paternogbc
commented
6 years ago Hey @gijsbertwerner , I got the following error when trying to run model = "BM" in tree_continous:
#' #Load data:
data("primates")
#' #Model trait evolution accounting for phylogenetic uncertainty
adultMass<-primates$data$adultMass
names(adultMass)<-rownames(primates$data)
tree_cont<-tree_continuous(data = adultMass,phy = primates$phy,
model = "BM",n.tree=10,n.cores = 2,track = TRUE)
Error or in data.frame(j, sigsq, optpar, z0, aicc, stringsAsFactors = F) :
object 'optpar' not foundShould I just include the following line of code to fix the issue?:
if (model == "BM"){optpar <- NA}
Or the model BM is trully not possible?
caterinap
gijsbertwerner
Anything we find wrong or need to be done, please lets post here =) We could follow Caterina style (and check things when they are done).
Remember to always pull and re-build the package before testing. =)
[x] 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 )[x] When running check, got error: checking whether package 'sensiPhy' can be installed ... ERROR Installation failed.
[x] '::' or ':::' import not declared from: ‘geiger’
[x] Missing link or links in documentation object 'sensi_plot.sensiTree.TraitEvol.Rd': ‘[sensiPhy]{tree_fitDiscrete}’ ‘[sensiPhy]{tree_fitContinuous}’ See section 'Cross-references' in the 'Writing R Extensions' manual.
[x] checking R code for possible problems ... NOTE sensi_plot.sensiClade.TraitEvol: no visible binding for global variable ‘estimate’ sensi_plot.sensiClade.TraitEvol: no visible binding for global variable ‘model’ sensi_plot.sensiInflu.TraitEvol: no visible global function definition for ‘median’ sensi_plot.sensiSamp.TraitEvol: no visible binding for global variable ‘sigsq’ sensi_plot.sensiSamp.TraitEvol: no visible binding for global variable ‘q12’ sensi_plot.sensiSamp.TraitEvol: no visible binding for global variable ‘q21’ sensi_plot.sensiTree.TraitEvol: no visible global function definition for ‘median’ tree_continuous: no visible binding for global variable ‘median’ tree_continuous: no visible binding for global variable ‘sd’ tree_discrete: no visible binding for global variable ‘median’ tree_discrete: no visible binding for global variable ‘sd’ Undefined global functions or variables: estimate median model q12 q21 sd sigsq Consider adding importFrom("stats", "median", "sd") to your NAMESPACE file.
[x] checking Rd line widths ... NOTE
Rd file 'clade_discrete.Rd': \examples lines wider than 100 characters: clade_disc_2<-clade_discrete(data=primates$data,phy = primates$phy[[1]],model="ARD",transform="kappa",
Rd file 'influ_continuous.Rd': \examples lines wider than 100 characters:
Print summary statistics for the transitions rates, aic-values and (if applicable) optimisation parameter
Rd file 'influ_discrete.Rd': \examples lines wider than 100 characters:
Print summary statistics for the transitions rates, aic-values and (if applicable) optimisation parameter
Rd file 'samp_continuous.Rd': \examples lines wider than 100 characters:
Print summary statistics for the transitions rates, aic-values and (if applicable) optimisation parameter
Rd file 'samp_discrete.Rd': \examples lines wider than 100 characters:
Print summary statistics for the transitions rates, aic-values and (if applicable) optimisation parameter
Rd file 'tree_continuous.Rd': \examples lines wider than 100 characters:
Print summary statistics for the transitions rates, aic-values and (if applicable) optimisation parameter
Rd file 'tree_discrete.Rd': \examples lines wider than 100 characters:
Print summary statistics for the transitions rates, aic-values and (if applicable) optimisation parameter