hopkinsidd / idspatialstats

IDSpatialStats

This GitHub repository provides source code for the IDSpatialStats R package, which is designed to help epidemiologists assess the scale of spatial and temporal dependence in epidemic case occurrence data.

The current implementation of the package includes a function which simulates infectious disease spread as a spatial branching process, along with two novel spatial statistics that estimate: 1) the mean of the spatial transmission kernel, which is a measure of fine-scale spatial dependence between two cases, and 2) the tau-statistic, a measure of global clustering based on pathogen subtype.

Detailed description of the methods can be found here:

The IDSpatialStats R package: Quantifying spatial dependence of infectious disease spread (Giles et al. 2019)

Measuring spatial dependence for infectious disease epidemiology (Lessler et al. 2016)

Estimating infectious disease transmission distances using the overall distribution of cases (Salje et al. 2016)

Installation

To install the offical release of the IDSpatialStats package, open R and type:

install.packages('IDSpatialStats')

To install the install the development version, first install the devtools package and then install IDSpatialStats from source via GitHub:

install.packages('devtools')
devtools::install_github('HopkinsIDD/IDSpatialStats')

Troubleshooting

For general questions, contact package maintainers Justin Lessler ([email protected]) or John Giles ([email protected]).

To report bugs or problems with documentation, please go to the Issues page associated with this GitHub page and click new issue.

If you wish to contribute to IDSpatialStats, please get in touch via email and then fork the latest version of the package. After committing your code to your own forked version, submit a pull request when you are ready to share.

idspatialstats's Issues

Error in quantile.default(newX[, i], ...) : missing values and NaN's not allowed if 'na.rm' is FALSE

Hello John,

Thanks very much to the team for updating the package, and the helpful R journal article. I have been successfully running the package until recently when I encountered this error, after about an hour of runtime (using some data on cholera cases over a 1-year period).

I am unable to trace its origin, so far, but I think it's related to the get.tau.ci function and adding add na.rm = TRUE in the quantile() call for constructing the CIs. Indeed, I'm not sure if it's an issue with the package. Thank you for any insight you may be able to provide.

Error:

Error in quantile.default(newX[, i], ...) : 
  missing values and NaN's not allowed if 'na.rm' is FALSE
Called from: quantile.default(newX[, i], ...)

From traceback:

eval(substitute(browser(skipCalls = pos)
get_tau.ci
get_tau_and_cis
run_main_analysis