simjoly / coursecomparativemethods Goto Github PK

Hi,
thanks for making all this material available, I learn quite a bit through your lectures!

I have an issue with code from lecture 4, more specifically this line:
height.dat<-data.frame(code=rownames(seedplantsdata),height=as.numeric(seedplantsdata$height))
which throws this warning message:
In data.frame(code = rownames(seedplantsdata), height = as.numeric(seedplantsdata$height)) : NAs introduced by coercion
which makes sense since height is factor (small, medium, large) and can't be cast as numeric (or?)
Is there an error in the script or am I making a stupid mistake somewhere?

Thanks again!

install.packages("~/Desktop/lecture1/data/phyloch_1.5-3_R_x86_64-apple-darwin10.8.0.tar", repos = NULL)
Installing package into ‘/Users/lixingguang/Library/R/x86_64/4.1/library’
(as ‘lib’ is unspecified)
Error in install.packages : type == "both" cannot be used with 'repos = NULL'

Thank you so much for making all the lectures available online! I have learnt alot from them!

I was wondering if its possible (R package already available) to plot the variation in a tree using variable rate model?
I ran BayesTrait and found that there is a strong evidence of variation of trait with time. The analysis also generates a Output tree file. But it only stretches/shrinks the tree with different rate of change. I wanted to ask if there is a way to map it on a tree using heatmap? [like contMap in phytools]