Nothing
### Initial
suppressMessages(library(pbdDEMO, quietly = TRUE))
library(phyclust, quietly = TRUE)
### Load data
data.path <- paste(.libPaths()[1], "/phyclust/data/pony524.phy", sep = "")
pony.524 <- read.phylip(data.path)
X <- pony.524$org
K0 <- 1
Ka <- 2
### Find MLEs
if(comm.rank() == 0){
ret.K0 <- find.best(X, K0)
ret.Ka <- find.best(X, Ka)
} else{
ret.K0 <- NULL
ret.Ka <- NULL
}
### Broadcast fitted models to all workers
ret.K0 <- bcast(ret.K0)
ret.Ka <- bcast(ret.Ka)
LRT <- -2 * (ret.Ka$logL - ret.K0$logL)
### The user defined function
FUN <- function(jid){
X.b <- bootstrap.seq.data(ret.K0)$org
### find.best is recommended, but more time-consuming
# ret.K0 <- find.best(X.b, K0)
# ret.Ka <- find.best(X.b, Ka)
ret.K0 <- phyclust(X.b, K0)
repeat{
ret.Ka <- phyclust(X.b, Ka)
if(ret.Ka$logL > ret.K0$logL){
break
}
}
LRT.b <- -2 * (ret.Ka$logL - ret.K0$logL)
# cat("comm.rank:", comm.rank(), " jid:", jid, "LRT:", LRT.b, "\n")
LRT.b
}
### Task pull and summary
ret <- task.pull(1:100, FUN)
if(comm.rank() == 0){
LRT.B <- unlist(ret)
cat("K0: ", K0, "\n",
"Ka: ", Ka, "\n",
"logL K0: ", ret.K0$logL, "\n",
"logL Ka: ", ret.Ka$logL, "\n",
"LRT: ", LRT, "\n",
"p-value: ", mean(LRT > LRT.B), "\n", sep = "")
}
### Finish
finalize()
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