in the loop)
  • Non-linearity (Lizzie and Dan)
  • Deadlines: Aim to have your tasks done by 12 June (Wednesday) so Ailene can send new draft on 18 June (Tuesday), comments by 25 June (Tuesday)

At our next meeting (26 April 2019)

At our next meeting (9 April 2019)

Important: Please post issues and files people need to review here before the meeting!

  • Give Ailene feedback a plot of marginal effects using our chillport and utah models (issue #242). A little explanation: the line for "forcing" is changing the forcing temperature, but keeping the chilling at its mean level; line for "chilling" is changing chilling temperature, keeping forcing at its mean level; "both" is altering both simulataneously. The 3d figure keeps photoperiod at 8 hrs. Please come with answers to: 1) What are the main (1-3) messages you get from this figure? 2) Which version do we want in main vs sup (3d or 2d; utah vs chill)?
  • Question about range models. I tried to put together a datasheet that merges species level effect size estimates from the bb model with the range data nacho put together. Does this seem like the right data format to answer our questions (seehere)

At our meeting (27 March 2019)

Small quick issues:

At our meeting (13 March 2019)

  • Updates on bbpercent issue?

  • Bigger comments on photoperiod MS, or any comments that we should discuss (big or small)?

  • Divvy any tasks on budburst MS?

  • Updates on other issues?

  • Any issues to close?

  • Coding challenge!

  • If time allows ... review other issues (though I doubt it).

At our meeting (27 February 2019)

  • Review traits progress! link here
  • Updates on papers! Photoperiod, limiting cues, budburst

Issues:

  • Issue #235: I think could wrap up if Ailene would track down answers ....
  • Issue #247: PEP data
  • Issue #244: Cold tolerance -- can someone transcribe the data (incl. metadata and ref issue)? Then we can close.
  • New issue: Help on treatments that could test interactions.
  • If time allows ... review other issues.

At our next meeting (6 February 2019)

  • Updates not on this list?
  • Limiting cues paper work
  • Range work (#197)
  • Cold tolerance data update (#244)
  • Weinberger updates (#126)
  • Latitude model
  • Issue #235 (photoperiod by Lizzie)
  • Chilling and forcing from PEP data (#238)
  • Model plotting updates

At our meeting (23 January 2019)

  • Traits! Deirdre and Darwin lead discussion: update traits wiki page, start with sensitivity then go to photo/chill and force. Get cold tolerance traits data ...
  • Updates on ranges (issue #197, Nacho is working on)
  • Updates on models and plots, round-robin
  • If time allows, run through issues!

At our meeting (9 January 2019)

  • Housekeeping on lab meeting
  • Review the photoperiod figure located here
  • Discuss next steps for issue #234 (papers).
  • Updates on issue #233 (traits)
  • Species range updates? #197
  • Updates on PEP 725 (#238)
  • Latitude model #121
  • Review models and model plots briefly
  • Discuss approaches for forecasting chilling and forcing (issue #242)
  • Anything else?

At our meeting (12 December 2018)

  • Nacho gave updates on range code, next steps are chilling.
  • Phylogeny: Lots of progress, next steps are to better understand what the model is doing.
  • Chilling is done! Moving onto models.
  • Next steps sorted for: weinberger (plotting), latitude models (plotting), adding papers, traits, photo vs. force and main models (plotting). Did I hear plotting anyone?

At the retreat (4-9 December)

Day 6 (Sunday)

  • Updates on ranges from Dan: Next steps are listed in issue #197
  • Updates on traits from Deirdre and Darwin. Issue #233.
  • Updates on adding papers. See issue #234.
  • Updates on chilling from Ailene #183
  • Updates on Weinberger from Dan, Ailene, Lizzie: Next steps are listed in #126.
  • Updates on latitude model from Cat: #121 ... will have plots soon!
  • Updates on separating photo and force (Cat): Updates to come.
  • Updates on budburst models from Lizzie: Next steps are more model fits (#232 and #239) and projections....

