spacetime: Spatio-temporal maps from incidence objects

In reconhub/epimaps: Mapping Tools for Epidemics

Description

This function implements similar features to the S4 generic stplot from the spacetime package for incidence objects (from the incidence package), which are stratified by locations.

Usage

spacetime(obj, sf, type = c("map", "heatmap"), breaks = NULL,
  field = "NAME_2", pal = viridis::viridis, ...)

Arguments

obj	An incidence objects, as generated by the codeincidence package, stratified by geographic units matching that of a provided shapefile.
sf	A shapefile stored as a SpatialPolygonsDataFrame object from the sp package.
type	A character string indicating the type of graphics to produce: a map ("map"), or a heatmap ("heatmap").
breaks	A numeric vector indicating break points for the color scale.
field	A character string indicating the field containing the name of the spatial units to be used for plotting - the same as the ones used for incidence stratification.
pal	A color palette to be used for plotting.
...	Further arguments to be passed to stplot.

Value

The function returns a plot with extra attributes:

• incience_mat: an incidence matrix

• stfdf_obj: an stfdf object

Author(s)

Isobel Blake ([e-mail]) and Thibaut Jombart ([e-mail])

See Also

• getData to fetch shapefiles freely available from GDAM

• the incidence package documented at: http://www.repidemicsconsortium.org/incidence/

Examples

## Not run: 
if (require("sp") &&
    require("raster") &&
    require("outbreaks") &&
    require("incidence")) {

## fetch shapefiles for different admin levels
adm2data <- raster::getData('GADM', country = 'SLE', level = 2)
adm1data <- raster::getData('GADM', country = 'SLE', level = 1)
adm0data <- raster::getData('GADM', country = 'SLE', level = 0)

## plot data
plot(adm2data, border = "grey")
plot(adm1data, add = TRUE)
plot(adm0data, add = TRUE, lwd = 2)
text(sp::coordinates(adm2data), labels = adm2data$NAME_2, cex = 0.6)

## make fake data
dat <- ebola_sim$linelist

## randomly assign district location
p <- c(0.15,0.1,0.01,0.01,0.02,0,0,0.05,0.01,0,0.05,0.1,0.25,0.25)
dat$adm2 <- sample(adm2data$NAME_2, size = nrow(dat),
                   replace = TRUE, prob = p)

## make an incidence object
x <- incidence::incidence(dat$date_of_onset, 30, groups = dat$adm2)

## make plot
res <- spacetime(x, adm2data)
res

## extra data stored in attributes
attributes(res)
}

## End(Not run)

reconhub/epimaps documentation built on May 7, 2019, 1:30 p.m.