Theo Pepler

Software

The software packages listed below are for the R programming language for statistical computing. You will therefore need a working installation of R (freely downloadable from one of the many CRAN mirrors), from which you can follow the installation instructions given here.

Some additional packages are available in repositories on my GitHub account.

cpc: Common principal component (CPC) analysis and applications
This package contains tools for common principal component (CPC) analysis and applications of the CPC model to various other statistical techniques. Functions are available for covariance matrix estimation, discriminant analysis and biplots, all under the CPC model.
EPIC.SimInf: EPIC package for epidemiological simulation modelling using SimInf
Extract and tidy data from the EPIC server, to be used for epidemiological simulation modelling with the SimInf R package. This package was developed as an extension of the SimInf package for use by members of the Scottish Government's Centre of Expertise on Animal Disease Outbreaks (EPIC).
harbin: Harbin quantification for RT-qPCR data
Performs Harbin quantification for reverse transcription quantitative PCR (RT-qPCR) data. Currently offers support only for files produced by the Qiagen Rotor-Gene Q thermal cycler, but the package can be extended per request to support other technologies.
nonpar: Collection of methods for non-parametric analysis
This package contains methods for non-parametric data analysis. At the moment only some tests for the two-sample location-scale problem are given, but more will be added in future versions.
ssaCUSUM: SSA-CUSUM for surveillance of time series data
Functions to perform the SSA-CUSUM (Singular Spectrum Analysis CUmulative SUM) procedure on a univariate time series. It is a nonparametric technique, useful for the monitoring of surveillance data with/without seasonal (or other types of cyclical) variation.
theolib: Collection of auxiliary functions
A collection of various auxiliary functions to ease matrix manipulation in R. This package may contain code for functions (and wrappers for functions) already implemented in other R packages, but is mostly for my personal use.