Error: sensi_plot for clade_continous

[paternogbc]

CRAN TESTS:

Error: clade_continous()

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: clade_continuous
> ### Title: Influential Clade Detection - Trait Evolution Continuous
> ###   Characters
> ### Aliases: clade_continuous
> 
... 420 lines ...
1  Callitrichidae         9 1.871823 0.20413705       12.2      1.725941
  Pval.randomization
3          0.3666667
2          0.5000000
4          0.5666667
1          0.2666667

> sensi_plot.sensiClade.TraitEvol(clade_cont2)
Error in sensi_plot.sensiClade.TraitEvol(clade_cont2) : 
  could not find function "sensi_plot.sensiClade.TraitEvol"
Execution halted

[paternogbc]

New Error:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: influ_discrete
> ### Title: Influential Species Detection - Trait Evolution Discrete
> ###   Characters
> ### Aliases: influ_discrete
> 
> ### ** Examples
> 
> #Load data:
> data("primates")
> #Create a binary trait factor 
> adultMass_binary<-ifelse(primates$data$adultMass > 7350, "big", "small")
> adultMass_binary<-as.factor(as.factor(adultMass_binary))
> names(adultMass_binary)<-rownames(primates$data)
> #Model trait evolution accounting for phylogenetic uncertainty
> influ_binary<-influ_discrete(data = adultMass_binary,phy = primates$phy[[1]],
+ model = "SYM",transform = "none",cutoff = 2,n.cores = 2,track = T)
Error in influ_discrete(data = adultMass_binary, phy = primates$phy[[1]],  : 
  T used instead of TRUE
Execution halted

[gijsbertwerner]

Hmm, the influ one is strange because nothing should have changed there. This is probably because with the previous ncores error, it simply quite before even getting to this bit already? Will try and change the T to true, and see if that changes!

[caterinap]

Just changed the two on my computer. No error anymore. Want me to push? It's just two very small things

[paternogbc]

I am working on all the issues, just posting here to keep track. Managed to fix these.

[gijsbertwerner]

No worries, was just working on it myself, and making a few other changes. Will push in a few minutes!

[gijsbertwerner]

Hahaha, ok, we are cross-posting! Have just pushed something which I think should work now, but will leave you to it! :-)

[caterinap]

hhehe ok just tag our names when you need help :)

[gijsbertwerner]

Should be all done now, the other one was easy to, it was simply me accidentally putting the full name sensi_plot.sensiClade.TraitEvol() in the example, rather than sensi_plot().

I think it should all be fine now, perhaps you can pull and redo the CRAN test, @paternogbc ? I am afraid I sort of don't really know anymore how to do it :-(

[paternogbc]

hahhaha =) Yep sure! Thanks a lot =) I think I will be finished with fixing all Errors tonight.

[paternogbc]

Hey @gijsbertwerner , Yep, I will have a look on what you have done and what I have done and try to organize/merge. There still small errors (which are usually easy to fix, like those above) that appear after we fix the first ones... heheh. So it is probably easier if I continue the tests from here. But I can incorporate what you have pushed without conflicting with changes I have done.

I am sure it will be all tight =) and thanks a lot for helping with the solutions. I will tag you guys to ask for help ;).

[gijsbertwerner]

Sounds great, @paternogbc! I will not touch it anymore unless you specifically tag me, so as to prevent conflicting changes :-)

[caterinap]

@paternogbc and @gijsbertwerner : Don't want to interfere with your current commit and create problems when merging or other stuff so just report here things to change:

• [ ] Correct example description in clade, influ, samp(both continuous and discrete): #Model trait evolution accounting for phylogenetic uncertainty (replace with _influentialclades, influential species, sampling size )

[paternogbc]

Awesome, thanks!

On Wed, 6 Dec 2017 at 20:41 Caterina Penone notifications@github.com wrote:

@paternogbc https://github.com/paternogbc and @gijsbertwerner https://github.com/gijsbertwerner : Don't want to interfere with your current commit and create problems when merging or other stuff so just report here things to change:

• Correct example description in clade, influ, samp(both continuous and discrete):

  Model trait evolution accounting for phylogenetic uncertainty

  (replace with influential_clades, influential species, sampling size )

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/paternogbc/sensiPhy/issues/175#issuecomment-349586417, or mute the thread https://github.com/notifications/unsubscribe-auth/AJMWOeFYlvYqSjQvGvhSLNhKaSNabQh_ks5s9mFWgaJpZM4Q1ePH .

--

Gustavo Brant Paterno Doutorando em Ecologia Departamento de Ecologia Universidade Federal do Rio Grande do Norte

email : paternogbc@gmail.com Google Citations: https://scholar.google.com/citations?user=uNxyHMkAAAAJ&hl=pt-BR https://scholar.google.com/citations?user=uNxyHMkAAAAJ&hl=pt-BR Research Gate: https://www.researchgate.net/profile/Gustavo_Paterno2 https://www.researchgate.net/profile/Gustavo_Paterno2 Github: https://github.com/paternogbc Blog : www.Raprendiz.wordpress.com Skype : gustavopaterno Lattes: http://lattes.cnpq.br/3661227833522004

[paternogbc]

@gijsbertwerner and @caterinap all errors wree fixed (working on warnings and notes). I merged both trait_evol and new_diver branches and pushed everything to master. A new issue #176 can be used to post anything we find wrong from now on. IT would be good if we all run cran tests on our machines and post problems there so I can work on the issues at simultaneously.