revgadget issue for "Environmental-dependent Speciation & Extinction Rates"

[claudiavaga]

Dear all,

I am trying to use RevGadget to plot the results of the Environmental-dependent Speciation & Extinction Rates analyses.
The original code in the tutorial is the following:

library(RevGadgets)
tree <- read.tree("data/primates.tre")

the CO2 values as a reference in our plot
co2 <- c(297.6, 301.36, 304.84, 307.86, 310.36, 312.53, 314.48, 316.31, 317.42, 317.63, 317.74, 318.51, 318.29, 316.5, 315.49, 317.64, 318.61, 316.6, 317.77, 328.27, 351.12, 381.87, 415.47, 446.86, 478.31, 513.77, 550.74, 586.68, 631.48, 684.13, 725.83, 757.81, 789.39, 813.79, 824.25, 812.6, 784.79, 755.25, 738.41, 727.53, 710.48, 693.55, 683.04, 683.99, 690.93, 694.44, 701.62, 718.05, 731.95, 731.56, 717.76)

MAX_VAR_AGE = 50
NUM_INTERVALS = length(co2)
co2_age <- MAX_VAR_AGE * (1:NUM_INTERVALS) / NUM_INTERVALS
predictor.ages <- co2_age
predictor.var <- co2

rev_out <- rev.process.div.rates(speciation_times_file = "output/primates_EBD_Corr_speciation_times.log",
speciation_rates_file = "output/primates_EBD_Corr_speciation_rates.log",
extinction_times_file = "output/primates_EBD_Corr_extinction_times.log",
extinction_rates_file = "output/primates_EBD_Corr_extinction_rates.log",
tree=tree,
burnin=0.25,numIntervals=100)
pdf("EBD_Corr.pdf")
par(mfrow=c(2,2))
rev.plot.div.rates(rev_out, predictor.ages=co2_age, predictor.var=co2, use.geoscale=TRUE)
dev.off()

Which I tried to modify (following the current version of the RevGadget function to plot branch data) into this:

library(RevGadgets)
tree <- read.tree("291species-50p-sclera.newick.tre")

temp <- c(11.44, 16.94, 20.62, 23.60, 23.78, 24.06, 22.07, 23.44, 23.40, 26.08, 28.03, 26.99, 32.28, 33.59, 25.60, 28.85, 24.51, 28.13, 31.42, 32.26, 35.56, 34.14, 26.01, 32.00, 30.52, 27.27, 28.25, 27.00, 27.27, 24.47, 23.88, 20.11, 17.77, 21.39, 23.20, 26.37, 24.10, 25.06, 22.32, 25.02, 23.43, 19.18, 25.82, 28.50, 18.02, 22.19, 18.68, 13.50, 18.70, 20.76, 20.80, 20.25, 16.55, 14.46, 18.09, 14.08, 12.02, 12.83, 21.75, 23.76, 27.91, 25.67, 22.49, 25.29, 28.81, 33.25, 34.05, 25.60, 20.97, 19.90, 24.36, 19.48, 20.80, 27.85, 27.31, 31.00, 30.90, 31.53, 32.10)

MAX_VAR_AGE = 482
NUM_INTERVALS = length(temp)
temp_age <- MAX_VAR_AGE * (1:NUM_INTERVALS) / NUM_INTERVALS
predictor.ages <- temp_age
predictor.var <- temp

speciation_time_file <- "scleractinia_temp_corr_speciation_times.log"
speciation_rate_file <- "scleractinia_temp_corr_speciation_rates.log"
extinction_time_file <- "scleractinia_temp_corr_extinction_times.log"
extinction_rate_file <- "scleractinia_temp_corr_extinction_rates.log"

rates <- processDivRates(speciation_time_log = speciation_time_file,
speciation_rate_log = speciation_rate_file,
extinction_time_log = extinction_time_file,
extinction_rate_log = extinction_rate_file,
tree=tree,
burnin=0.25,numIntervals=100)

pdf("sclera_temp_corr.pdf")
par(mfrow=c(2,2))
plotDivRates(rates, predictor.ages=temp_age, predictor.var=temp, use.geoscale=TRUE)
dev.off()

However, I am running into this error:

plotDivRates(rates, predictor.ages=temp_age, predictor.var=temp, use.geoscale=TRUE)
Error in plotDivRates(rates, predictor.ages = temp_age, predictor.var = temp, :
unused arguments (predictor.ages = temp_age, predictor.var = temp, use.geoscale = TRUE)

Error in processDivRates(speciation_time_log = speciation_time_file, speciation_rate_log = speciation_rate_file, :
unused argument (tree = tree)

Can anyone help me figure out how to troubleshoot this code?

Thanks in advance for the help!
Claudia