envelope: Envelope plot

Description

Envelope plot of the posterior densities of a vector of parameter nodes, in which the sequential order of nodes is important, such as a time series.

This produces a plot of overlayed shaded strips, each corresponding to a given interval width (defaults to 50 percent and 95 percent), with an overlayed median line.

Usage

envelope(
  df,
  p = NULL,
  x = NA,
  row = NULL,
  column = NULL,
  median = TRUE,
  ci = c(0.5, 0.95),
  col = 4,
  add = FALSE,
  dark = 0.3,
  outline = FALSE,
  xlab = "",
  ylab = "",
  main = NULL,
  ylim = NULL,
  transform = c("none", "exp", "expit"),
  ...
)

Value

NULL

Arguments

df: Output object returned from jagsUI::jags(); or alternately, two-dimensional data.frame or matrix in which parameter node element is given by column and MCMC iteration is given by row.
p: Parameter name, if input to df is a jagsUI output object.
x: Vector of X-coordinates for plotting.
row: Row to subset, in the case of a 2-d matrix of parameter nodes in-model.
column: Column to subset, in the case of a 2-d matrix of parameter nodes in-model.
median: Whether to include median line
ci: Vector of intervals to overlay. Defaults to 50 percent and 95 percent.
col: Color for plotting
add: Whether to add to existing plot
dark: Opacity (0-1) for envelopes. Note that multiple overlapping intervals will darken the envelope.
outline: Whether to just envelope outlines
xlab: X-axis label
ylab: Y-axis label
main: Plot title. If the default (NULL) is accepted and argument p is used, p will be used for the title.
ylim: Y-axis limits for plotting. If the default (NULL) is accepted, these will be determined automatically.
transform: Should the y-axis be (back)transformed? Options are "exp", indicating exponential, or "expit", indicating inverse-logit. Defaults to "none", indicating no transformation. Note: if transform="exp"is used, consider adding additional plotting argument log="y".
...: additional plotting arguments or arguments to lines()

Author

Matt Tyers

Examples

Run this code

## usage with input data.frame
trend <- jags_df(SS_out, p="trend")
envelope(trend, x=SS_data$x)

## usage with jagsUI object
envelope(SS_out, p="trend")

## usage with 2-d jagsUI object
envelope(SS_out, p="cycle_s", column=1, main="cycle")
envelope(SS_out, p="cycle_s", column=2, col=2, add=TRUE)  ## overlay

## scale transformation
envelope(SS_out, p="trend", transform="exp", ylab="exp transform")
envelope(SS_out, p="trend", transform="exp", ylab="exp transform", log="y")