The FLQuant class is a six-dimensional array designed to store most quantitative data used in fisheries and population modelling.

FLQuant(object, ...)

# S4 method for missing
FLQuant(object, dim = rep(1, 6),
  dimnames = "missing", quant = NULL, units = "NA", iter = 1)

# S4 method for vector
FLQuant(object, dim = rep(1, 6),
  dimnames = "missing", quant = NULL, units = "NA", iter = 1,
  fill.iter = TRUE)

# S4 method for array
FLQuant(object, dim = rep(1, 6),
  dimnames = "missing", quant = NULL, units = "NA", iter = 1,
  fill.iter = TRUE)

# S4 method for matrix
FLQuant(object, dim = lapply(dimnames, length),
  dimnames = "missing", ...)

# S4 method for FLQuant
FLQuant(object,
  quant = attributes(object)[["quant"]],
  units = attributes(object)[["units"]],
  dimnames = attributes(object)[["dimnames"]], iter = dim(object)[6],
  fill.iter = TRUE, dim = attributes(object)[["dim"]])

Arguments

object

Input numeric object

...

Additional arguments

dim

Vector of dimension lengths

dimnames

List of dimension names

quant

Character vector for name of first dimension

units

Character vctor of units of measurement, see uom

iter

Number of iterations, i.e. length of the 6th dimension

fill.iter

Should iterations be filled with the same content as the first?

Details

The six dimensions are named. The name of the first dimension can be altered by the user from its default, quant. This could typically be age or length for data related to natural populations. The only name not accepted is 'cohort', as data structured along cohort should be stored using the FLCohort class instead. Other dimensions are always names as follows: year, for the calendar year of the datapoint; unit, for any kind of division of the population, e.g. by sex; season, for any temporal strata shorter than year; area, for any kind of spatial stratification; and iter, for replicates obtained through bootstrap, simulation or Bayesian analysis.

In addition, FLQuant objects contain a units attribute, of class character, intended to contain the units of measurement relevant to the data.

Slots

.Data

A 6-D array for numeric data. array.

units

Units of measurement. character.

Validity

Dimensions:

Array must have 6 dimensions

Content:

Array must be of class numeric

Dimnames:

Dimensions 2 to 6 must be named "year", "unit", "season", "area" and "iter"

Constructor

The FLQuant method provides a flexible constructor for objects of the class. Inputs can be of class:

vector:

A numeric vector will be placed along the year dimension by default.

matrix:

A matrix will be placed along dimensions 1 and 2, unless otherwise specified by 'dim'. The matrix dimnames will be used unless overriden by 'dimnames'.

array:

As above

missing:

If no input is given, an empty FLQuant (NA) is returned, but dimensions and dimnames can still be specified.

Additional arguments to the constructor:

units:

The units of measurement, a character string.

dim:

The dimensions of the object, a numeric vector of length 6.

dimnames:

A list object providing the dimnames of the array. Only those different from the default ones need to be specified.

quant:

The name of the first dimension, if different from 'quant', as a character string.

