SIRE Precision Calculator (SIRE-PC)

Disease transmission experiments consist of multiple closed groups of individuals in which initially infected "seeder" individuals transmit their infection to a "contact" population. Data from these experiments can be used by epidemiologists to understand disease spread and the factors affecting it.

SIRE-PC takes as inputs details of a given experimental design (in particular the number and genetic composition of seeders and contacts in each group and the number of replicates being carried out) and outputs analytical estimates for the standard deviations in SNP or vaccination effect parameters affecting the susceptibility, infectivity and recoverability of individuals.

Establishing good experimental design is achieved by adjusting the input values, subject to any limitations imposed on the experiment being carried out (e.g. the number individuals per group may be fixed), with the aim of minimising these output standard deviations. To facilitate this process the tool includes the optimal solutions for five experimental designs as well as providing the option for arbitrary user-defined designs to be investigated.

It is important to note that the estimates provided by this tool represent lower bounds on the standard deviations of model parameters. Environmental noise, confounding with fixed effect and incomplete data (e.g. only individual death events known) will all act to increase these standard deviations, and so reduce the statistical power with which SNP or vaccination-based associations can be made.

SIRE-PC is provided freely for anyone to use under a GNU General Public License. We only request that those who use SIRE-PC analysis in their publications cite this tool. It can run in the web browser by clicking on the open icon: