Remove standardizedVitalRates

[patrickbarks]

standardizedVitalRates calls four other Rage functions in sequence: rearrangeMatrix, reprodStages, collapseMatrix, then vitalRates. The first 3 convert an MPM to a standardized format, and the 4th extracts averaged vital rates.

I see no reason to group these 4 components into a single function:

• The main reason is that each component function has it's own set of optional arguments (e.g. reprodStages has different options for dealing with propagule and post-reproductive stages, vitalRates has different options for how to split and weight vital rates). standardizedVitalRates doesn't currently support any of these — it simply uses the defaults of the component functions. Adding this support would make standardizedVitalRates overly complicated, in my opinion.

• Second, the four component functions may each fail for different reasons. Combining them in a single function makes debugging more difficult.

• Third, a user that wants to extract vital rates from a standardized matrix is likely to want to calculate other things from that standardized matrix as well. But the standardized matrix is not returned by standardizedVitalRates.

Therefore, I suggest we remove standardizedVitalRates and encourage users to use the four component functions separately (e.g. with an example on the website or vignette). We could alternatively bundle the first 3 component functions into a new function (e.g. standardizeMatrix), which I think would be more useful to users, and not quite as complicated.

[jonesor]

Looks good.