I have MCMC output chains A and B for example, I want to produce trace plots for them using the boa command line... #loads boa boa.init() #reads in chains boa.chain.add(boa.importMatrix('A'), 'A') boa.chain.add(boa.importMatrix('B'), 'B') #plot trace plot problems arise here! I know I can get trace plots using boa.plot('trace') but this plots the parameter chains on the same plot- I want separate plots using boa.plot.trace() #from the manual.. boa.plot.trace(lnames, pname, annotate = boa.par("legend")) lnames: Character vector giving the name of the desired MCMC sequence in the working session list of sequences. pname: Character string giving the name of the parameters to be plotted. annotate: Logical value indicating that a legend be included in the plot. I tried boa.plot.trace(B) and boa.plot.trace(B,"B") but both do not give me a trace plot for chain B and print FALSE. I am obviously misinterpreting lnames and pnames. Can anyone help please? Thanks in advance Emma -- View this message in context: http://r.789695.n4.nabble.com/more-boa-plots-questions-tp3330312p3330312.html Sent from the R help mailing list archive at Nabble.com.