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realTimeSurv (version 1.0)

Real Time Disease Surveillance Using Geospatial Statistical Modelling

Description

Convenient tools and data for the real-time surveillance of infectious disease and various visualisation and reporting tools. The package serves as a wrapper to a variety of geostatistical ('lgcp', 'sp', 'rgeos', etc.) and plotting packages ('ggplot2', 'ggmap', 'ggspatial', etc. ) for R, and is intended to enable rapid deployment of real-time surveillance statistical software.

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Version

Install

install.packages('realTimeSurv')

Monthly Downloads

1

Version

1.0

License

CC BY-SA 4.0

Maintainer

Sam Watson

Last Published

May 18th, 2021

Functions in realTimeSurv (1.0)

lgcpST

Alternative to lgcpPredictSpatioTemporalPlusPars
plot.lgcpReal

Real-time surveillance plot
dat

Simulated point process data set
plot_data

Create spatial pixels data frame
plot_hotspot

Hotspot mapping and visualisation
plot_hotspot_data

Produce hotspot spatial pixels data
plot_lgcp_dat

Extract data from an lgcpReal object
print.lgcpReal

Print function for lgcpReal
print.lgcpRealSumm

Print function for lgcpRealSumm
print.lgcpRealPlot

Print function for lgcpRealPlot
summary.lgcpReal

Summarise lgcp output
mincontrast_st

Minimum constrast spatio-temporal estimation
vpc

Variance partition coefficient
square_pop

Simulated population density across unit square
square

A unit square spatial polygon
convergence

MCMC convergence diagnostics
infecSim

Infection simulation
aggregator_data

Create spatial polygons data frame
lgcp

Spatio-temporal Log-Gaussian Cox Process Model
geocode_st

Generate geocoded and time-stamped data
aggregator

Aggregate lgcp output to larger geography
get_map2

Alternative get_map function
lgcpExtract

Extract samples from lgcp model
get_day

Get day of the week