See also

FLQuant

Examples

# creating a new FLQuant flq <- FLQuant() flq <- FLQuant(1:10, dim=c(2,5)) summary(flq)
#> An object of class "FLQuant" with: #> dim : 2 5 1 1 1 1 #> quant: quant #> units: NA #> #> Min : 1 #> 1st Qu.: 3.25 #> Mean : 5.5 #> Median : 5.5 #> 3rd Qu.: 7.75 #> Max : 10 #> NAs : 0 %
# Vectors are used column first... dim(FLQuant(1:10))
#> [1] 1 10 1 1 1 1
# ...while matrices go row first. dim(FLQuant(matrix(1:10)))
#> [1] 10 1 1 1 1 1
FLQuant(matrix(rnorm(100), ncol=20))
#> An object of class "FLQuant" #> , , unit = unique, season = all, area = unique #> #> year #> quant 1 2 3 4 5 6 7 #> 1 0.671420 1.250601 -1.574575 -1.653281 -0.386304 -2.377515 -0.205677 #> 2 1.230022 -1.876237 -0.196319 -2.761868 -0.242499 -0.065409 0.234881 #> 3 1.645468 -0.368788 0.915060 0.264369 0.220593 -0.469705 0.110628 #> 4 -0.182926 -2.129297 1.078637 1.024572 -1.481090 -0.280516 0.274202 #> 5 -1.379258 0.337646 1.452803 -0.659186 0.724691 0.574837 1.574920 #> year #> quant 8 9 10 11 12 13 14 #> 1 0.567768 -0.579388 -0.420207 1.138668 -0.096206 0.427619 -0.395441 #> 2 -0.059612 0.942199 -0.255375 0.190523 0.694509 -0.566479 -0.130702 #> 3 -0.149588 -0.706361 -0.369238 -1.366394 -0.474591 -0.833835 -1.999494 #> 4 0.266169 -1.275402 1.212448 -1.298103 1.763131 0.398259 -0.995931 #> 5 0.528403 0.733260 -0.445363 -2.137098 2.025846 -1.474538 0.420114 #> year #> quant 15 16 17 18 19 20 #> 1 -0.062862 -0.780270 1.513670 -0.610945 -0.144902 -0.094504 #> 2 -0.080132 -1.776959 0.033989 1.251884 -0.324447 0.032556 #> 3 -0.032283 -0.427835 0.740793 0.250319 -0.172565 0.461290 #> 4 -0.718981 -2.031027 -1.270808 -1.705582 -1.236063 1.381400 #> 5 -1.116561 2.750765 -0.163564 -0.855413 -1.902304 -0.416476 #> #> units: NA
FLQuant(array(rnorm(100), dim=c(5,2,1,1,1,10)))
#> An object of class "FLQuant" #> iters: 10 #> #> , , unit = unique, season = all, area = unique #> #> year #> quant 1 2 #> 1 -0.25995(1.298) 0.34655(0.434) #> 2 -0.46356(0.383) -0.57083(1.013) #> 3 -0.22391(1.044) -0.61925(0.631) #> 4 -0.51552(0.419) -0.46943(0.615) #> 5 -0.23508(0.617) 0.39845(0.978) #> #> units: NA
FLQuant(array(rnorm(100), dim=c(5,2)), iter=10)
#> An object of class "FLQuant" #> iters: 10 #> #> , , unit = unique, season = all, area = unique #> #> year #> quant 1 2 #> 1 0.696270(0) -0.830808(0) #> 2 2.008870(0) 1.402474(0) #> 3 -0.056978(0) -0.723869(0) #> 4 0.240416(0) 1.330580(0) #> 5 -0.021890(0) -0.811333(0) #> #> units: NA
# working with FLQuant objects flq <- FLQuant(rnorm(200), dimnames=list(age=1:5, year=2000:2008), units='diff') summary(flq)
#> An object of class "FLQuant" with: #> dim : 5 9 1 1 1 1 #> quant: age #> units: diff #> #> Min : -1.69018 #> 1st Qu.: -0.715704 #> Mean : -0.02313333 #> Median : -0.08009077 #> 3rd Qu.: 0.5949239 #> Max : 1.915691 #> NAs : 0 %
flq[1,]
#> An object of class "FLQuant" #> , , unit = unique, season = all, area = unique #> #> year #> age 2000 2001 2002 2003 2004 2005 2006 2007 #> 1 -0.27494 0.81959 -0.38404 -0.34301 0.47958 -0.79594 -0.94297 -0.18924 #> year #> age 2008 #> 1 -0.45863 #> #> units: diff
flq[,1]
#> An object of class "FLQuant" #> , , unit = unique, season = all, area = unique #> #> year #> age 2000 #> 1 -0.27494 #> 2 0.48545 #> 3 0.91698 #> 4 -0.98534 #> 5 -1.49119 #> #> units: diff
flq[1,1] <- 0 units(flq)
#> [1] "diff"
quant(flq)
#> [1] "age"
plot(flq)
FLQuant()
#> An object of class "FLQuant" #> , , unit = unique, season = all, area = unique #> #> year #> quant 1 #> all NA #> #> units: NA
summary(FLQuant())
#> An object of class "FLQuant" with: #> dim : 1 1 1 1 1 1 #> quant: quant #> units: NA #> #> Min : NA #> 1st Qu.: NA #> Mean : NA #> Median : NA #> 3rd Qu.: NA #> Max : NA #> NAs : 100 %
FLQuant(1:10)
#> An object of class "FLQuant" #> , , unit = unique, season = all, area = unique #> #> year #> quant 1 2 3 4 5 6 7 8 9 10 #> all 1 2 3 4 5 6 7 8 9 10 #> #> units: NA
FLQuant(array(rnorm(9), dim=c(3,3,3)))
#> An object of class "FLQuant" #> , , unit = 1, season = all, area = unique #> #> year #> quant 1 2 3 #> 1 0.971396 0.225973 0.334415 #> 2 -0.579663 -0.514857 -0.093491 #> 3 1.604180 -0.823788 0.304062 #> #> , , unit = 2, season = all, area = unique #> #> year #> quant 1 2 3 #> 1 0.971396 0.225973 0.334415 #> 2 -0.579663 -0.514857 -0.093491 #> 3 1.604180 -0.823788 0.304062 #> #> , , unit = 3, season = all, area = unique #> #> year #> quant 1 2 3 #> 1 0.971396 0.225973 0.334415 #> 2 -0.579663 -0.514857 -0.093491 #> 3 1.604180 -0.823788 0.304062 #> #> units: NA
FLQuant(matrix(rnorm(12), nrow=3, ncol=3))
#> An object of class "FLQuant" #> , , unit = unique, season = all, area = unique #> #> year #> quant 1 2 3 #> 1 -0.476508 -1.555644 -0.129409 #> 2 -0.241312 0.093501 0.407796 #> 3 0.824156 -0.366949 -0.583969 #> #> units: NA
FLQuant(FLQuant(array(rnorm(9), dim=c(3,3,3)), units='kg'), units='t')
#> An object of class "FLQuant" #> , , unit = 1, season = all, area = unique #> #> year #> quant 1 2 3 #> 1 0.357236 -1.609575 0.176436 #> 2 0.550428 -1.049710 1.128307 #> 3 0.038402 2.052034 0.435002 #> #> , , unit = 2, season = all, area = unique #> #> year #> quant 1 2 3 #> 1 0.357236 -1.609575 0.176436 #> 2 0.550428 -1.049710 1.128307 #> 3 0.038402 2.052034 0.435002 #> #> , , unit = 3, season = all, area = unique #> #> year #> quant 1 2 3 #> 1 0.357236 -1.609575 0.176436 #> 2 0.550428 -1.049710 1.128307 #> 3 0.038402 2.052034 0.435002 #> #> units: t