https://github.com/mrc-ide/squire.page

Extra functions for use with squire and nimue fits
https://github.com/mrc-ide/squire.page

Last synced: about 2 months ago
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Extra functions for use with squire and nimue fits

• Host: GitHub
• URL: https://github.com/mrc-ide/squire.page
• Owner: mrc-ide
• License: other
• Created: 2021-11-16T18:07:14.000Z (about 3 years ago)
• Default Branch: main
• Last Pushed: 2023-05-09T10:43:23.000Z (over 1 year ago)
• Last Synced: 2023-10-17T07:17:40.863Z (about 1 year ago)
• Language: C
• Homepage: https://mrc-ide.github.io/squire.page/
• Size: 27.7 MB
• Stars: 2
• Watchers: 2
• Forks: 3
• Open Issues: 4
• Metadata Files:
  • Readme: README.Rmd
  • License: LICENSE

Awesome Lists containing this project

README

        
---

output: github_document

---

```{r, include = FALSE}

knitr::opts_chunk$set(

  collapse = TRUE,

  comment = "#>",

  fig.path = "man/figures/README-",

  out.width = "100%"

)

```

# squire.page

This package stores miscellaneous R functions used in the repo [global-lmic-reports](https://github.com/mrc-ide/global-lmic-reports-orderly) 

and other repos that use [nimue](https://github.com/mrc-ide/nimue) fits. The 

thinking behind storing these as an external package means that they can be kept

consistent across multiple repos and [orderly](https://github.com/vimc/orderly)

tasks. The majority of functions are variations on the fitting functions in

[squire](https://github.com/mrc-ide/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](https://mrc-ide.github.io/squire.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](https://github.com/mrc-ide/nimue) and

[squire](https://github.com/mrc-ide/squire).

You can install squire.page like so:

``` r

#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