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fitContinuous - input argument names and documentation names are very confusing #25

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lukejharmon opened this issue Apr 15, 2016 · 1 comment

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@lukejharmon
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When people discuss evolutionary trends in the literature, they usually mean changes in the mean trait value through time. But in fitContinuous this is called "drift" - which conjures genetic drift and, probably, is confusing to everyone. Then what we call the trend model is a trend in the rate, and is very similar to EB - but there is really no way to know that from the documentation.

This is a bit of a sad state. I suggest changing this but in a way that maintains backwards compatibility with people's code - that is, add two new arguments for these two models that are more intuitive, like meanTrend and rateTrend, and (silently) accept the old arguments as well.

@liamrevell
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I made this changes - but called the models "mean_trend" and "rate_trend" while maintaining backward compatibility (that is, "drift" and "trend" are still accepted).

I then went to update the model names in fitContinuousMCMC - but I discovered they are all totally different & gave up!

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