Usage
add.summary(runjags.object, vars = NA, mutate = NA, psrf.target = 1.05,
normalise.mcmc = TRUE, modeest.opts = list(), confidence = c(0.95),
autocorr.lags = c(10), custom = NULL,
silent.jags = runjags.getOption("silent.jags"),
plots = runjags.getOption("predraw.plots"), plot.type = c("trace", "ecdf",
"histogram", "autocorr", "key", "crosscorr"), col = NA,
summary.iters = 10000, trace.iters = 1000, separate.chains = FALSE,
trace.options = list(), density.options = list(),
histogram.options = list(), ecdfplot.options = list(),
acplot.options = list())## S3 method for class 'runjags':
summary(object, ...)
## S3 method for class 'runjags':
plot(x, plot.type = c("trace", "ecdf", "histogram",
"autocorr", "key", "crosscorr"), vars = NA,
layout = runjags.getOption("plot.layout"),
new.windows = runjags.getOption("new.windows"), file = "",
mutate = NULL, col = NA, trace.iters = NA, separate.chains = NA,
trace.options = NA, density.options = NA, histogram.options = NA,
ecdfplot.options = NA, acplot.options = NA, ...)
## S3 method for class 'runjags':
print(x, vars = NA, digits = 5, ...)
## S3 method for class 'runjagsplots':
print(x, layout = runjags.getOption("plot.layout"),
new.windows = runjags.getOption("new.windows"), file = "", ...)
## S3 method for class 'runjagsplots':
plot(x, layout = runjags.getOption("plot.layout"),
new.windows = runjags.getOption("new.windows"), file = "", ...)
Arguments
vars
an optional character vector of variable names. If supplied, only variable names in the object supplied with a partial match to anything in 'vars' will be used. Note that regular expressions are not allowed, but the caret (^) token can be used to specif
mutate
either a function or a list with first element a function and remaining elements arguments to this function. This can be used to add new variables to the posterior chains that are derived from the directly monitored variables in JAGS. This allows the var
psrf.target
the desired cutoff for 'convergence' as determined Gelman and Rubin's convergence diagnostic (see gelman.diag). This is somewhat arbitrary, but 1.05 is a commonly used figure. normalise.mcmc
an option test transformations of the monitored variable for improved normality, which is an assumption of the Gelman and Rubin statistic. Setting this option to FALSE will likely cause problems with calculating the psrf for highly skewed variables.
modeest.opts
arguments to be passed to the mlv function to calculate the mode of continuous variables. Ignored if the mode.continuous option in runjags.options confidence
a numeric vector of probabilities (between 0 and 1) on which to base confidence interval calculations.
autocorr.lags
a numeric vector of integers on which to base the autocorrelation diagnostic. See also the autocorr plot type.
custom
a custom function which takes a numeric object as input and outputs a single summary statistic. This statistic will be included with the others in the print and summary method outputs.
silent.jags
option to suppress feedback text produced by the summary function when summary statistics must be recalculated.
plots
option to pre-draw the plots given by plot.type to facilitate more convinient assessment of convergence after the model has finished running, at the expense of requiring a larger object to stored. The default value uses the option given in
plot.type
a character vector of plots to produce, from 'trace', 'density', 'ecdf', 'histogram', 'autocorr', 'crosscorr', 'key' or 'all'. These are all based on the equivalent plots from the lattice package wi col
a vector of colours to use for the different chains. This will be used for all plot types (where relevant), including the 'key' plot which functions to label the chain numbers of the various colours. The default uses the standard lattice colour palatte
summary.iters
the number of iterations to thin the chains to before calculating summary statistics (including all plots except the trace plot). Setting too high a value will cause a long delay while calculating these statistics.
trace.iters
the number of iterations to thin the chains to before producing traceplots. Setting too high a value will cause large file sizes and delays displaying the trace plots.
separate.chains
option to display each plot separately for different chains (except crosscorr and key). If FALSE, either the separate chains will be shown on the same plot (for trace, density, and ecdf) or as a single plot with combined chains (for histogram and autocor
trace.options
a list of arguments to be passed to the underlying plot function that creates the trace plots. A colour specification should be specified using the 'col' argument above to ensure that this is the same across plot types.
density.options
a list of arguments to be passed to the underlying plot function that creates the density plots. A colour specification should be specified using the 'col' argument above to ensure that this is the same across plot types.
histogram.options
a list of arguments to be passed to the underlying plot function that creates the histogram plots. A colour specification should be specified using the 'col' argument above to ensure that this is the same across plot types.
ecdfplot.options
a list of arguments to be passed to the underlying plot function that creates the ecdf plots. A colour specification should be specified using the 'col' argument above to ensure that this is the same across plot types.
acplot.options
a list of arguments to be passed to the underlying plot function that creates the autocorr plots. A colour specification should be specified using the 'col' argument above to ensure that this is the same across plot types.
...
additional arguments to be passed to pdf for the plot.runjags method, or the default print method for the print.runjags method. layout
the layout of the runjags plots to print, a numeric vector of length 2 stating the number of rows and columns of plots. The default value is taken from runjags.options. new.windows
option to produce each plot (or matrix of plots) on a new graphics window rather than over-writing the previous plots. For R interfaces where plots can be cycled through (e.g. the OS X GUI and RStudio), it is likely to be preferable to produce all plots
file
an optional filename to which plots can be saved using pdf. The default "" means produce plots in the active graphics device. digits
the number of digits to display for printed numerical output.