overlayenvelope: Overlay envelope plots

In jagshelper: Extracting and Visualizing Output from 'jagsUI'

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"),
  ...
)

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()

Value

NULL

Author(s)

Matt Tyers

See Also

envelope, crossplot

Examples

## 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")

jagshelper documentation built on Oct. 22, 2024, 1:06 a.m.