ojwatson / squire.page

Extra functions for use with squire and nimue fits

squire.page

This package stores miscellaneous R functions used in the repo global-lmic-reports and other repos that use nimue fits. The thinking behind storing these as an external package means that they can be kept consistent across multiple repos and orderly tasks. The majority of functions are variations on the fitting functions in squire. These are not added to the base squire or nimue packages as they are too specific in their usage.

Named after the position typically held before a becoming a squire.

Contents

Please see the GitHub page for more information.

Likelihood and MCMC functions for the excess mortality fitting. These account for fitting to weekly data and not daily, and also allow for poisson instead of negative binomial fitting.

Likelihood functions for the LMIC-reports. These allow fitting to cases at the tail of the epidemic and time varying hospitalisation modifiers (should be added to squire at some point).

Functions to simulate draws from model output given different numbers of vaccines. Also a similar function from the LMICs (should simplify this).

Functions for setting up future scenarios in the LMIC projections.

A different method for fitting any squire/nimue model by adjusting Rt values over short periods of time.

Various functions for plotting R and deaths over time, should be compatible with any version of the fits.

Installation

This package depends on both nimue and squire. You can install squire.page like so:

#devtools::install_github("mrc-ide/squire")
#devtools::install_github("mrc-ide/nimue")
devtools::install_github("mrc-ide/squire.page")

To Do:

• Ensure all functions are documented