hisse

checkRd: (-1) generateMiSSEGreedyCombinations.Rd:25: Lost braces
    25 | Estimating extinction rates is hard. This affects all diversification models (even if all you want and look at is speciation rate, extinction rate estimates still affect what this is as they affect the likelihood). It is most noticeable in MiSSE with eps, the extinction fraction (extinction rate divided by speciation rate). One option, following Magallon & Sanderson (2001), is to set extinction fraction at set values. By default, we use theirs, 0 (meaning a Yule model - no extinction) or 0.9 (a lot of extinction, though still less than paleontoligists find). You can set your own in \code{fixed.eps.tries}. If you only want to use fixed values, and not estimate, get rid of the NA, as well. However, don't \dQuote{cheat} -- if you use a range of values for fixed.eps, it's basically doing a search for this, though the default AICc calculation doesn't dQuote{know} this to penalize it for another parameter.
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four hidden states. They can be constrained: the easiest way is to have, say, turnover having an independent rate for each hidden state and eps having the same rate for all the hidden states. If \code{vary.both} is set to FALSE, all models are of this sort: if turnover varies, eps is constant across all hidden states, or vice versa. Jeremy Beaulieu prefers this. If \code{vary.both} is set to TRUE, both can vary: for example, there could be five hidden states for both turnover and eps, but turnover lets each of these have a different rate, but eps only allows three values (so that eps_A and eps_D might be forced to be equal, and eps_B and eps_E might be forced to be equal). Brian O'Meara would consider allowing this, while cautioning you about the risks of too many parameters.
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Found calls to structure() using deprecated special names:
  hisse/R/simulateHisse.R (.Dim: 1, .Names: 1)
'.Dim' should be changed to 'dim'.
'.Names' should be changed to 'names'.