Post tagged: reproducibility

by Paul Agapow
in science

tagged knitr, r, reproducibility, restructured-text

Writing knitr in restructured text

Swapping out Markdown for a different markup.

knitr is a useful R package/tool for documenting analysis. Basically, it allows the embedding of R code "chunks" within a simple text document. This document can then be "knitted", which means that the R code is interpreted and reinserted in the document along with the results of that code …

by Paul Agapow
in software

tagged reproducibility, python, software

psicons.core

A tool for documentable and reproducible analysis and research.

Note

Although I used psicons heavily for a while, better and more humane tools have come along. In particular, I'd recommend snakemake. This page is left here for historical interest

Background

Scientific analysis can be problematic:

  • It may involve multiple steps, each using the results of the previous stage.  Making …