FLQuant class for numerical data

Description

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

The sixth 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. 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.

Extends

FLArray array

Methods

[(base) :

Extract elements

signature(x=FLQuant,i=ANY,j=ANY,drop=missing)

[<-(base) :

Substitute elements

signature(x=FLQuant,i=ANY,j=ANY,value=missing)

apply(base) :

Operate with a function along certain dimensions

signature(X=FLQuant,MARGIN=missing,FUN=missing)

Arith(base) :

Arithmetic operations

signature(e1=FLQuant,e2=FLQuant)

as.data.frame(base) :

Convert to a data.frame with 7 columns

signature(x=FLQuant,row.names=ANY,optional=ANY)

as.FLQuant(FLCore) :

Convert into an FLQuant

signature(x=missing)

barchart(lattice) :

Plot a barchart following the given formula

signature(x=formula,data=FLQuant)

bubbles(FLCore) :

Plot a bubble following the given formula, with size of the bubbles given by the values in the object

signature(x=formula,data=FLQuant)

bwplot(lattice) :

Describe method

signature(x=formula,data=FLQuant)

catch<-(FLCore) :

Describe method

signature(object=FLCatch,value=FLQuant)

catch<-(FLCore) :

Describe method

signature(object=FLStock,value=FLQuant)

catch.n<-(FLCore) :

Describe method

signature(object=FLCatch,value=FLQuant)

catch.n<-(FLCore) :

Describe method

signature(object=FLStock,value=FLQuant)

catch.n<-(FLCore) :

Describe method

signature(object=FLIndex,value=FLQuant)

catch.wt<-(FLCore) :

Describe method

signature(object=FLCatch,value=FLQuant)

catch.wt<-(FLCore) :

Describe method

signature(object=FLStock,value=FLQuant)

catch.wt<-(FLCore) :

Describe method

signature(object=FLIndex,value=FLQuant)

coerce(methods) :

Describe method

signature(from=NULL,to=FLQuant,strict=missing)

cv(FLCore) :

Describe method

signature(object=missing)

dimnames<-(base) :

Describe method

signature(x=missing,value=missing)

dims(FLCore) :

Describe method

signature(obj=missing)

discards<-(FLCore) :

Describe method

signature(object=FLCatch,value=FLQuant)

discards<-(FLCore) :

Describe method

signature(object=FLStock,value=FLQuant)

discards.n<-(FLCore) :

Describe method

signature(object=FLCatch,value=FLQuant)

discards.n<-(FLCore) :

Describe method

signature(object=FLStock,value=FLQuant)

discards.wt<-(FLCore) :

Describe method

signature(object=FLCatch,value=FLQuant)

discards.wt<-(FLCore) :

Describe method

signature(object=FLStock,value=FLQuant)

dotplot(lattice) :

Describe method

signature(x=formula,data=FLQuant)

E(FLCore) :

Describe method

signature(object=missing)

fec<-(FLCore) :

Describe method

signature(object=FLBiol,value=FLQuant)

FLCatch(FLCore) :

Describe method

signature(object=missing)

FLCohort(FLCore) :

Describe method

signature(object=missing)

FLMetier(FLCore) :

Describe method

signature(catches=missing)

FLQuant(FLCore) :

Describe method

signature(object=missing)

FLQuantPoint(FLCore) :

Describe method

signature(object=missing)

FLSR(FLCore) :

Describe method

signature(object=FLQuant,model=missing)

FLSR(FLCore) :

Describe method

signature(object=FLQuant,model=character)

FLSR(FLCore) :

Describe method

signature(object=FLQuant,model=function)

FLSR(FLCore) :

Describe method

signature(object=FLQuant,model=formula)

harvest<-(FLCore) :

Describe method

signature(object=FLStock,value=FLQuant)

histogram(lattice) :

Describe method

signature(x=formula,data=FLQuant)

iter(FLCore) :

