# Software and Toolkit

This page gives links to my software and projects I am working on, and describes the tools I use for data analysis and modelling.

# Personal

- Github: My personal github page
- ggfan Github homepage of the R package I authored for the plotting of probability distributions. Based on
`fanplot`

# Software and toolkit

This section describes the tools I use for research and data analysis.

## R

R is a free and open source statistical programming language

- CRAN R's home. Repository for R packages.
- Tidyverse Suite of R libraries for the tidy analysis of data. Tidy data is data store as a table where every column represents one variable and every row represents one (and only one) observation. Storing data in this way makes data processing and visualisation The tidy data allows data processing and analysis task to be written in an easily understandable way. Each step in the analysis can be represented by a function, which are generally named after the verb which describes the task they perform (e.g. "filter", "summarise"). The complete anaylsis is then just a chain (or pipeline) of such functions.
- rmarkdown Markdown is a simple syntax for the writing of documents in plain text. R markdown allows one to interweave markdown documents with R code chunks.
- knitr Knitr runs code chunks in documents written in rmarkdown or in latex and inserts their outputs, or a reference to the relevant figures.

## Python

- jupyter Python notebooks
- sympy Symbolic maths package for python. Allows for symbolic manipulation of mathematical expressions, including differentiation and integration.
- pymc3 Bayesian Sampling package for python, utilising Theano.
- pelican Static website generator with which this blog is constructed.

## Other

- ubuntu Linux OS distribution.
- pandoc Coverts between markdown, .doc, html, latex and various other formats.
- sublime Text editor in which I am writing this!
- stan Bayesian Sampling
- mingw Linux Command line tools for windows.
- git Decentralised version control system.
- hg Another decentralised version control system.

I use the University of Southampton's supercomputer, `iridis`

, to do heavy computational lifting. Mostly this involves embarrassingly parallel tasks such as running simulations over experimental design points, or running variants of a family of statistical models for purposes of model comparison.