The R code is not reproducible. I got stuck on the first few lines.

Line 40 - TB <- read.csv('TB_data.csv')
Error in file(file, "rt") : cannot open the connection
In addition: Warning message:
In file(file, "rt") :
cannot open file 'TB_data.csv': No such file or directory

I tried to use the file that was there but I ended up with an error from the join -
TB<-read.csv("TB_dataset_SAB_Tree.csv")
# join TB and climate
data <- left_join(TB, climate, by=c("Location_elev"="loc_elev_match_correct"))

# remove rows with missing TB or temperature data
data <- data[!is.na(data$TB),] dim(data)# 209 66 data <- data[!is.na(data$annual_range),] # n = 214
dim(data)# 0 66
I assume this is the incorrect file.

Please provide reproducible code and the correct data.

Please see the attached file

Great stuff! Thank you for making those changes.
There are a few small things that need to be changed-

first, please do not use rm(list=ls()). This is actually bad practice (despite being on every blog and "help" source for R!) By doing this (if I dont notice) you can delete all my day's work in one line of code. If you think the user needs to start a new session to make the models run then please add a comment- although in your case this is not needed (for my system at least).

The second thing is a missing comma in the code block header in Tbr_analysis block 2 (package loading).

The third is that sessionInfo() shows my sessionInfo not yours - you will need to paste it in as text.

Finally in line 2407: # Calculate phylogenetic signal (Blomberg’s K)
result <- phylosignal(trait, species_tree_resolved,nsim=999) You need to change nsim to "reps" (I suspect this is a version mismatch)

Thanks again for making these changes - the code runs great now and is fully reproducible.