Reproducible

Common Workflow Language (CWL)

Workflow systems turn raw data into scientific knowledge. Pipeline, Snakemake, Docker, Galaxy, Python, Conda, Workflow Definition Language (WDL), Nextflow. The best is to embed the workflow in a container; see Developing reproducible bioinformatics analysis workflows for heterogeneous computing environments to support African genomics by Baichoo 2018.

R

Rcwl package

Rmarkdown

Rmarkdown package

packrat

R packages → packrat

Docker & Singularity

Docker

Misc

• digest: Create Compact Hash Digests of R Objects
• memoise: Memoisation of Functions. Great for shiny applications. 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(n=1e5) { 
  a <- rnorm(n)
  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