If na.rm=TRUE
(the default) then elements of a variable that
are missing (NA
) for any iteration in at least one chain will
be dropped.
This argument was added to handle incompletely defined variables.
From JAGS version 4.0.0, users may monitor variables that are not
completely defined in the BUGS language description of the model,
e.g. if y[i]
is defined in a for
loop starting from
i=3
then y[1], y[2]
are not defined. The user may still
monitor variable y
and the monitored values corresponding to
y[1], y[2]
will have value NA
for all iterations in all
chains. Most of the functions in the coda package cannot handle
missing values so these variables are dropped by default.