The tsir from adbecker

tsir's Introduction

tsiR: An R package for time-series Susceptible-Infected-Recovered models of epidemics

Information regarding this package and a short tutorial can be found here: http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0185528

If you've found the package useful in your research, I ask that you cite the above PLOS ONE paper.

This package can be installed via CRAN. Updates to the package post the PLOS ONE paper will follow below as they occur.

Note : 03/15/2019

This warning message was added to V.0.4.1 but worth adding here as well -- if you find very unreasonable reporting rates along either endpoints or in highly variable epidemic regions using a gaussian regression, it may be worth reducing 'sigmamax' in either runtsir or estpars away from the default of 3 close to 0.5 or so.

Update V.0.4.1 : Minor update 01/29/2019

The tsiR package has been updated to include further warning messages, bug fixes, and further annotations.

Update V.0.4.0 : Lyapunov Analysis 08/20/2018

The tsiR package has been updated to include Global and Local Lyapunov Exponents. You can learn more and find examples of how to use this function for the London data by typing ?TSIR_LE ?TSIR_LLE and ?plotLLE in the R console. This updateis now on CRAN.

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tsir's Issues

Error: Either ymin or ymax must be given as an aesthetic. in plotres(LondonRes)

I am trying your example in the documentation and while running the following code:

library(tsiR)
LondonMeas <- twentymeas[["London"]]

LondonRes <- runtsir(data=LondonMeas, IP = 2,
                     xreg = 'cumcases', regtype='gaussian',
                     alpha = NULL, sbar = NULL,family = 'gaussian', link = 'identity', method = 'negbin', nsim = 100)
plotres(LondonRes)

only first four plot is published and I get this error:

plotres(LondonRes)
Error: Either ymin or ymax must be given as an aesthetic.
Run rlang::last_error() to see where the error occurred.
In addition: Warning message:
Ignoring unknown aesthetics: fill

Interested in using for NYT COVID model

I came across your package in a search for a time series approach on modeling the NYT COVID data https://github.com/nytimes/covid-19-data.

After reading https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0185528 I still think I have not used the tsiRdata function correctly.

Ideally we would like to use mcmcestpars followed by simulatetsir, correct?

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