R: Bivariate Plot of Posterior Densities

crossplot {jagshelper}

R Documentation

Bivariate Plot of Posterior Densities

Description

Bivariate plot of the posterior densities of corresponding vectors of parameter nodes. Three plotting methods are provided, that may be overlayed if desired.

If drawcross == TRUE, caterpillar-like plots will be produced, with quantile intervals in the x- and y- directions.
If drawx == TRUE, caterpillar-like plots will be produced, but rotated along the standardized principal component axes. This may be useful to draw if correlation is present.
If drawblob == TRUE, smoothed polygons will be produced, each containing approximately ⁠ci=⁠ x100% of the associated MCMC samples.

All methods can overlay multiple bars or polygons, depending on the length of ⁠ci=⁠.

Usage

crossplot(
  dfx,
  dfy = NULL,
  p = NULL,
  col = 4,
  drawcross = TRUE,
  drawx = FALSE,
  drawblob = FALSE,
  blobres = NULL,
  blobsmooth = NULL,
  outline = FALSE,
  ci = c(0.5, 0.95),
  lwd = 1,
  mean = FALSE,
  link = FALSE,
  linklwd = 1,
  labels = FALSE,
  labelpos = NULL,
  labelcex = 0.7,
  whichx = NULL,
  rowx = NULL,
  columnx = NULL,
  whichy = NULL,
  rowy = NULL,
  columny = NULL,
  xlab = NULL,
  ylab = NULL,
  main = NULL,
  xlim = NULL,
  ylim = NULL,
  transformx = c("none", "exp", "expit"),
  transformy = c("none", "exp", "expit"),
  add = FALSE,
  ...
)

Arguments

`dfx`	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. A vector may also be used, that expresses MCMC iterations of a single parameter node. If used with `⁠dfy=⁠`, this will be plotted in the x-direction.
`dfy`	Optionally, a two-dimensional `data.frame` or matrix in which parameter node element is given by column and MCMC iteration is given by row. A vector may also be used, that expresses MCMC iterations of a single parameter node. If used, this will be plotted in the y-direction.
`p`	Vector of parameter names, if input to `dfx` is a `jagsUI` output object. If used, this must be of length 2.
`col`	Color for plotting, or recyclable vector of colors. Defaults to `4`. If `col == "random"`, rcolors will be used to generate a random vector of colors.
`drawcross`	Whether to draw quantile bars in the x- and y-directions. Defaults to `TRUE`.
`drawx`	Whether to draw quantile bars along the standardized principal component axes. Defaults to `FALSE`.
`drawblob`	Whether to draw smoothed quantile polygons. Defaults to `FALSE`.
`blobres`	Optional tuning parameter for drawing quantile polygons, and corresponds to the number of polygon vertices. If the default `NULL` is accepted, the function will supply a value based on the number of MCMC samples.
`blobsmooth`	Optional tuning parameter for drawing quantile polygons, and corresponds to half the number of polygon vertices used for local smoothing. If the default `NULL` is accepted, the function will supply a value based on the number of MCMC samples and the number of vertices.
`outline`	Whether to draw quantile polygons as lines rather than filled regions. Defaults to `FALSE`.
`ci`	Vector of intervals to overlay. Defaults to 50 percent and 95 percent.
`lwd`	Base line width for plotting. Defaults to 1.
`mean`	Whether to include points for means. Defaults to `FALSE`.
`link`	Whether to link medians in sequence. Defaults to `FALSE`.
`linklwd`	Line width to use for linking. Defaults to `1`.
`labels`	Whether to add labels, or a vector of labels to add. Defaults to `FALSE`.
`labelpos`	Optionally, an argument to `pos` in text for labels. Defaults to `NULL`.
`labelcex`	Optional character expansion for labels. Defaults to `0.7`.
`whichx`	Element to subset for x, if only one element of a vector of parameter nodes is desired for plotting.
`rowx`	Row to subset for x, in the case of a 2-d matrix of parameter nodes in-model.
`columnx`	Column to subset for x, in the case of a 2-d matrix of parameter nodes in-model.
`whichy`	Element to subset for x, if only one element of a vector of parameter nodes is desired for plotting.
`rowy`	Row to subset for y, in the case of a 2-d matrix of parameter nodes in-model.
`columny`	Column to subset for y, in the case of a 2-d matrix of parameter nodes in-model.
`xlab`	X-axis label. If the default `NULL` is accepted, this will be drawn automatically.
`ylab`	Y-axis label. If the default `NULL` is accepted, this will be drawn automatically.
`main`	Plot title.
`xlim`	X-axis limits. If the default (`NULL`) is accepted, the limits will be determined automatically.
`ylim`	Y-axis limits. If the default (`NULL`) is accepted, the limits will be determined automatically.
`transformx`	Should the x-axis be (back)transformed? Options are `"exp"`, indicating exponential, or `"expit"`, indicating inverse-logit. Defaults to `"none"`, indicating no transformation. Note: if `transformx="exp"`is used, consider adding additional plotting argument `log="x"` or `log="xy"`.
`transformy`	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 `transformy="exp"`is used, consider adding additional plotting argument `log="y"` or `log="xy"`.
`add`	Whether to add to existing plot
`...`	additional plotting arguments

Value

NULL

Author(s)

Matt Tyers

Examples

## basic functionality with cross geometry
crossplot(SS_out, p=c("trend","rate"))

## default labels
crossplot(SS_out, p=c("trend","cycle"), labels=TRUE)

## showing:
## - link lines
## - blob geometry (smoothed confidence polygons)
## - random colors with col="random"
crossplot(SS_out, p=c("trend","cycle"),
          labels=SS_data$x, labelpos=1, link=TRUE, drawblob=TRUE,
          col="random")

## adding x geometry and showing usage with a single vector element (41)
crossplot(SS_out, p=c("trend","cycle"),
          whichx=41, whichy=41,
          drawblob=TRUE, drawx=TRUE)

## single vectors (or data.frames or 2d matrices) can also be used
xx <- SS_out$sims.list$trend[,41]
yy <- SS_out$sims.list$cycle[,41]

par(mfrow = c(2, 2))
plot(xx, yy, col=adjustcolor(1, alpha.f=.1), pch=16, main="cross geometry")
crossplot(xx, yy, add=TRUE, col=1)
plot(xx, yy, col=adjustcolor(1, alpha.f=.1), pch=16, main="x geometry")
crossplot(xx, yy, add=TRUE, col=1,
          drawcross=FALSE, drawx=TRUE)
plot(xx, yy, col=adjustcolor(1, alpha.f=.1), pch=16, main="blob geometry")
crossplot(xx, yy, add=TRUE, col=1,
          drawcross=FALSE, drawblob=TRUE)
plot(xx, yy, col=adjustcolor(1, alpha.f=.1), pch=16, main="blob outlines")
crossplot(xx, yy, add=TRUE, col=1,
          drawcross=FALSE, drawblob=TRUE, outline=TRUE)

[Package jagshelper version 0.3.1 Index]