Questions while running GUI

[smhoban]

Question 1: how is the "Select Simulation Root Directory" on tab 1 different from the "Subdirectory for actual simulation" on tab 3?

[smhoban]

Question 2: A small thing, but on this screen of the GUI: https://github.com/christianparobek/skeleSim/blob/master/doc/scenario-1.png

Within this main tab of all the parameters, we've got the 3 sub tabs going left to right: "Population characteristics," "Among population migration rate" and "Locus characteristics". But on the left we've got these a little out of order from top to bottom- they go "population stuff", "locus stuff", "migration stuff". Can we just shift the order of those on the left to be "population stuff", "migration stuff", "locus stuff". It'll be easier to explain in the vignette if these go in order.

[smhoban]

Question 3: When doing the rmetasim locus details, I can't define the full allele frequency distribution? I click on radio button this and nothing happens.

Also if I try the plus/minus buttons here it all crashes with this error: Warning: Error in rep: invalid 'times' argument Stack trace (innermost first): 66: FUN [rmetasim-server.R#76] 65: lapply [rmetasim-server.R#76] 64: observeEventHandler [rmetasim-server.R#76] 2: runApp 1: skeleSimGUI

[smhoban]

Another way to break it... On the tab "Scenario Conf" if I accidentally click "scenario number" down arrow to 0 or less, it all crashes. Obviously you can't have a scenario 0 or -1, but it shouldn't crash, so a catch is needed here. This is the trace:

Warning: Error in [[: attempt to select less than one element Stack trace (innermost first): 69: reactive hst [simcoal-server.R#14] 58: hst 57: observeEventExpr 2: runApp 1: skeleSimGUI Warning: Error in [[: attempt to select less than one element Stack trace (innermost first): 57: observeEventExpr 2: runApp 1: skeleSimGUI

[smhoban]

Lastly, I might be missing out on something but now that I've got my test skelesim object prepared, with two scenarios, I click "Run simulation" and nothing happens. Well, I get "Wrote skeleSim parameter file: '/home/user/Documents/test.20160308.1230.6079.params.rdata'" but this just has my skelesim object but no results.

Can someone try to load this object and run it, and tell me what I'm missing :) I'll put this object in the main directory: test.20160308.1226.2546.params.rdata

[MichelleDBG]

Sean - I'm following your workflow and I can't get shiny to let me change the population sizes within the boxes in Scenario Conf/Population characteristics. You have this problem before?

[smhoban]

I am able to change them. It takes couple clicks sometimes not sure why but eventually it lets me :)

It won't let you change migration rates unless you click "user defined"

On Wed, Mar 9, 2016 at 1:08 PM, Michelle DePrenger-Levin < notifications@github.com> wrote:

Sean - I'm following your workflow and I can't get shiny to let me change the population sizes within the boxes in Scenario Conf/Population characteristics. You have this problem before?

— Reply to this email directly or view it on GitHub https://github.com/christianparobek/skeleSim/issues/26#issuecomment-194456338 .

Sean Hoban Tree Conservation Biologist The Morton Arboretum http://www.mortonarb.org/ 4100 Illinois Rt 53, 3rd Floor Research Bldg, room 324, Lisle, IL 630-719-2419

New publications!! Accounting for the nested nature of genetic variation http://onlinelibrary.wiley.com/doi/10.1111/oik.02760/abstract Oikos 2016 Exploring seaweed population dynamics http://onlinelibrary.wiley.com/doi/10.1111/jpy.12366/abstract Journal of Phycology 2016 Loci under selection in expanding tree populations http://onlinelibrary.wiley.com/doi/10.1111/mec.13234/abstract Molecular Ecology 2015 Designing optimal seed collection protocols http://www.sciencedirect.com/science/article/pii/S0006320715001767 Biological Conservation 2015 Using ABC to understand invasive species establishment http://www.nature.com/hdy/journal/vaop/ncurrent/full/hdy201538a.html Heredity 2015

research webpage: http://sites.google.com/site/hoban3/ ResearchGate Profile: http://www.researchgate.net/profile/Sean_Hoban/ food blog: http://cuisineraveclevin.blogspot.it/ blog about invasive species: http://invasivore.org/

[stranda]

Try highlighting the rate and typing in a new one. Should not depend on user defined migration

[MichelleDBG]

Yaarggg, I can't change any numbers in any of the internal tab boxes. I'll go through and see if something needs updating...

