Extract input checking and transforming from functions used in loops

[Bisaloo]

Internal functions used in loops (via optim() ) include input checking which will have to run in every single iteration of the loop:

epiparameter/R/extract_param.R

Lines 307 to 327 in 18e9dd8

	dist <- match.arg(dist)
	cumulative <- switch(dist,
	lnorm = stats::plnorm,
	gamma = stats::pgamma,
	weibull = stats::pweibull,
	norm = stats::pnorm
	)
	density <- switch(dist,
	lnorm = stats::dlnorm,
	gamma = stats::dgamma,
	weibull = stats::dweibull,
	norm = stats::dnorm
	)
	param_names <- switch(dist,
	lnorm = c("meanlog", "sdlog"),
	gamma = c("shape", "scale"),
	weibull = c("shape", "scale"),
	norm = c("mean", "sd")
	)

epiparameter/R/extract_param.R

Lines 365 to 377 in 18e9dd8

	dist <- match.arg(dist)
	cumulative <- switch(dist,
	lnorm = stats::plnorm,
	gamma = stats::pgamma,
	weibull = stats::pweibull,
	norm = stats::pnorm
	)
	param_names <- switch(dist,
	lnorm = c("meanlog", "sdlog"),
	gamma = c("shape", "scale"),
	weibull = c("shape", "scale"),
	norm = c("mean", "sd")

From a performance point of view, it would be much better to do this once before the loop is initiated. Since they are internal functions, we don't have to worry about checking their inputs.

It would also potentially reduce duplication across these two functions.