trace_ACF_plot {bayesMRM} | R Documentation |
bmrm
objectProduce trace and Auto-Correlation Function plots (along with Effective sample size) of MCMC samples of elements of A, nonzero elements of P, elements of Sigma.
trace_ACF_plot(x,var="P", ACF=FALSE, nplot=0,irow=1, icol=1, saveFile=FALSE,...)
x |
an object of class |
var |
name of a variable to which the plots apply. It should be one of "A" (source contribution matrix), "P" (source composition matrix), "Sigma" (error variance). |
ACF |
TRUE/FALSE if TRUE ACF plots will be provided along with effective sample sizes(dafault: FALSE) |
nplot |
number of elements of 'var' for trace and/or ACF plots. If 'nplot' is smaller than the total number of elements of 'var' then plots of 'nplot' selected elements will be drawn. Otherwise, trace and/or ACF plots of all elements will be drawn. (default=0 implies that all elements will be selected if var="P" or "Sigma", and the first 12 elements will be selected if var="A") |
irow |
row index of A/P matrix or index of element of Sigma vector. Plots of 'nplot' elements starting from (irow, icol) element of A/P or elements starting from irow element of Sigma will be drawn (default=1). |
icol |
column number of A/P matrix. Plots of 'nplot' elements starting from (irow, icol) element of A/P will be drawn (default=1). |
saveFile |
TRUE/FALSE, save the plots in file 'var'-trace.pdf (default=FALSE) |
... |
arguments to be passed to methods |
plot
data(Elpaso); Y=Elpaso$Y ; muP=Elpaso$muP ; q=nrow(muP)
out.Elpaso <- bmrm(Y,q,muP, nAdapt=1000,nBurnIn=5000,nIter=5000,nThin=1)
trace_ACF_plot(out.Elpaso,"Sigma", ACF=TRUE)
trace_ACF_plot(out.Elpaso,"P", ACF=TRUE)
trace_ACF_plot(out.Elpaso,"A",ACF=TRUE, nplot=12, irow=2, icol=3)