vignettes/profile_calc_act.R

In beast-dev/RBeast: Create BEAST and BEAST2 input files and parse their output

## ------------------------------------------------------------------------
library(RBeast)

## ------------------------------------------------------------------------
trace <- sin(seq(from = 0.0, to = 2.0 * pi, length.out = 10))

## ------------------------------------------------------------------------
n_sizes <- 6
n_types <- 2
elapseds <- data.frame(
  type = as.factor(rep(c("cpp", "r"), times = n_sizes)),
  size = rep(NA, times = n_sizes * n_types),
  t_sec = rep(NA, times = n_sizes * n_types)
)


for (i in seq(1, n_sizes))
{
  # Duplicate input
  trace <- c(trace, trace)
  
  # Measure again
  t_r <- rbenchmark::benchmark(
    RBeast::calc_act_r(trace, sample_interval = 2),
    replications = 1,
    columns = c("elapsed")
  )$elapsed
  t_cpp <- rbenchmark::benchmark(
    RBeast::calc_act(trace, sample_interval = 2),
    replications = 1,
    columns = c("elapsed")
  )$elapsed

  elapseds$size[(i * 2) - 1] <- length(trace)  
  elapseds$size[i * 2]  <- length(trace)
  elapseds$t_sec[(i * 2) - 1] <- t_cpp  
  elapseds$t_sec[i * 2] <- t_r
}

## ------------------------------------------------------------------------

ggplot2::ggplot(
 data = elapseds,
 ggplot2::aes(x = size, y = t_sec, color = type)
) + ggplot2::geom_line() + 
  ggplot2::geom_point() + 
  ggplot2::ggtitle("cpp version is faster")