dimSummaries: Summaries by dimension

In flr/FLCore: Core Package of FLR, Fisheries Modelling in R

Summaries by dimension

Description

Methods to compute various summary calculations (sum, mean, variance) over selected dimensions of objects from any array-based classes (e.g. FLQuant). These methods return an object of the same dimensions as the input but with length one in the dimension chosen to operate along.

Usage

quantSums(x, ...)

yearSums(x, ...)

unitSums(x, ...)

seasonSums(x, ...)

areaSums(x, ...)

iterSums(x, ...)

dimSums(x, ...)

quantMeans(x, ...)

yearMedians(x, ...)

yearMeans(x, ...)

unitMeans(x, ...)

seasonMeans(x, ...)

areaMeans(x, ...)

iterMeans(x, ...)

dimMeans(x, ...)

quantVars(x, ...)

yearVars(x, ...)

unitVars(x, ...)

seasonVars(x, ...)

areaVars(x, ...)

iterVars(x, ...)

dimVars(x, ...)

iterMedians(x, ...)

iterCVs(x, ...)

iterProb(x, ...)

## S4 method for signature 'FLQuant'
quantSums(x, na.rm = TRUE)

## S4 method for signature 'FLQuant'
yearSums(x, na.rm = TRUE)

## S4 method for signature 'FLQuant'
unitSums(x, na.rm = TRUE)

## S4 method for signature 'FLQuant'
seasonSums(x, na.rm = TRUE)

## S4 method for signature 'FLQuant'
areaSums(x, na.rm = TRUE)

## S4 method for signature 'FLQuant'
iterSums(x, na.rm = TRUE)

## S4 method for signature 'FLQuant'
quantMeans(x, na.rm = TRUE)

## S4 method for signature 'FLQuant'
yearMeans(x, na.rm = TRUE)

## S4 method for signature 'FLQuant'
unitMeans(x, na.rm = TRUE)

## S4 method for signature 'FLQuant'
seasonMeans(x, na.rm = TRUE)

## S4 method for signature 'FLQuant'
areaMeans(x, na.rm = TRUE)

## S4 method for signature 'FLQuant'
iterMeans(x, na.rm = TRUE)

## S4 method for signature 'FLQuant'
yearMedians(x, na.rm = TRUE)

## S4 method for signature 'FLQuant'
iterMedians(x, na.rm = TRUE)

## S4 method for signature 'FLQuant'
quantVars(x, na.rm = TRUE)

## S4 method for signature 'FLQuant'
yearVars(x, na.rm = TRUE)

## S4 method for signature 'FLQuant'
unitVars(x, na.rm = TRUE)

## S4 method for signature 'FLQuant'
seasonVars(x, na.rm = TRUE)

## S4 method for signature 'FLQuant'
areaVars(x, na.rm = TRUE)

## S4 method for signature 'FLQuant'
iterVars(x, na.rm = TRUE)

## S4 method for signature 'FLQuant'
iterCVs(x, na.rm = TRUE)

## S4 method for signature 'FLQuant'
iterProb(x, na.rm = TRUE)

## S4 method for signature 'FLQuantDistr'
yearSums(x, na.rm = TRUE)

## S4 method for signature 'FLQuantDistr'
unitSums(x, na.rm = TRUE)

## S4 method for signature 'FLQuantDistr'
seasonSums(x, na.rm = TRUE)

## S4 method for signature 'FLQuantDistr'
areaSums(x, na.rm = TRUE)

## S4 method for signature 'FLQuantDistr'
yearMeans(x, na.rm = TRUE)

## S4 method for signature 'FLQuantDistr'
unitMeans(x, na.rm = TRUE)

## S4 method for signature 'FLQuantDistr'
seasonMeans(x, na.rm = TRUE)

## S4 method for signature 'FLQuantDistr'
areaMeans(x, na.rm = TRUE)

## S4 method for signature 'FLQuantDistr'
iterMeans(x, na.rm = TRUE)

## S4 method for signature 'FLQuantDistr'
iterMedians(x, na.rm = TRUE)

## S4 method for signature 'FLQuantDistr'
quantVars(x, na.rm = TRUE)

## S4 method for signature 'FLQuantDistr'
yearVars(x, na.rm = TRUE)

## S4 method for signature 'FLQuantDistr'
unitVars(x, na.rm = TRUE)

## S4 method for signature 'FLQuantDistr'
seasonVars(x, na.rm = TRUE)

## S4 method for signature 'FLQuantDistr'
areaVars(x, na.rm = TRUE)

## S4 method for signature 'FLQuantDistr'
iterVars(x, na.rm = TRUE)

## S4 method for signature 'FLPar'
iterMeans(x, na.rm = TRUE)

## S4 method for signature 'FLPar'
iterMedians(x, na.rm = TRUE)

## S4 method for signature 'FLPar'
iterVars(x, na.rm = TRUE)

## S4 method for signature 'FLPar'
iterSums(x, na.rm = TRUE)

Arguments

x	An object.
na.rm	Should NAs be removed before calculation? Defaults to TRUE.

Details

This set of methods computes three different summaries (sum, mean and variance) of an FLQuant object along each of the six dimensions (quant, year, unit, season, area, or iter). Medians and CVs can also be computed along the sixth dimension, iter.

These methods encapsulate a call to apply with the corresponding dimensions and function: mean, median, var, and sum, while iterCVs are computed as sqrt(iterVars) / iterMeans.

In contrast with R standard behaviour, the sum of a dimension where all elements are NA will be NA and not 0. See example below.

Methods working along the iter dimension are also defined for objects of class FLPar.

Methods to operate over the first dimension refer to it as the quant dimension, regardless of the actual name used in the object.

Generic methods

quantSums(x), quantMeans(x), quantVars(x) yearSums(x), yearMeans(x), yearVars(x) unitSums(x), unitMeans(x), unitVars(x) seasonSums(x), seasonMeans(x), seasonVars(x) areaSums(x), areaMeans(x), areaVars(x) iterMeans(x), iterVars(x), iterMedians(x), iterSums(x) dimSums(x), dimMeans(x), dimVars(x)

Author(s)

The FLR Team

See Also

FLQuant, sum, mean, var

Examples

flq <- FLQuant(rnorm(4000), dim=c(5,10,2,2,2,10), quant='age')

quantSums(flq)
quantMeans(flq)
yearSums(flq)
iterMeans(flq)
dim(quantSums(flq))

# NA dims stay as NA when summed along
x <- FLQuant(c(NA, NA, NA, rnorm(6)), dim=c(3, 3))
quantSums(x)
# although in fact a sum of no elements (as na.rm=TRUE) is zero
apply(x, 2:6, sum, na.rm=TRUE)

flr/FLCore documentation built on May 4, 2024, midnight