caterpillar: Caterpillar plot

Description

Caterpillar plot of the posterior densities of a vector of parameter nodes, in which the sequential order of nodes might not be important, such as vector of random effects.

This produces a set of overlayed interval bars (default values are 50 percent and 95 percent), with overlayed median markings, for each of a vector of parameter nodes.

Usage

caterpillar(
  df,
  p = NULL,
  x = NA,
  row = NULL,
  column = NULL,
  median = TRUE,
  mean = FALSE,
  ci = c(0.5, 0.95),
  lwd = 1,
  col = 4,
  add = FALSE,
  xlab = "",
  ylab = "",
  main = NULL,
  ylim = NULL,
  xax = NA,
  transform = c("none", "exp", "expit"),
  medlwd = lwd,
  medwd = 1,
  ...
)

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. A vector may also be used, that expresses MCMC iterations of a single parameter node.
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 medians
mean: Whether to include means
ci: Vector of intervals to overlay. Defaults to 50 percent and 95 percent.
lwd: Base line width for plotting. Defaults to 1.
col: Color for plotting
add: Whether to add to existing plot
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. If the default (NULL) is accepted, the limits will be determined automatically.
xax: Vector of possible x-axis tick labels. Defaults to the data.frame column names.
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".
medlwd: Line width of median line
medwd: Relative width of median line. Defaults to 1, perhaps smaller numbers will look better?
...: additional plotting arguments

Author

Matt Tyers

Examples

Run this code

## usage with input data.frame
a <- jags_df(asdf_jags_out, p="a")

caterpillar(a)
caterpillar(a, ci=seq(.1,.9,by=.1))
caterpillar(a, lwd=2)
caterpillar(a, xax=c("effect 1", "effect 2", "effect 3"))


## usage with input as jagsUI object
caterpillar(asdf_jags_out, p="a")
caterpillar(SS_out, p="rate")

## usage with a 2-d parameter matrix
caterpillar(SS_out, p="cycle_s", column=1)
caterpillar(SS_out, p="cycle_s", column=2)

## usage with an exponential transformation
caterpillar(SS_out, p="trend", transform="exp", ylab="exp transform")
caterpillar(SS_out, p="trend", transform="exp", ylab="exp transform", log="y")
caterpillar(SS_out, p="trend", transform="expit", ylab="expit (inv logit) transform")