FabienCondamine
commented
4 years ago Dear Kateryn,
One simple way to do this is as follows:
missing.lineages <- # a numerical value for your total clade species diversity trees <- read.tree("Posteriors_trees.tre") #Can be read.nexus() especially if posterior trees come from a BEAST analysis subsampled.trees <- sample(trees, 100)
for (i in 1:length(subsampled.trees)) { tree <- subsampled.trees[[i]] tot_time <- max(node.age(tree)$ages) f <- Ntip(tree)/(Ntip(tree)+missing.lineages) cond = "crown"
print("BTempVar EXPO") f.lamb<-function(t,x,y){y[1]exp(y[2]x)} f.mu<-function(t,x,y){0} lamb_par<-c(0.1,0.0) mu_par<-c() cst.lamb=F; cst.mu=T; expo.lamb=F; expo.mu=F; fix.mu=T
tree_BTempVar_EXPO <- fit_env(tree, env_data, tot_time, f.lamb, f.mu,lamb_par, mu_par, f=f, cst.lamb=cst.lamb, cst.mu=cst.mu, expo.lamb=expo.lamb, expo.mu=expo.mu, fix.mu=fix.mu, cond=cond, dt=1e-3)
print(tree_BTempVar_EXPO)}
Of course, you need to create an object (list, vector, matrix) to store the results for each tree of your distribution. Also, you need to load the temperature data, here named env_data in the fit_env function (e.g. data(InfTemp)).
I hope this helps. Don't hesitate if you have any questions.
Best regards,
KaterynPino
JClavel
Hello,
I want to fit the environmental-dependent models in RPANDA, but with a sample of trees, but I don't know-how. All the examples I found are with a single tree. There is some script to do this?. A lot of thanks!
Cheers,
Kateryn