DPLYR 1.0.6 issue analyzing biogeobears outputs

[coyotree]

I'm not skilled at cross posting but if you receive the error "Error in DataMask$new(.data, caller_env) : argument "caller_env" is missing, with no default", consider loading dplyr 1.0.5. That fixed my problem when analyzing BioGeoBEARS data using RevGadgets.

Post with correction:
YuLab-SMU/ggtree#399

[RhettRautsaw]

@coyotree How did you convert BioGeoBEARS output list "res" to treedata that can be read and plotted by RevGadgets?

[coyotree]

This all came from @cmt2! The script to convert is attached (or should be, I'm bad at github). It also be found in RevGadgets but I am not sure.

library(devtools)
#install_github(repo="nmatzke/BioGeoBEARS")
library(BioGeoBEARS)
#install_github("cmt2/RevGadgets")
#install_github("GuangchuangYu/ggtree")
library(RevGadgets)
#install.packages("tidytree")
library(tidytree)
#install.packages("tidyverse")
library(tidyverse)
#install.packages("naniar")
library(naniar)
#install_github("willgearty/deeptime")
library(deeptime)

setwd("working_directory")

source("bgb_to_revgadgets.R")

# Begin RevGadgets plotting section
results_path <- "DECJ.Rdata"
geo_data_path <- "geography.file.phy"
tree_path <- "tree.tre"

res_formatted <- bgb_to_revgadgets(results_path = results_path,
                                   geo_data_path = geo_data_path,
                                   tree_path = tree_path)

# gonna need a lot of colors 
n <- length(attributes(res_formatted)$state_labels) 
col_vector <- colorRampPalette(colFun(12))(n)
names(col_vector) <- attributes(res_formatted)$state_labels

pdf("plot1.pdf", width = 10, height = 40)
plotAncStatesMAP(t = res_formatted, cladogenetic = F, tip_labels_size = 1, node_labels_as = "state", 
                 node_labels_size = 1, node_shape = 15, node_labels_centered = T, tip_labels_offset = 5, node_color = col_vector, node_size_as = NULL,
                 node_size = 2, tip_labels_states = T, tip_labels_states_size = 1, tip_labels_states_offset = 1,
                 timeline = T, state_transparency = 1)
dev.off()

pdf("plot2.pdf", width = 10, height = 20)
plotAncStatesPie(t = res_formatted, cladogenetic = TRUE, node_pie_size = .3, tip_labels_states = T, 
                 tip_pies = FALSE, tip_labels_size = 1, timeline =T, node_labels_as = "state",
                 tip_labels_offset = 2, pie_colors = col_vector) +
  ggplot2::theme(legend.position = c(0.2, 0.8)) +
  ggplot2::theme(legend.text = element_text(size = 2))

dev.off()

bgb_to_revgadgets.txt

[RhettRautsaw]

Thanks @coyotree!! I haven't seen this function anywhere, but that is very useful.