Plots a network of the relative transmission probabilities

Source: R/visualizeResults.R

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.

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 pVar), individual IDs (columns <indIDVar>.1 and <indIDVar>.2), and the dates of observation (columns <dateVar>.1 and <dateVar>.2).

indIDVar

The name (in quotes) of the individual ID columns (data frame df must have variables called <indIDVar>.1 and <indIDVar>.2).

dateVar

The name (in quotes) of the columns with the dates that the individuals are observed (data frame df must have variables called <dateVar>.1 and <dateVar>.2).

pVar

The name (in quotes) of the column with transmission probabilities.

clustMethod

The method used to cluster the infectors; one of "none", "n", "kd", "hc_absolute", "hc_relative" where "none" or not specifying a value means use all pairs with no clustering (see clusterInfectors for detials on clustering methods).

cutoff

The cutoff for clustering (see clusterInfectors).

blackAndWhite

A logical. If TRUE, then the edges are colored in greyscale, if FALSE, then the edges are colored with shades of blue.

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).

Examples


# \donttest{
## 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()
#> null device 
#>           1 


## 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()         
#> null device 
#>           1 
# }