plot_nosoHazard: Plot daily risk of nosocomial infection per patient

In MESuRS-Lab/mwss: Stochastic simulations of infectious disease spread in healthcare systems structured as a networked metapopulation

Plot daily risk of nosocomial infection per patient

Description

plot_nosoHazard function returns a network plot of the wards whose colors represent the average daily risk of contracting a nosocomial infection for one patient of the ward . This average daily risk is calculated by dividing the average daily incidence by the average daily turnover (number of beds divided by the average length of stay). Associated risk-colors grade from white to red.

Usage

plot_nosoHazard(
       trajmwss, ward_names, pop_size_P, LS,
       matContact, layout = "with_fr", vertexsize = 0.5,
       vertexlabelsize = 0.03, edgearrowsize = 0.4, addtitle = FALSE,
       maxcolors = FALSE, verbose = TRUE)

Arguments

trajmwss	list of trajectories generated by multisim function
ward_names	string vector of ward names
pop_size_P	numerical vector of patient population sizes
LS	numerical vector of length of stay
matContact	Matrix reporting the proportion of time spent by health care workers in the different wards.
layout	String. Graph layout (details: ? igraph::layout_). Default is "with_fr". Options: "as_star","as_tree","in_circle","nicely","on_grid","on_sphere", "randomly","with_dh","with_fr","with_gem","with_graphopt", "with_kk","with_lgl", "with_mds", "with_sugiyama"
vertexsize	Integer. Defines the nodes/ward size (default is 0.5).
vertexlabelsize	Integer. Defines the nodes/ward names size (default is 0.03).
edgearrowsize	Integer. Defines the edge arrows size (default is 0.4).
addtitle	logical for optional title. Default is FALSE,
maxcolors	integer. Limit the number of colors displayed in the legend (default is FALSE)
verbose	Default is TRUE

Value

Igraph plot.

Examples

data("toydata")
list2env(toydata,envir=.GlobalEnv)
gdata <- build_gdata()

model <- mwss(ward_names, pop_size_P, pop_size_H, nVisits, LS, gdata, tSim = 30)
results <- multisim(model, 5, ward_names)

matContact <- randomContacts(pop_size_H, ward_names)$contactMat

plot_nosoHazard(results,
                ward_names,
                pop_size_P,
                LS,
                matContact,
                layout = "nicely",
                vertexsize = 0.5,
                vertexlabelsize = 0.03,
                edgearrowsize = 0.4,
                addtitle = TRUE,
                maxcolors = FALSE,
                verbose = FALSE)

MESuRS-Lab/mwss documentation built on Sept. 12, 2023, 12:08 a.m.