nbNetwork {nbTransmission} | R Documentation |
Plots a network of the relative transmission probabilities
Description
The function nNetwork
plots a network of the transmission probabilities.
The nodes are the individuals and the edges represent possible transmission pairs.
The darker the edge, the higher the probability that the pair is a transmission link.
If a cluster method is specified using clustMethod
and cutoff
, only edges
that are in the high probability cluster of infectors will be drawn.
Usage
nbNetwork(
df,
indIDVar,
dateVar,
pVar,
clustMethod = c("none", "n", "kd", "hc_absolute", "hc_relative"),
cutoff = NA,
blackAndWhite = FALSE,
probBreaks = c(-0.01, 0.001, 0.005, 0.01, 0.05, 0.1, 0.25, 0.5, 0.75, 1)
)
Arguments
df |
The name of the dateset with transmission probabilities (column |
indIDVar |
The name (in quotes) of the individual ID columns
(data frame |
dateVar |
The name (in quotes) of the columns with the dates that the individuals are
observed (data frame |
pVar |
The name (in quotes) of the column with transmission probabilities. |
clustMethod |
The method used to cluster the infectors; one of
|
cutoff |
The cutoff for clustering (see |
blackAndWhite |
A logical. If |
probBreaks |
A numeric vector containing between 3 and 10 elements specifying the boundaries used to classify the probabilities and color the edges. The first element should be less than 0 and the last should be 1. |
Details
Users have the option of specifying how the probabilities should be grouped into different
color shades through the argument probBreaks
. The probabilities are split into groups by
using probBreaks
as the breaks
argument in cut
with the default options.
The length of the vector should be between 3 and 10 and the first element should be less than 0 and
the last 1 so that all probabilities are guarenteed to be classified.
The colors are defined with the code brewer.pal(length(probBreaks) - 1, "Blues")
(where "Blues" is replaced by "Greys" if blackAndWhite
is set to TRUE
).
See Also
nbProbabilities
clusterInfectors
Examples
## Network of all pairs in color with the default probability breaks
par(mar = c(0, 0, 0.2, 0))
nbNetwork(nbResults, indIDVar = "individualID", dateVar = "infectionDate",
pVar = "pScaled", clustMethod = "none")
dev.off()
## Network of just the top cluster of infectors, black and white, changing the probability breaks
par(mar = c(0, 0, 0.2, 0))
nbNetwork(nbResults, indIDVar = "individualID", dateVar = "infectionDate",
pVar = "pScaled", clustMethod = "hc_absolute", cutoff = 0.05,
blackAndWhite = TRUE, probBreaks = c(-0.01, 0.01, 0.1, 0.25, 0.5, 1))
dev.off()