Dendroica

Dendroica estimations for diversity-dependence model

setwd("~/Dropbox/Code/dmea/dat4")
dendroica =  read.csv(file = 'Dendroica_branchtimes.csv',header = F,sep = ',')
dendroica = rev(as.numeric(matrix(dendroica)))
bt = diff(dendroica )
init_pars = c(1,0.03,0.2)
pars=init_pars

EM_phylo(wt=bt,init_par = pars,n_trees=300,tol=0.01,parallel = T)

## [1] 1.00 0.03 0.20
## [1] "iteration 1 took 9.663 seg"
## [1] 1.1003453 0.0341850 0.1764066
## [1] "iteration 2 took 9.313 seg"
## [1] 1.08407452 0.03342843 0.17132256
## [1] "iteration 3 took 9.55 seg"

## $pars
## [1] 1.09271430 0.03375342 0.17492664

Foraminifera estimations for diversity-dependence model

setwd("~/Dropbox/Code/dmea/dat4")
foraminifera = read.csv(file='foraminifera_branchtimes.csv',header=F,sep=',')
foraminifera = rev(as.numeric(matrix(foraminifera)))
bt = diff(foraminifera)
pars=init_pars

EM_phylo(wt=bt,init_par = pars,n_trees=300,tol=0.01,parallel = T)

## [1] 1.00 0.03 0.20
## [1] "iteration 1 took 22.396 seg"
## [1] 0.225214652 0.006417795 0.030670503
## [1] "iteration 2 took 19.046 seg"
## [1] 0.132868672 0.003405879 0.011342998
## [1] "iteration 3 took 16.57 seg"
## [1] 0.112722051 0.002889775 0.009103474
## [1] "iteration 4 took 13.507 seg"
## [1] 0.101881979 0.002680743 0.007255854
## [1] "iteration 5 took 13.464 seg"

## $pars
## [1] 0.097294380 0.002629404 0.005775224