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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.
The text was updated successfully, but these errors were encountered:
standardizedVitalRates
calls four other Rage functions in sequence:rearrangeMatrix
,reprodStages
,collapseMatrix
, thenvitalRates
. 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 makestandardizedVitalRates
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.The text was updated successfully, but these errors were encountered: