issue with ph_aot with phylo files:

[Jez-R]

Session Info

version R version 3.6.0 (2019-04-26) os macOS 10.15.1 system x86_64, darwin15.6.0 ui RStudio language (EN) collate en_AU.UTF-8 ctype en_AU.UTF-8 date 2019-11-19

I'm having an issue with ph_aot trying to import phylogenies from phylo files:

Error in seq.default(from = grep("Trait conservatism by node", out) + : 'from' must be of length 1

The example from the vignette - readLines(phylo_file) - works fine, but I can't figure out the issue importing phylo objects. Apologies in advance if this is something basic.

Example code below:

library(ape)
data(bird.orders)
tree <- (bird.orders)

traits <- data.frame("name" = 1:23)

traits$name <- tree$tip.label
traits$traitA <- rbinom(23, 1,.5)
traits$traitB <- rbinom(23, 1,.5)
traits$traitC <- rbinom(23, 1,.5)
traits$traitD <- as.integer(floor(runif(23, 1,5)))

tree$tip.label %in% traits$name
tree2 <- write.tree(tree)

ph_aot(traits = traits, phylo = tree)
ph_aot(traits = traits, phylo = tree2)

[sckott]

thanks for the report - for session info what we mean is, load the package in question first, then run session info, so we know what versions of packages you have installed. What version of phylocomr do you have?

[Jez-R]

Sorry about that (long time listener, first time caller). Hope this is correct.

R version 3.6.0 (2019-04-26)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS  10.15.1

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib

locale:
[1] en_AU.UTF-8/en_AU.UTF-8/en_AU.UTF-8/C/en_AU.UTF-8/en_AU.UTF-8

attached base packages:
[1] parallel  grid      stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] phylocomr_0.2.0

[sckott]

working on a solutino

[Jez-R]

Many thanks! Also with the above code, it should be:

data(bird.orders) tree <- (bird.orders)

[sckott]

right, i figured that out 😉

[sckott]

@Jez-R reinstall remotes::install_github("ropensci/phylocomr") and try again