Change depletion() to use data=()

[droglenc]

The current version of depletion() uses vectors of catch and effort as the first two arguments. While this may be useful if catch and effort were entered into separate stand-alone vectors it is cumbersome if catch and effort data are in a data.frame (see examples with SMBassLS). Alternatively, it may be more useful to have a formula version that uses data=. For backward compatibility, the current use of vectors should be maintained (I think this is the case with catchCurve(), so check that code for an example).

This stems from a question from Keane Flynn about wanting to do something like group_by() |> depletion() to efficiently perform the analysis for multiple groups of data. A current hacky work-around for that situation is below (probably could have used split() and lapply() here as well). Adding the formula notation with data= should make this easier.

## Dummy example data (grp="A" is SMBassLS example ... just FYI)
tmpdf <- data.frame(ct=c(131,69,99,78,56,76,49,42,63,47,
                         117,75,87,67,58,67,42),
                    ft=c(7,7,7,7,7,7,7,7,7,7,
                         5,7,5,5,4,6,5),
                    grp=as.factor(c("A","A","A","A","A","A","A","A","A","A",
                                    "B","B","B","B","B","B","B")))
str(tmpdf)

## Initialize a results data.frame
res <- data.frame("grp"=factor(),
                  "No"=double(),"No.se"=double(),
                  "q"=double(),"q.se"=double())

## Use a loop to process groups individually
for (i in levels(tmpdf$grp)) {
  tmp <- dplyr::filter(tmpdf,grp==i)
  tmpres <- FSA::depletion(tmp$ct,tmp$ft,method="Leslie")
  res <- dplyr::add_row(res,"grp"=i,
                        No=tmpres$est["No","Estimate"],
                        No.se=tmpres$est["No","Std. Err."],
                        q=tmpres$est["q","Estimate"],
                        q.se=tmpres$est["q","Std. Err."])
}

## See the result
res