overlayenvelope: Overlay envelope plots

Description

Overlays multiple envelope plots of posterior data.frames, or outputs returned from jagsUI. This would be best suited to a set of posterior data.frames or 2-d matrices representing sequential vectors of parameter nodes.

Here a single envelope plot is defined as a set of overlayed shaded strips, each corresponding to a given interval width (defaults to 50 percent and 95 percent), with an overlayed median line.

Usage

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

Value

NULL

Arguments

df: Primary input can be specified in a number of ways: either a list() of posterior data.frames or matrices, a list of output objects returned from jagsUI::jags(), a 3-dimensional array in which the input matrices to plot are separated according to the 3rd array dimension, or a single output object returned from jagsUI::jags() with multiple arguments passed to p, following.
p: Parameter name, if input to df is a list of jagsUI output objects; or a vector of parameter names, if input to df is a single jagsUI output object.
x: Optional 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: Vector of colors for plotting
add: Whether to add to existing plot
dark: Opacity (0-1) for envelopes. Note that multiple overlapping intervals will darken the envelope. Defaults to 0.3.
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.
legend: Whether to automatically try to add a legend. Defaults to TRUE.
legendnames: Optional vector of names for a legend.
legendpos: Position for optional legend. Defaults to "topleft".
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 list of input data.frames
overlayenvelope(df=list(SS_out$sims.list$cycle_s[,,1],
                            SS_out$sims.list$cycle_s[,,2]))

## usage with a 3-d input array
overlayenvelope(df=SS_out$sims.list$cycle_s)

## usage with a jagsUI output object and parameter name (2-d parameter)
overlayenvelope(df=SS_out, p="cycle_s")

## usage with a single jagsUI output object and multiple parameters
overlayenvelope(df=SS_out, p=c("trend","rate"))

## exponential transformation
overlayenvelope(df=SS_out, p="cycle_s", transform="exp",
                ylab="exp transform")
overlayenvelope(df=SS_out, p="cycle_s", transform="exp",
                ylab="exp transform", log="y")