simLenSelect: Simulate sampling fish based on length selectivity.
In droglenc/FSAsim: Simulate Data for Fisheries Stock Assessment Methods

Description Usage Arguments Details Value See Also Examples

Constructs a sample of fish based on a user-supplied length-based selectivity curve. The selectivity curve can be supplied via a parametric model (the beta distribution) or manually for various length categories.

simLenSelectP(lens, alpha = 1, beta = 1, max.height = 1, show = FALSE)

simLenSelectM(
  lens,
  breaks,
  probs = rep(max.height, length(breaks)),
  max.height = 1,
  interact = TRUE,
  digits = 2
)

`lens`	A vector containg the lengths of individual fish.
`alpha`	A numeric shape parameter to the beta distribution. See `dbeta`.
`beta`	A numeric shape parameter to the beta distribution. See `dbeta`.
`max.height`	A numeric that controls the maximum height of the probability distribution – i.e., this will be the maximum probability of capture.
`show`	A logical indicating whether a graphic of the selectivity curve should be shown (`=TRUE`) or not (`=TRUE`; default).
`breaks`	A numeric vector of lower values for the break points of the length categories.
`probs`	A numeric vector of capture probabilities (i.e., selectivities) for each length category. Default is a vector containing all ones – i.e., no selectivity by length category.
`interact`	A logical indicating whether the capture probabilities (i.e., selectivities) should be chosen by the user interacting with a selectivity plot. See details.
`digits`	A numeric indicating the number of digits that should be used when selecting the capture probabilities. Smaller values represent coarser choices.

NEED DETAIL HERE.

If simLenSelectP is used then a vector of logicals indicating whether each fish was sampled (TRUE) or not. If simLenSelectM is used then a list that contains the following three items is returned:

smpld a vector of logicals indicating whether each fish was sampled (TRUE) or not.
breaks the vector of length category breaks sent in breaks.
probs the vector of capture probabilities that corresponds to the length categories in breaks. This vector may not equal the supplied probs vector if the user changed the capture probabilities with the interactive graphic (i.e., using interact=TRUE).

simAges, simLenFromAge

## Load FSA package for Summarize()
library(FSA)

## set seed for repeatability
set.seed(5234734)

## Simulated individual ages (random)
#    see simAges functions
bg.ages <- simAges(N0=500,A=0.35)

## Simulated lengths, given the above ages
bg.lens <- simLenFromAge(bg.ages,228,0.206,0,8)

## Simulated samplings given the above lengths and 
##   selectivities from a beta(3,5)
bg.smpl <- simLenSelectP(bg.lens,3,5)
# append ages, lengths, and samplings into one data frame
bg.df1 <- data.frame(age=bg.ages,len=bg.lens,smpld=bg.smpl)
# get only those that were sampled
bg.df1a <- Subset(bg.df1,smpld)
# Summaries
Summarize(len~age,data=bg.df1,digits=1)
Summarize(len~age,data=bg.df1a,digits=1)

## Simulated samplings given the above lengths and user supplied selectivities
bg.brks <- seq(20,230,10)
bg.prbs1 <- c(0.0,0.0,0.0,0.1,0.3,0.6,0.9,0.9,1.0,1.0,1.0,1.0,1.0,1.0,1.0,0.9,
 0.8,0.6,0.3,0.2,0.1,0.0)
bg.smpl1 <- simLenSelectM(bg.lens,bg.brks,bg.prbs1,interact=FALSE)
bg.df2 <- data.frame(age=bg.ages,len=bg.lens,smpld=bg.smpl1$smpld)
bg.df2a <- Subset(bg.df2,smpld)
Summarize(len~age,data=bg.df2,digits=1)
Summarize(len~age,data=bg.df2a,digits=1)

## Simulated samplings given the above lengths and selectivities from interactive choices
#  NOT RUN because of interactive choices
## Not run: 
bg.brks <- seq(20,230,10)
bg.smpl2 <- simLenSelectM(bg.lens,bg.brks)
bg.df3 <- data.frame(age=bg.ages,len=bg.lens,smpld=bg.smpl2$smpld)
bg.df3a <- Subset(bg.df3,smpld)
Summarize(len~age,data=bg.df3,digits=1)
Summarize(len~age,data=bg.df3a,digits=1)

## End(Not run)