'plot.chains' plots the chains for parameters saved in a call to 'bugs'.

ARGUMENTS:

'param' is one of three things:  If 'bugs.out' is the output to a call to 'bugs'/'jags' in the R2OpenBUGS, R2WinBUGS or R2jags package or the output from a previous call to 'extract.chains', then 'param' must be the name of a parameter that was saved in this output.  This name can be specified either by means of the name given to it by OpenBUGS/WinBUGS/JAGS, or by the R-legal name that was created by the 'extract.chains' function.  If 'bugs.out' is NA, then 'param' is either a matrix of chains or it is a list whose sole component is a matrix of chains.

'bugs.out' is either NA or it is the output from a call to 'bugs'/'jags' in the R2OpenBUGS, R2WinBUGS or R2jags package or it is the output from a previous call to 'extract.chains'. If 'bugs.out' is NA, then 'param' must be either a matrix of chains or a list whose sole component is a matrix of chains (as in the output of 'extract.chains'.  

'xlim.f = NA' (default) means that 'plot.chains' plots all of the iterations for the chains.  Alternatively, set 'xlim.f' to the lower and upper bounds on the x-axis, e.g., 'xlim.f = c(200, 300)' to plot the iterations from 200 to 300.

'ylim.f = NA' (default) means that 'plot.chains' determines the limits on the y-axis.  Alternatively, set 'ylim.f' to the lower and upper limit on the y-axis, e.g., 'ylim.f = c(.2, .8).

'legend = FALSE' (default) then no legend is plotted.  If 'legend = TRUE', a legend is printed across the top of the graph to show the correspondence between the line colors and chains.

'add.labels = TRUE' (default) to have 'plot.chains' generate the axis labels.  If FALSE, the axis labels are omitted.

'cex.lab = 1.5' controls the character size for the axis labels.

'plot.jm' makes the JM default plot.  The default range is 0 to 100 on both axes, but this can be changed.  If 'no.margins = TRUE', the plotting area has no space for margins.  This is preferred when making text plots or diagrams.  Other argument for 'plot' can be passed to 'plot' via ....