Plots dynamic network model diagnostics calculated in
netdx
.
Usage
# S3 method for class 'netdx'
plot(
x,
type = "formation",
method = "l",
sims,
stats,
duration.imputed = TRUE,
sim.lines = FALSE,
sim.col,
sim.lwd,
mean.line = TRUE,
mean.smooth = TRUE,
mean.col,
mean.lwd = 2,
mean.lty = 1,
qnts = 0.5,
qnts.col,
qnts.alpha = 0.5,
qnts.smooth = TRUE,
targ.line = TRUE,
targ.col,
targ.lwd = 2,
targ.lty = 2,
plots.joined,
legend,
grid = FALSE,
...
)
Arguments
- x
An
EpiModel
object of classnetdx
.- 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 tonetdx
; fortype = "duration", "dissolution"
,stats
are among those of the dissolution model (withoutoffset()
). 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 toTRUE
whentype = "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 ifFALSE
.- legend
If
TRUE
, plot default legend.- grid
If
TRUE
, a grid is added to the background of plot (seegrid
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.
Examples
if (FALSE) { # \dontrun{
# 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")
} # }