From Ape's log,
chronogram has indeed been deprecated.
CHANGES IN APE VERSION 2.5-2
DEPRECATED & DEFUNCT
o evolve.phylo() and plot.ancestral() have been removed.
o chronogram(), ratogram(), and NPRS.criterion() have been removed.
But as mentionned in this page (thanks @cpad0112), using the parameter
chronos is similar to applying the NPRS.
[EDIT] After looking at the function's code and confirming by reading Sanderson 2002, lambda is the level of penalization of the loglikelihood. So the higher the lambda, the closer you are from NPRS. I am pretty sure the page I quoted here is wrong. Here is the function of interest (penalized likelihood with correlated rate), in chronos:
correlated = function(rate,
loglik <- log.lik.poisson(rate, node.time)
if (!is.finite(loglik)) return(-1e+100)
loglik - lambda * (sum((rate[ind1] - rate[ind2])^2) +