Day 5 (Saturday was free day)

Day 3 (Thursday)

  • Updates on the models from yesterday
  • Read photoperiod paper: Really coming along, we discussed some improvements to box, to figures and to text.
  • Limiting cues: Lizzie will prep data for finalizing PEP 725 figure.
  • Afternoon was reading Chesson 2000 over beers and settling in

Day 4 (Friday)

  • Nacho is using Zanne tree and making great progress. He realized we may want to fit each cue separately to estimate lambda usefully. We agreed he should try all four models (all three cues together and a model for each cue)
  • Worked on conceptual figure
  • Worked through the issues. We are really coming along!

Day 2 (Wednesday)

Morning meeting

  • Start with the models and types of designs (exp vs. ramped vs. all) ... Let's start by thinking through photo ... Can we dummy variable exp vs. ramped vs. all types (or will this have issues since most species have only one of these types and we must nest species within EACH type not across types)? If we cannot do that should we present — say — two models: one with exp only and one with all? ... We decided to just focus on exp and ramped! We can present other models in supp as needed.
  • Clean bbstanleadin.R (this was useful)
  • Made some phylogeny decisions ... we will use all species from studies that manipulated forcing and photo (both cues manipulated within the same study) and include Dan Flynn's data

Day 1 (Tuesday)

Previous meetings

At our meeting (21 November 2018) ...

  • Photoperiod manuscript feedback overview
  • Model updates and next steps
  • Issues run through
  • OSPREE t-shirt updates
  • Retreat logistics

At our meeting (24 October 2018) ...

Issues:

  • bbleadin.R discussion and related issues (#217, #218, #219 ... also we have two files called speciesxomplex.R)
  • Check the data updates (#201) ... and try to run through ALL related issues
  • Photoperiod paper update (#193)
  • Limitingcues figures updates
  • Latitude model updates?
  • Other updates?
  • Next steps/topics for OSPREE (#195 todo list review)

At our meeting (10 October 2018) ...

  • Scheduling! Retreat is scheduled! Who is coming so I can book appropriate number of beds
  • Welcome Deirdre and Darwin to OSPREE!
  • Do we need OSPREE t-shirts?! (Dan? Cat?)

Issues:

  • Check the data updates (#201)
  • Photoperiod paper update (#193)
  • Limitingcues figures updates
  • Latitude model updates?
  • Impute updates?
  • New data/species (#196)
  • Next steps/topics for OSPREE (#195 todo list review)

At our meeting (26 September 2018) ...

  • Scheduling! Discuss transition to lab meeting schedule with OSPREE every other week.
  • Scheduling! Discuss retreat: ~4-9 December link here

More issues:

  • Impute updates
  • Limitingcues figures updates
  • Latitude model updates
  • Next steps/topics for OSPREE

At our meeting (12 September 2018) ...

  • Scheduling! Transition to lab meeting schedule with OSPREE every other week.
  • Scheduling! Late October/early November or post-Veterans Day retreat (potentially early December). Check poll, discuss.

Some small issues to run through:

  • Issue #176 (freeze treatment) -- finish Basler? Columns correct? -- DONE!
  • Issue #191 -- what is up with Atlantic lat/long? -- fixed!
  • Issue #192 -- updates on Ribes (Lizzie, Cat)
  • Issue #191 -- updates on Picea/is code matching species correctly? (Dan)
  • Issue #185 -- BRMS diffs (Ailene)

More issues:

  • Impute updates
  • Limitingcues figures updates
  • Latitude model updates
  • Next steps/topics for OSPREE

At our meeting (20 August 2018) ...

  • Scheduling! Two meetings in September, then transition to lab meeting schedule with OSPREE every other week?
  • Scheduling! Late October/early November or post-Veterans Day retreat? Some small issues to run through:
  • Issue #176 (freeze treatment) -- finish Basler? Columns correct?
  • Issue #191 -- what is up with Atlantic lat/long?
  • Issue #192 -- updates on Ribes (Cat)
  • Issue #191 -- updates on Picea (Lizzie)
  • Issue #185 -- BRMS diffs (Ailene, Lizzie)

More issues:

  • Impute updates?
  • Divide and conquer on limitingcues figures?
  • Ailene: update/questions about nonlinearities for limiting cues (#190)
  • Latitude model updates?
  • Next steps/topics for OSPREE

At our meeting (7 August 2018) ...

