cmt2

# randomly sample a tree for this example
t <- rtree(10)
# check that the example tree is a phylo object
class(t) == "phylo"
# convert to RevGadgets plotting format 
t_td <- convertTreeFormat(t) # [note, run the function code below before executing this line of code]


# The function:
# `tree` is the argument for your phylo object.

cmt2

##### Script to check if the authors of a paper have co-authored with 
##### a potential reviewer within the past 4 years (following COI for 
##### NSF and various journals). I make o guarantees this will work, 
##### as name changes, variations in spellings, etc. might interfere
##### with the code. Please note that this does not check for other 
##### potential conflicts such as mentorship relationships, etc.


library(lubridate)
library(scholar)

cmt2

readStochasticMaps <- function(map_paths, 
                               burnin = 0.1,
                               combine_runs = TRUE) {
  
  # read in map logs and remove burnin
  maps <- vector("list", length = length(map_paths))
  for (i in 1:length(map_paths)) {
    message(paste0("Reading in map log file ", i, "\n",
                   "This may take a while."))
    maps[[i]] <- read.table(file = map_paths[i], 

cmt2

bgb_to_revgadgets <- function(results_path, geo_data_path, tree_path, area_names = NULL) {
  # load biogeobears results object
  load(results_path)
  # change data directories in results object
  res[["inputs"]]$geogfn <- geo_data_path
  res[["inputs"]]$trfn <- tree_path
  
  ##### Process data for plotting ##### 
  
  # read in tree separately