## Run this file by sourcing it, ot doing
## Rscript bm-timing.R
##
## This caches the timing results (which takes about ) in some .Rdata files.
library(diversitree)
source("bm-timing-fun.R")
n.taxa <- 2^(4:12)
obj <- run.cached("timings.Rdata",
timings(n.taxa, 10))
obj.err <- run.cached("timings-err.Rdata",
timings(n.taxa, 10, states.sd=1e-7))
times <- sapply(obj, sapply, function(x) mean(x[,"t.each"]))
times.err <- sapply(obj.err, sapply, function(x) mean(x[,"t.each"]))
to.pdf("bm-timing.pdf", 5, 5,
fig.timing(n.taxa, times, times.err))
if ( FALSE ) { # don't run by default
## Here is the estimated exponent of qudratic growth:
i <- (length(n.taxa)-1):(length(n.taxa))
diff(log(times[i,]))/diff(log(n.taxa[i]))
diff(log(times.err[i,]))/diff(log(n.taxa[i]))
## Timing ratios:
times[9,1] / times[9,]
times.err[9,1] / times.err[9,]
}
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