  • Issue #176 (freeze treatment) -- finish Basler and close
  • Check in on Caffara11b (#118) -- CLOSED
  • Dan: Update on photocurves (#171) -- CLOSED
  • Lizzie's update on limitingcues, best figures for paper
  • Ailene: update/questions about nonlinearities for limiting cues (#190)
  • All: Report on Stan models for days to BB
    • Diffs between BRMS and rstan (Dan) -- all the same params?
    • Imputation (Nacho/Ailene) -- Ailene is BRMS model imputation; Nacho is doing means!
    • Updates on Picea abies (#191) -- Dan
    • Updates on Ribes nigrum (#192) -- Cat
  • Latitude model: check out collinearity (Cat) next up run with 7 species, check effect of lat x chill
  • All: Report on next steps/topics for OSPREE ... what do we want to accomplish with database before making it public?

At our meeting (3 July 2018) ...

  • Check in on issue #176 (freeze treatment) -- almost done!
  • Ailene: photoperiod outline/figures questions
  • Lizzie: Update on limitingcues, including figure updates (incl. Nacho for interannual temp variation on PEP725 figures)
  • Dan: Update on photocurves (#171) and fixing Caffarra data - looks close!
  • Cat: Progress on 3D figure (#165) -- what is up with late days to BB in OSPREE -- nice work! Close whenever ready.
  • All: Report on Stan models for days to BB
    • Effects of apple (Cat) -- done!
    • Chill portions or hours (Ailene) -- keep working on both!
    • Diffs between BRMS and rstan (Dan) -- it's not due to diffs between iter and warmups
    • Imputation (Nacho)
  • Latitude model: check out collinearity (Cat)
  • As always, try to: run through issues!

At our meeting (13 June 2018) ...

  • Ailene's update on Fig. 1 for photoperiod paper
  • Lizzie: Update on limitingcues, including figure updates (incl. Nacho for interannual temp variation on PEP725 figures)
  • Dan: Update on photocurves (#171)
  • Cat: Progress on 3D figure (#165) -- check out how rescaling days to BB looks
  • All: Report on Stan models for days to BB -(Related: Ailene chilling estimates)
  • Latitude model: increase to all provenance studies?
  • Ailene: photoperiod outline/figures questions

NOTES: Picea abies is the most widely planted outside its range ... check its range vs where our OSPREE data.

Followup:

  • Lizzie: check on #125 and #30! -- Cat cleaned one issue we found but otherwise -99 (or -999) is days to BB value with no budburst, and NA means there was no treatment or such.

At our meeting (29 May 2018) ...

  • Ailene's update on Fig. 1 for photoperiod paper -- keep working on it, add insets
  • Dan: Update on photocurves (#171) -- use base R to build figure!
  • Lizzie: Update on limitigcues, including figure help needed -- many news tasks added, see issue #174
  • Cat: Progress on 3D figure (#165) -- let's go 2D!

Wrapup ....

  • Cat: Basler temp (issue #170) - closed

At our meeting (1 May 2018) ...

  • All: Comments on limitingcues paper
  • Ailene updates map for photoperiod paper (#162) and finish table (#151 and #139)
  • Cat: Progress on 3D figure (#165) -- great!
  • Nacho: Updates on 2012 vs 2013 (#144) -- done, we like 2009 better
  • Ailene: daily climate data and forcing questions.update (#130) including questions on no.response etc.
  • Lizzie: Some brief model updates ...

At our 10 April 2018 meeting

  • Code!
  1. Dan: Update on missing chill for charrier11 and cook05 and ALL updates on issue #147 (very close!)
  2. Lizzie and Dan: gheraldini10 updates (it's fixed)
  3. Ailene: clean up bb_daily prep code (very close!)
  4. Nacho & Lizzie: bbperctodays.R updates (and why one of Lizzie's tasks below is not done) -- Lizzie is checking
  5. Group: review bb_cleanmergeall.R, do we still need imput_chilling.R? If not, can we mv notes to bbcleaning_README.txt and delete
  6. Very quick run through on issues 6a. Ailene: a few little questions about forcing. can be done when we get to issue #130.

