sample4ALK: Sample fish for construction of an age-length key.
In droglenc/FSAsim: Simulate Data for Fisheries Stock Assessment Methods

Description Usage Arguments Value Examples

Samples fish from a data frame of lengths and ages to simulate selecton of fish to be used to construct an age-length key. Fish can either be selected as a fixed number per length category (e.g., 5 fish per 10-mm length category) or as a random sample from the population.

sample4ALK(
  formula,
  data,
  type = c("fixed", "random"),
  n.fixed = 10,
  n.random = 100,
  w = 1,
  startcat = NULL,
  breaks = NULL
)

`formula`	A formula of the form `age~length` where “age” generically represents a variable in `data` that contain the observed ages and “length” generically represents a variable in `data` that contains the observed length measurements.
`data`	A data.frame that minimally contains the observed age and length measurements in the `formula`.
`type`	A string indicating the type of sampling to conduct. See details.
`n.fixed`	A single numeric that indicates the number of fish to sample per length category when `type="fixed"`.
`n.random`	A single numeric that indicates the total number of fish to sample when `type="random"`.
`w`	A single numeric that indicates the width of length categories to create when `type="fixed"`.
`startcat`	A single numeric that indicates the beginning of the first length category when `type="fixed"`.
`breaks`	A numeric vector of lower values for the break points of the length categories when `type="fixed"`.

A data.frame similar to data but where some of the ages have been replaced with NA to simulate fish that have NOT been sampled for ages.

## get FSA library for lencat
require(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)

## Combine lengths and ages into one data.frame
df <- data.frame(age=bg.ages,len=bg.lens)
# length frequency (10-mm) of the "population"
df$LCat <- lencat(df$len,w=10)
( popLF <- xtabs(~LCat,df) )
round(prop.table(popLF),2)

## Simulate some fish having ages -- random selection of 200 individuals
dfage1 <- sample4ALK(age~len,data=df,type="random",n.random=200)
# length frequency (10-mm) of the "aged" fish
( smpl1LF <- xtabs(~LCat,Subset(dfage1,!is.na(age))) )
round(prop.table(smpl1LF),2)

## Simulate some fish having ages -- 10 fish per 10-mm length category
dfage2 <- sample4ALK(age~len,data=df,type="fixed",w=10,n.fixed=10)
# length frequency (10-mm) of the "aged" fish
( smpl2LF <- xtabs(~LCat,Subset(dfage2,!is.na(age))) )
round(prop.table(smpl2LF),2)

## Example age-length key from the last sample
# get age-sample
df.age <- Subset(dfage2,!is.na(age))
al.raw <- xtabs(~LCat+age,data=df.age)
al.key <- prop.table(al.raw,margin=1)
round(al.key,2)