CRTspat (version 1.4.0)

plotCRT: Graphical displays of the geography of a CRT

Description

plotCRT returns graphical displays of the geography of a CRT or of the results of statistical analyses of a CRT

Usage

plotCRT(
  object,
  map = FALSE,
  distance = "nearestDiscord",
  fill = "arms",
  showLocations = FALSE,
  showClusterBoundaries = TRUE,
  showClusterLabels = FALSE,
  showBuffer = FALSE,
  cpalette = NULL,
  buffer_width = NULL,
  maskbuffer = 0.2,
  labelsize = 4,
  legend.position = NULL
)

Value

graphics object produced by the ggplot2 package

Arguments

object

object of class 'CRTanalysis' produced by CRTanalysis()

map

logical: indicator of whether a map is required

distance

measure of distance or surround with options:

"nearestDiscord"	distance to nearest discordant location (km)
"disc"	disc
"hdep"	Tukey's half space depth
"sdep"	simplicial depth

fill

fill layer of map with options:

'cluster'	cluster assignment
'arms'	arm assignment
'nearestDiscord'	distance to the nearest discordant location
'disc'	disc measure of surround
'hdep'	Tukey's half space depth
'sdep'	simplicial depth
'prediction'	model prediction of the outcome
'none'	No fill

showLocations

logical: determining whether locations are shown

showClusterBoundaries

logical: determining whether cluster boundaries are shown

showClusterLabels

logical: determining whether the cluster numbers are shown

showBuffer

logical: whether a buffer zone should be overlayed

cpalette

colour palette (to use different colours for clusters this must be at least as long as the number of clusters.

buffer_width

width of buffer zone to be overlayed (km)

maskbuffer

radius of buffer around inhabited areas (km)

labelsize

size of cluster number labels

legend.position

(using ggplot2::themes syntax)

Details

If map = FALSE and the input is a trial data frame or a CRTsp object, containing a randomisation to arms, a stacked bar chart of the outcome grouped by the specified distance is produced. If the specified distance has not yet been calculated an error is returned.

If map = FALSE and the input is a CRTanalysis object a plot of the estimated spillover function is generated. The fitted spillover function is plotted as a continuous green/blue line against the measure of the surround or of the distance to the nearest discordant location. Using the same axes, data summaries are plotted for ten categories of distance from the boundary. Both the average of the outcome and confidence intervals are plotted.If spillover limits have been estimated then these limits are used to delimit a shaded rectangular overlay, providing they fall within the range of distances in the data. If the spillover limits fall outside the range of the data then the range of distances in the data define the boundaries of the shaded area.

• For analyses with logit link function the outcome is plotted as a proportion.
  

• For analyses with log or cloglog link function the data are plotted on a scale of the Williams mean (mean of exp(log(x + 1))) - 1) rescaled so that the median matches the fitted curve at the midpoint.
  

If map = TRUE a thematic map corresponding to the value of fill is generated.

• fill = 'clusters' or leads to thematic map showing the locations of the clusters

• fill = 'arms' leads to a thematic map showing the geography of the randomization

• fill = 'distance' leads to a raster plot of the distance to the nearest discordant location.

• fill = 'prediction' leads to a raster plot of predictions from an 'INLA' model.

If showBuffer = TRUE the map is overlaid with a grey transparent layer showing which areas are within a defined distance of the boundary between the arms. Possibilities are:

• If the trial has not been randomised or if showBuffer = FALSE no buffer is displayed

• If buffer_width takes a positive value then buffers of this width are displayed irrespective of any pre-specified or spillover limits.

• If the input is a 'CRTanalysis' and spillover limits have been estimated then these limits are used to define the displayed buffer providing they fall within the range of distances in the data.

• If buffer_width is not specified and no spillover limits are available, then any pre-specified buffer (e.g. one generated by specify_buffer()) is displayed.

A message is output indicating which of these possibilities applies.

Examples

{example <- readdata('exampleCRT.txt')
#Plot of data by distance
plotCRT(example)
#Map of locations only
plotCRT(example, map = TRUE, fill = 'none', showLocations = TRUE,
           showClusterBoundaries=FALSE, maskbuffer=0.2)
#show cluster boundaries and number clusters
plotCRT(example, map = TRUE, fill ='none', showClusterBoundaries=TRUE,
           showClusterLabels=TRUE, maskbuffer=0.2, labelsize = 2)
#show clusters in colour
plotCRT(example, map = TRUE, fill = 'clusters', showClusterLabels = TRUE,
          labelsize=2, maskbuffer=0.2)
#show arms
plotCRT(example, map = TRUE,
fill = 'arms', maskbuffer=0.2, legend.position=c(0.8,0.8))
#spillover plot
analysis <- CRTanalysis(example)
 plotCRT(analysis, map = FALSE)
}