plot.netdx: Plot Dynamic Network Model Diagnostics

In EpiModel: Mathematical Modeling of Infectious Disease Dynamics

Plot Dynamic Network Model Diagnostics

Description

Plots dynamic network model diagnostics calculated in netdx.

Usage

## S3 method for class 'netdx'
plot(
  x,
  type = "formation",
  method = "l",
  sims = NULL,
  stats = NULL,
  duration.imputed = TRUE,
  sim.lines = FALSE,
  sim.col = NULL,
  sim.lwd = NULL,
  mean.line = TRUE,
  mean.smooth = TRUE,
  mean.col = NULL,
  mean.lwd = 2,
  mean.lty = 1,
  qnts = 0.5,
  qnts.col = NULL,
  qnts.alpha = 0.5,
  qnts.smooth = TRUE,
  targ.line = TRUE,
  targ.col = NULL,
  targ.lwd = 2,
  targ.lty = 2,
  plots.joined = NULL,
  legend = NULL,
  grid = FALSE,
  ...
)

Arguments

x	An EpiModel object of class netdx.
type	Plot type, with options of "formation" for network model formation statistics, "duration" for dissolution model statistics for average edge duration, or "dissolution" for dissolution model statistics for proportion of ties dissolved per time step.
method	Plot method, with options of "l" for line plots and "b" for box plots.
sims	A vector of simulation numbers to plot.
stats	Statistics to plot. For type = "formation", stats are among those specified in the call to netdx; for type = "duration", "dissolution", stats are among those of the dissolution model (without offset()). The default is to plot all statistics.
duration.imputed	If type = "duration", a logical indicating whether or not to impute starting times for relationships extant at the start of the simulation. Defaults to TRUE when type = "duration".
sim.lines	If TRUE, plot individual simulation lines. Default is to plot lines for one-group models but not for two-group models.
sim.col	Vector of any standard R color format for simulation lines.
sim.lwd	Line width for simulation lines.
mean.line	If TRUE, plot mean of simulations across time.
mean.smooth	If TRUE, use a loess smoother on the mean line.
mean.col	Vector of any standard R color format for mean lines.
mean.lwd	Line width for mean lines.
mean.lty	Line type for mean lines.
qnts	If numeric, plot polygon of simulation quantiles based on the range implied by the argument (see details). If FALSE, suppress polygon from plot.
qnts.col	Vector of any standard R color format for polygons.
qnts.alpha	Transparency level for quantile polygons, where 0 = transparent and 1 = opaque (see adjustcolor function).
qnts.smooth	If TRUE, use a loess smoother on quantile polygons.
targ.line	If TRUE, plot target or expected value line for the statistic of interest.
targ.col	Vector of standard R colors for target statistic lines, with default colors based on RColorBrewer color palettes.
targ.lwd	Line width for the line showing the target statistic values.
targ.lty	Line type for the line showing the target statistic values.
plots.joined	If TRUE, combine all statistics in one plot, versus one plot per statistic if FALSE.
legend	If TRUE, plot default legend.
grid	If TRUE, a grid is added to the background of plot (see grid for details), with default of nx by ny.
...	Additional arguments to pass.

Details

The plot function for netdx objects will generate plots of two types of model diagnostic statistics that run as part of the diagnostic tools within that function. The formation plot shows the summary statistics requested in nwstats.formula, where the default includes those statistics in the network model formation formula specified in the original call to netest.

The duration plot shows the average age of existing edges at each time step, up until the maximum time step requested. The age is used as an estimator of the average duration of edges in the equilibrium state. When duration.imputed = FALSE, edges that exist at the beginning of the simulation are assumed to start with an age of 1, yielding a burn-in period before the observed mean approaches its target. When duration.imputed = TRUE, expected ages prior to the start of the simulation are calculated from the dissolution model, typically eliminating the need for a burn-in period.

The dissolution plot shows the proportion of the extant ties that are dissolved at each time step, up until the maximum time step requested. Typically, the proportion of ties that are dissolved is the reciprocal of the mean relational duration. This plot thus contains similar information to that in the duration plot, but should reach its expected value more quickly, since it is not subject to censoring.

The plots.joined argument will control whether the statistics are joined in one plot or plotted separately, assuming there are multiple statistics in the model. The default is based on the number of network statistics requested. The layout of the separate plots within the larger plot window is also based on the number of statistics.

See Also

netdx

Examples

## Not run: 
# Network initialization and model parameterization
nw <- network_initialize(n = 500)
nw <- set_vertex_attribute(nw, "sex", rbinom(500, 1, 0.5))
formation <- ~edges + nodematch("sex")
target.stats <- c(500, 300)
coef.diss <- dissolution_coefs(dissolution = ~offset(edges) +
                  offset(nodematch("sex")), duration = c(50, 40))

# Estimate the model
est <- netest(nw, formation, target.stats, coef.diss, verbose = FALSE)

# Static diagnostics
dx1 <- netdx(est, nsims = 1e4, dynamic = FALSE,
             nwstats.formula = ~edges + meandeg + concurrent +
                                nodefactor("sex", levels = NULL) +
                                nodematch("sex"))
dx1

# Plot diagnostics
plot(dx1)
plot(dx1, stats = c("edges", "concurrent"), mean.col = "black",
     sim.lines = TRUE, plots.joined = FALSE)
plot(dx1, stats = "edges", method = "b",
     col = "seagreen3", grid = TRUE)

# Dynamic diagnostics
dx2 <- netdx(est, nsims = 10, nsteps = 500,
             nwstats.formula = ~edges + meandeg + concurrent +
                                nodefactor("sex", levels = NULL) +
                                nodematch("sex"))
dx2

# Formation statistics plots, joined and separate
plot(dx2, grid = TRUE)
plot(dx2, type = "formation", plots.joined = TRUE)
plot(dx2, type = "formation", sims = 1, plots.joined = TRUE,
     qnts = FALSE, sim.lines = TRUE, mean.line = FALSE)
plot(dx2, type = "formation", plots.joined = FALSE,
     stats = c("edges", "concurrent"), grid = TRUE)

plot(dx2, method = "b", col = "bisque", grid = TRUE)
plot(dx2, method = "b", stats = "meandeg", col = "dodgerblue")

# Duration statistics plot
par(mfrow = c(1, 2))
# With duration imputed
plot(dx2, type = "duration", sim.line = TRUE, sim.lwd = 0.3,
     targ.lty = 1, targ.lwd = 0.5)
# Without duration imputed
plot(dx2, type = "duration", sim.line = TRUE, sim.lwd = 0.3,
     targ.lty = 1, targ.lwd = 0.5, duration.imputed = FALSE)

# Dissolution statistics plot
plot(dx2, type = "dissolution", qnts = 0.25, grid = TRUE)
plot(dx2, type = "dissolution", method = "b", col = "pink1")

## End(Not run)

EpiModel documentation built on Oct. 12, 2024, 1:06 a.m.