[smhoban]

Maybe a shiney thing then?

On Wed, Mar 9, 2016 at 1:40 PM, Michelle DePrenger-Levin < notifications@github.com> wrote:

Yaarggg, I can't change any numbers in any of the internal tab boxes. I'll go through and see if something needs updating...

— Reply to this email directly or view it on GitHub https://github.com/christianparobek/skeleSim/issues/26#issuecomment-194472233 .

Sean Hoban Tree Conservation Biologist The Morton Arboretum http://www.mortonarb.org/ 4100 Illinois Rt 53, 3rd Floor Research Bldg, room 324, Lisle, IL 630-719-2419

New publications!! Accounting for the nested nature of genetic variation http://onlinelibrary.wiley.com/doi/10.1111/oik.02760/abstract Oikos 2016 Exploring seaweed population dynamics http://onlinelibrary.wiley.com/doi/10.1111/jpy.12366/abstract Journal of Phycology 2016 Loci under selection in expanding tree populations http://onlinelibrary.wiley.com/doi/10.1111/mec.13234/abstract Molecular Ecology 2015 Designing optimal seed collection protocols http://www.sciencedirect.com/science/article/pii/S0006320715001767 Biological Conservation 2015 Using ABC to understand invasive species establishment http://www.nature.com/hdy/journal/vaop/ncurrent/full/hdy201538a.html Heredity 2015

research webpage: http://sites.google.com/site/hoban3/ ResearchGate Profile: http://www.researchgate.net/profile/Sean_Hoban/ food blog: http://cuisineraveclevin.blogspot.it/ blog about invasive species: http://invasivore.org/

[MichelleDBG]

Ha ha! updated shiny and now I can add text.

[MichelleDBG]

I enter 0 for each migration matrix and it recalculates with 1s. I tried changing the distance function and slipped on dexp. Now I don't have any other options in that drop down and can only get three zeros and one 1.

[smhoban]

Hmm under migration model I could choose 'user' and that worked

On Wed, Mar 9, 2016 at 2:05 PM, Michelle DePrenger-Levin < notifications@github.com> wrote:

I enter 0 for each migration matrix and it recalculates with 1s. I tried changing the distance function and slipped on dexp. Now I don't have any other options in that drop down and can only get three zeros and one 1.

— Reply to this email directly or view it on GitHub https://github.com/christianparobek/skeleSim/issues/26#issuecomment-194481649 .

Sean Hoban Tree Conservation Biologist The Morton Arboretum http://www.mortonarb.org/ 4100 Illinois Rt 53, 3rd Floor Research Bldg, room 324, Lisle, IL 630-719-2419

New publications!! Accounting for the nested nature of genetic variation http://onlinelibrary.wiley.com/doi/10.1111/oik.02760/abstract Oikos 2016 Exploring seaweed population dynamics http://onlinelibrary.wiley.com/doi/10.1111/jpy.12366/abstract Journal of Phycology 2016 Loci under selection in expanding tree populations http://onlinelibrary.wiley.com/doi/10.1111/mec.13234/abstract Molecular Ecology 2015 Designing optimal seed collection protocols http://www.sciencedirect.com/science/article/pii/S0006320715001767 Biological Conservation 2015 Using ABC to understand invasive species establishment http://www.nature.com/hdy/journal/vaop/ncurrent/full/hdy201538a.html Heredity 2015

research webpage: http://sites.google.com/site/hoban3/ ResearchGate Profile: http://www.researchgate.net/profile/Sean_Hoban/ food blog: http://cuisineraveclevin.blogspot.it/ blog about invasive species: http://invasivore.org/

[stranda]

Right...I misunderstood. The elements in the matrix can only be changed under "user" migration model. I thought you were talking about the migration multiplier on the left hand column. It gets multiplied throughout the migration matrix

[stranda]

I think that I have addressed the issues raised here.