Describe method

signature(object=missing)

iter<-(FLCore) :

Describe method

signature(object=missing,value=missing)

iters(FLCore) :

Describe method

signature(object=missing)

landings<-(FLCore) :

Describe method

signature(object=FLCatch,value=FLQuant)

landings<-(FLCore) :

Describe method

signature(object=FLStock,value=FLQuant)

landings.n<-(FLCore) :

Describe method

signature(object=FLCatch,value=FLQuant)

landings.n<-(FLCore) :

Describe method

signature(object=FLStock,value=FLQuant)

landings.wt<-(FLCore) :

Describe method

signature(object=FLCatch,value=FLQuant)

landings.wt<-(FLCore) :

Describe method

signature(object=FLStock,value=FLQuant)

m<-(FLCore) :

Describe method

signature(object=FLStock,value=FLQuant)

m<-(FLCore) :

Describe method

signature(object=FLBiol,value=FLQuant)

n<-(FLCore) :

Describe method

signature(object=FLBiol,value=FLQuant)

names(base) :

Describe method

signature(x=missing)

plot(graphics) :

Describe method

signature(x=FLQuant,y=missing)

price<-(FLCore) :

Describe method

signature(object=FLCatch,value=FLQuant)

print(base) :

Describe method

signature(x=missing)

propagate(FLCore) :

Describe method

signature(object=missing)

quant(FLCore) :

Describe method

signature(object=missing)

quant<-(FLCore) :

Describe method

signature(object=missing,value=missing)

quantile(stats) :

Describe method

signature(x=missing)

rlnorm(stats) :

Describe method

signature(n=numeric,meanlog=FLQuant,sdlog=FLQuant)

rlnorm(stats) :

Describe method

signature(n=numeric,meanlog=FLQuant,sdlog=numeric)

rlnorm(stats) :

Describe method

signature(n=numeric,meanlog=numeric,sdlog=FLQuant)

rnorm(stats) :

Describe method

signature(n=numeric,mean=FLQuant,sd=FLQuant)

show(methods) :

Describe method

signature(object=missing)

spwn<-(FLCore) :

Describe method

signature(object=FLBiol,value=FLQuant)

stripplot(lattice) :

Describe method

signature(x=formula,data=FLQuant)

summary(base) :

Describe method

signature(object=missing)

trim(FLCore) :

Describe method

signature(object=missing)

units(base) :

Describe method

signature(x=missing)

units<-(base) :

Describe method

signature(x=FLQuant,value=character)

window(stats) :

Describe method

signature(x=missing)

wt<-(FLCore) :

Describe method

signature(object=FLBiol,value=FLQuant)

xyplot(lattice) :

Describe method

signature(x=formula,data=FLQuant)

Author(s)

The FLR Team

See Also

[, [<-, apply, Arith, as.data.frame, as.FLQuant, barchart, bubbles, bwplot, catch<-, catch.n<-, catch.wt<-, coerce, cv, dimnames<-, dims, discards<-, discards.n<-, discards.wt<-, dotplot, E, fec<-, FLCatch, FLCohort, FLMetier, FLQuant, FLQuantPoint, FLSR, harvest<-, histogram, iter, iter<-, iters, landings<-, landings.n<-, landings.wt<-, m<-, n<-, names, plot, price<-, print, propagate, quant, quant<-, quantile, rlnorm, rnorm, show, spwn<-, stripplot, summary, trim, units, units<-, window, wt<-, xyplot, array

Examples

# creating a new FLQuant
flq <- FLQuant(rnorm(200), dimnames=list(age=1:5, year=2000:2008), units='diff')
summary(flq)

flq[1,]
flq[,1]
flq[1,1] <- 0

units(flq)
quant(flq)

xyplot(data ~ year, data=flq, type='b', main='FLQ Test Plot', groups=age,
  ylab='diff', xlab='', pch=19, auto.key=TRUE)