Assorted methods needed by FLa4a

getYidx(object, ...)

# S4 method for FLQuant
getYidx(object, year)

is.empty(object)

niters(object, ...)

# S4 method for FLModelSim
niters(object)

# S4 method for a4aGr
niters(object)

# S4 method for a4aStkParams
dims(obj)

replaceZeros(object, ...)

# S4 method for FLQuant
replaceZeros(object, fraction = 0.25)

# S4 method for FLStock
replaceZeros(object, fraction = 0.25)

# S4 method for FLIndex
replaceZeros(object, fraction = 0.25)

# S4 method for FLIndices
replaceZeros(object, fraction = 0.25)

Arguments

object: object of relevant class (see signature of method)
...: additional argument list that might never be used
year: numeric with year to be extracted
obj: an object
fraction: numeric with fraction of minimum to replace zeros

getYidx

Gets an FLQuant's numeric id for a vector of "years". For internal use and not very interesting for users. It takes an FLQuant object and vector of years and returns a numeric vector that can be used to subset the FLQuant.

is.empty

Method is.empty checks if an object is empty. It takes any object and returns a logical, TRUE, if the object is of length 0.

niters

Compute number of iterations. Takes an object of any FLR class and returns a numeric.

dims

Extracts the dims of the parameters.

replaceZeros

Replaces observations of 0 by a fraction of the minimum observed. It takes an FLQuant object and numeric of min fraction and returns a FLQuant with zeros replaced to be added to the FLStock or FLIndex objects.

Examples

#Example use of getYidx:
data(ple4)
flq <- catch(ple4)
getYidx(flq, 2000:2004)
#> [1] 44 45 46 47 48
flq[, getYidx(flq, 2000:2004)]
#> An object of class "FLQuant"
#> , , unit = unique, season = all, area = unique
#> 
#>      year
#> age   2000   2001   2002   2003   2004  
#>   all 145998 128107 143807 154029 140056
#> 
#> units:  t 
#Example use of is.empty:
is.empty(list())
#> [1] TRUE
is.empty(list(a=2))
#> [1] FALSE
#Example use of niters:
mm <- matrix(NA, ncol=3, nrow=3)
diag(mm) <- c(50, 0.001,0.001)
mm[upper.tri(mm)] <- mm[lower.tri(mm)] <- c(0.1,0.01,0.00004)
md <- ~linf*(1-exp(-k*(t-t0)))
imd <- ~t0-1/k*log(1-len/linf)
prs <- FLPar(linf=58.5, k=0.086, t0=0.001, units=c("cm","yr^-1","yr"))
vbObj <- a4aGr(grMod=md, grInvMod=imd, params=prs, vcov=mm, distr="norm")
# Generate 100 sample sets
vbObj <- mvrnorm(100,vbObj)
niters(vbObj)
#> [1] 100
#Example use of dims:
dims(FLPar())
#> $iter
#> [1] 1
#> 
#> $params
#> [1] ""
#> 
#Example use of getYidx:
data(ple4)
flq <- catch(ple4)
flq <- replaceZeros(flq, 0.25)
catch(ple4) <- flq