mapIncidence: Plot incidence time series using histograms
In Hackout2/incidence: Computation and Visualisation of Incidence from Line Lists

Description Usage Arguments Author(s) Examples

This function provides advanced plotting facilities for incidence time series using ggplot2

mapIncidence(x, dates, lon, lat, fill.by = NULL, col.pal = 0, alpha = 0.5,
  bin = 7, jitter = 0.01, source = "google", zoom = NULL,
  start.at = NULL, stop.at = NULL, xlab = NULL, ylab = "Incidence",
  date.format = "%d %b %Y", angle = 90, xbreaks = "1 week",
  heights = c(0.75, 0.25), ani.width = 800, ani.height = ani.width,
  point.size = 5, annot.size = 20, xy.annot = FALSE, path = tempdir())

`x`	a data.frame containing the data to be plotted.
`dates`	a character string or an integer indicating which column contains the dates to use
`lon`	a character string or an integer indicating which column contains longitudes ('x axis')
`lat`	a character string or an integer indicating which column contains latitudes ('y axis')
`fill.by`	a character string or an integer indicating which column to use to color the bars
`col.pal`	an integer between 1 and 8 indicating a color palette to be used; if 0 or NULL, the default color palette of ggplot2 is used
`alpha`	a numeric value between 0 and 1 handling transparency, with 0 being fulling transparent and 1 having no transparency
`bin`	an integer indicating the size of the time window (in days) to use for the incidence computation
`jitter`	a numeric value indicating the amount of random noise added to the locations of new cases
`source`	a character string indicating the type of maps to be used
`zoom`	an integer indicating the level of zoom to be used for the map, from 3 (continent) to 21 (building); see get_map
`start.at`	a starting date for the incidence; defaults to the earliest date of the dataset
`stop.at`	a stoping date for the incidence; defaults to the latest date of the dataset
`xlab`	a label for the x axis
`ylab`	a label for the y axis
`date.format`	a character string indicating the format of the dates
`angle`	an integer indicating the angle of the dates
`xbreaks`	a character string indicating the time interval between vertical lines
`heights`	a vector of two numbers summing to 1 indicating the relative heights of the map and the incidence time series
`ani.width`	an integer indicating the width of the image, in pixels
`ani.height`	an integer indicating the height of the image, in pixels; no-square images are not guaranteed to work
`point.size`	an integer indicating the size of point to be used for incidence
`annot.size`	an integer indicating the size of the text annotations
`xy.annot`	a logical indicating whether latitudes and longitudes should be shown
`path`	a character string indicating the path used to save the created files

Thibaut Jombart thibautjombart@gmail.com

## Not run: 

data(zombie_outbreak)
mapIncidence(head(zombie_outbreak,20000), 3,
            "x.coord","y.coord", fill.by="gender",
            jitter=0, zoom=15)


## End(Not run)