  • Everyone: New result figures given updated data! (See also updates to issue #167)

  • Cat and Dan: Updates on latitude model

  • Check in on Laube

  • Nacho: Green up maps (full map for 2013 (late) for the maps and difference map of 2012-2013)

  • Nacho: Finish limiting cues figures

  • Cat: 3D phenofit figure

  • See also below (last meeting's bigger bits)

DONE:

  • Lizzie: Double check on Worral67 for photperiod (fine)
  • Lizzie double checks the changes to clean_respvar.R (fine)

At our 26 March 2018 meeting ...

Small bits all DONE:

  • Ailene: Check on why li05 is still not 0 chill (short day controls): UPDATE: Fixed because of simple coding error
  • Ailene: Update on missing chill for heide93 (Corylus): UPDATE: It was because of wrong lat/long
  • Lizzie: updates GIAFNAGNA: UPDATE: has been corrected

Bigger bits:

  • Lizzie: work on resp and go through logical imputation (AND work on issue #147 — the response variable)
  • Lizzie/Nacho/Ailene/Cat/Dan: work on BB models
  • Ailene: check force temp is updating with daily data (YES, done)
  • Nacho: Finish greenup maps
  • Lizzie: work on limiting cues outline
  • Dan/Cat: latitude paper
  • Cat: 3D phenofit figure
  • Ailene/Cat: Figure 1 for photoperiod paper (DOY on horizontal; day hours on the vertical: do all 30 latitudes and put the dots for each study on it (to show change in space and time)
  • Dan: Gheraldini10 is almost fixed (ask Cat and Dan to confirm): Close!
  • Dan: response curves

At our next meeting (26 February 2018) ...

  • Update on resp issues (see also this issue)
  • Update on photoperiod maps (see also this issue)
  • Phenofit projections
  • photoperiod table/figure ideas
  • Retreat logistics: (1) Monday, (2) Tuesday timelines, (3) internet and electricity, (4) what to bring

At our last meeting (6 February 2018) ...

  • Review phenofit data from Isabelle (see this issue) and next steps
  • Updates on photoperiod maps from Dan (see this issue)
  • Updates on photoperiod, chill and forcing data (see this issue) ... for chilling we need to check in on this forcetemp issue
  • Let's do a sweep through issues
  • Goals for next meeting (26 February) (1) Try to re-run models (2) Nacho works on temperature data and works on some figures for that and/or photoperiod figure (phenofit) (3) Lizzie works on the respissues (4) Cat works on chilling (5) Dan works on greenup (6) Dan and Ailene work on chilling (7) Think on goals for retreat
  • Goals for retreat

Halloween: 31 October 2017

  • Lizzie (and Ailene?) updated all the big files now that we updated responsetime. Thank you all for your efforts!
  • Review limiting cues paper
    • Update on BBCH data from PEP
  • Review photoperiod paper (see issues)
    • Any new figures to discuss?
    • Daylength: any updates on MODIS, figures etc.?
    • Updated outline and table (Ailene has some questions, below)
      1. Which version of ospree should i use to make table (ospree_clean_respvar?)

At our previous meetings ...

17 October 2017

  • Yay, Nacho is here!
  • checkmeout_info.csv still has a lot of blanks, let's do a quick run-through together and see what we can fill in (I [Lizzie] just noticed some places I skipped!)
  • Review imputation info/progress (Lizzie) ... what are next steps?
  • Review limiting cues paper
    • How narrow do we want to be with BBCH? With years (#146)?
  • Review photoperiod paper (see issues)
    • New version of 3d figure (Nacho)
    • Daylength calculators and new figure by Dan
    • Updates on data for pheno changes and range shifts (Ailene and Nacho)
    • Updated outline and table (Ailene)
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