Reproducible

Rmarkdown

Rmarkdown package

packrat

R packages → packrat

Docker & Singularity

Docker

Misc

• digest: Create Compact Hash Digests of R Objects
• memoise: Memoisation of Functions. Need to understand how it works in order to take advantage. I modify the example from Efficient R by moving the data out of the function. The cache works in the 2nd call. I don't use benchmark() function since it performs the same operation each time (so favor memoise and mask some detail).

  library(ggplot2) # mpg 
  library(memoise) 
  plot_mpg2 <- function(mpgdf, row_to_remove) {
    mpgdf = mpgdf[-row_to_remove,]
    plot(mpgdf$cty, mpgdf$hwy)
    lines(lowess(mpgdf$cty, mpgdf$hwy), col=2)
  }
  m_plot_mpg2 = memoise(plot_mpg2)
  system.time(m_plot_mpg2(mpg, 12))
  #   user  system elapsed
  #  0.019   0.003   0.025
  system.time(plot_mpg2(mpg, 12))
  #   user  system elapsed
  #  0.018   0.003   0.024
  system.time(m_plot_mpg2(mpg, 12))
  #   user  system elapsed
  #  0.000   0.000   0.001
  system.time(plot_mpg2(mpg, 12))
  #   user  system elapsed
  #  0.032   0.008   0.047

And be careful when it is used in simulation.

f <- function() { 
  a <- rnorm(1e5)
  a
} 
system.time(f1 <- f())
mf <- memoise::memoise(f)
system.time(f2 <- mf())
system.time(f3 <- mf())
all.equal(f2, f3) # TRUE

• reproducible: A Set of Tools that Enhance Reproducibility Beyond Package Management