FLQuant class for numerical data

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

Usage

FLQuant(object, ...)

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

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

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

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

# S4 method for class '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.

Author

The FLR Team

Examples


# creating a new FLQuant
flq <- FLQuant()
flq <- FLQuant(1:10, dim=c(2,5))
summary(flq)
#> An object of class "FLQuant" with:
#> 
#> dim:    quant year unit season area iter 
#>         2     5    1    1      1    1 
#> units:  NA 
#> 
#>    Min. 1st Qu.  Median    Mean 3rd Qu.    Max.    %NAs 
#>     1.0     3.2     5.5     5.5     7.8    10.0     0.0 

# 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 x of class "FLQuant"
#> , , unit = unique, season = all, area = unique
#> 
#>      year
#> quant 1       2       3       4       5       6       7       8       9      
#>     1  0.6714  1.2506 -1.5746 -1.6533 -0.3863 -2.3775 -0.2057  0.5678 -0.5794
#>     2  1.2300 -1.8762 -0.1963 -2.7619 -0.2425 -0.0654  0.2349 -0.0596  0.9422
#>     3  1.6455 -0.3688  0.9151  0.2644  0.2206 -0.4697  0.1106 -0.1496 -0.7064
#>     4 -0.1829 -2.1293  1.0786  1.0246 -1.4811 -0.2805  0.2742  0.2662 -1.2754
#>     5 -1.3793  0.3376  1.4528 -0.6592  0.7247  0.5748  1.5749  0.5284  0.7333
#>      year
#> quant 10      11      12      13      14      15      16      17      18     
#>     1 -0.4202  1.1387 -0.0962  0.4276 -0.3954 -0.0629 -0.7803  1.5137 -0.6109
#>     2 -0.2554  0.1905  0.6945 -0.5665 -0.1307 -0.0801 -1.7770  0.0340  1.2519
#>     3 -0.3692 -1.3664 -0.4746 -0.8338 -1.9995 -0.0323 -0.4278  0.7408  0.2503
#>     4  1.2124 -1.2981  1.7631  0.3983 -0.9959 -0.7190 -2.0310 -1.2708 -1.7056
#>     5 -0.4454 -2.1371  2.0258 -1.4745  0.4201 -1.1166  2.7508 -0.1636 -0.8554
#>      year
#> quant 19      20     
#>     1 -0.1449 -0.0945
#>     2 -0.3244  0.0326
#>     3 -0.1726  0.4613
#>     4 -1.2361  1.3814
#>     5 -1.9023 -0.4165
#> 
#> units:  NA 

FLQuant(array(rnorm(100), dim=c(5,2,1,1,1,10)))
#> An x of class "FLQuant"
#> iters:  10 
#> 
#> , , unit = unique, season = all, area = unique
#> 
#>      year
#> quant 1             2            
#>     1 -0.260(1.298)  0.347(0.434)
#>     2 -0.464(0.383) -0.571(1.013)
#>     3 -0.224(1.044) -0.619(0.631)
#>     4 -0.516(0.419) -0.469(0.615)
#>     5 -0.235(0.617)  0.398(0.978)
#> 
#> units:  NA 
FLQuant(array(rnorm(100), dim=c(5,2)), iter=10)
#> An x of class "FLQuant"
#> iters:  10 
#> 
#> , , unit = unique, season = all, area = unique
#> 
#>      year
#> quant 1          2         
#>     1  0.6963(0) -0.8308(0)
#>     2  2.0089(0)  1.4025(0)
#>     3 -0.0570(0) -0.7239(0)
#>     4  0.2404(0)  1.3306(0)
#>     5 -0.0219(0) -0.8113(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:    age year unit season area iter 
#>         5   9    1    1      1    1 
#> units:  diff 
#> 
#>    Min. 1st Qu.  Median    Mean 3rd Qu.    Max.    %NAs 
#>  -1.690  -0.716  -0.080  -0.023   0.595   1.916   0.000 

flq[1,]
#> An x of class "FLQuant"
#> , , unit = unique, season = all, area = unique
#> 
#>    year
#> age 2000   2001   2002   2003   2004   2005   2006   2007   2008  
#>   1 -0.275  0.820 -0.384 -0.343  0.480 -0.796 -0.943 -0.189 -0.459
#> 
#> units:  diff 
flq[,1]
#> An x of class "FLQuant"
#> , , unit = unique, season = all, area = unique
#> 
#>    year
#> age 2000  
#>   1 -0.275
#>   2  0.485
#>   3  0.917
#>   4 -0.985
#>   5 -1.491
#> 
#> units:  diff 
flq[1,1] <- 0

units(flq)
#> [1] "diff"
quant(flq)
#> [1] "age"

plot(flq)



FLQuant()
#> An x 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:    quant year unit season area iter 
#>         1     1    1    1      1    1 
#> units:  NA 
#> 
#>    Min. 1st Qu.  Median    Mean 3rd Qu.    Max.    %NAs 
#>      NA      NA      NA      NA      NA      NA     100 

FLQuant(1:10)
#> An x 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 x of class "FLQuant"
#> , , unit = 1, season = all, area = unique
#> 
#>      year
#> quant 1       2       3      
#>     1  0.9714  0.2260  0.3344
#>     2 -0.5797 -0.5149 -0.0935
#>     3  1.6042 -0.8238  0.3041
#> 
#> , , unit = 2, season = all, area = unique
#> 
#>      year
#> quant 1       2       3      
#>     1  0.9714  0.2260  0.3344
#>     2 -0.5797 -0.5149 -0.0935
#>     3  1.6042 -0.8238  0.3041
#> 
#> , , unit = 3, season = all, area = unique
#> 
#>      year
#> quant 1       2       3      
#>     1  0.9714  0.2260  0.3344
#>     2 -0.5797 -0.5149 -0.0935
#>     3  1.6042 -0.8238  0.3041
#> 
#> units:  NA 
FLQuant(matrix(rnorm(12), nrow=4, ncol=3))
#> An x of class "FLQuant"
#> , , unit = unique, season = all, area = unique
#> 
#>      year
#> quant 1       2       3      
#>     1 -0.4765  0.0935 -0.5840
#>     2 -0.2413 -0.3669 -0.1934
#>     3  0.8242 -0.1294 -0.2695
#>     4 -1.5556  0.4078  0.0737
#> 
#> units:  NA 

FLQuant(FLQuant(array(rnorm(9), dim=c(3,3,3)), units='kg'), units='t')
#> An x of class "FLQuant"
#> , , unit = 1, season = all, area = unique
#> 
#>      year
#> quant 1       2       3      
#>     1  0.3572 -1.6096  0.1764
#>     2  0.5504 -1.0497  1.1283
#>     3  0.0384  2.0520  0.4350
#> 
#> , , unit = 2, season = all, area = unique
#> 
#>      year
#> quant 1       2       3      
#>     1  0.3572 -1.6096  0.1764
#>     2  0.5504 -1.0497  1.1283
#>     3  0.0384  2.0520  0.4350
#> 
#> , , unit = 3, season = all, area = unique
#> 
#>      year
#> quant 1       2       3      
#>     1  0.3572 -1.6096  0.1764
#>     2  0.5504 -1.0497  1.1283
#>     3  0.0384  2.0520  0.4350
#> 
#> units:  t