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FLQuant.R
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FLQuant.R
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# FLQuant.R - FLQuant class and methods
# FLCore/R/FLQuant.R
# Copyright 2003-2022 FLR Team. Distributed under the GPL 2 or later
# Maintainer: Iago Mosqueira (MWR)
# FLQuant(missing){{{
#' @rdname FLQuant
#' @aliases FLQuant,missing-method
#' @examples
#'
#' FLQuant()
#' summary(FLQuant())
setMethod("FLQuant", signature(object="missing"),
function(object, dim=rep(1,6), dimnames="missing", quant=NULL,
units="NA", iter=1) {
# no dim or dimnames
if (missing(dim) && missing(dimnames)) {
dim <- c(1,1,1,1,1,iter)
dimnames <- list(quant='all', year=1, unit='unique', season='all',
area='unique', iter=1:dim[6])
} else if (missing(dim)) {
# dim missing
dimnames <- filldimnames(dimnames, iter=iter)
dim <- as.numeric(sapply(dimnames, length))
} else if (missing(dimnames)) {
# dimnames missing
dim <- c(dim, rep(1,6))[1:6]
# but iter
if(!missing(iter))
dim[6] <- iter
dimnames <- list(
quant=if(dim[1]==1){"all"}else{1:dim[1]},
year=1:dim[2],
unit=if(dim[3]==1){"unique"}else{1:dim[3]},
season=if(dim[4]==1){"all"}else{1:dim[4]},
area=if(dim[5]==1){"unique"}else{1:dim[5]},
iter=1:dim[6])
} else {
# both missing
dim <- c(dim, rep(1,6))[1:6]
# but iter
if(!missing(iter))
dim[6] <- iter
dimnames <- filldimnames(dimnames, dim=dim, iter=iter)
}
flq <- new("FLQuant", array(as.numeric(NA), dim=dim, dimnames=dimnames),
units=units)
if (!is.null(quant))
quant(flq) <- quant
return(flq)
}
)# }}}
# FLQuant(vector){{{
#' @rdname FLQuant
#' @aliases FLQuant,vector-method
#' @examples
#'
#' FLQuant(1:10)
setMethod("FLQuant", signature(object="vector"),
function(object, dim=rep(1,6), dimnames="missing", quant=NULL, units="NA", iter=1,
fill.iter=TRUE) {
# no dim or dimnames
if (missing(dim) && missing(dimnames)) {
dim <- c(1,length(object),1,1,1,iter)
dimnames <- list(quant='all', year=1:length(object), unit='unique',
season='all', area='unique', iter=seq(1,iter))
}
# dim missing
else if (missing(dim)) {
dimnames <- filldimnames(dimnames, iter=iter)
dim <- as.numeric(sapply(dimnames, length))
}
# dimnames missing
else if (missing(dimnames)) {
dim <- c(dim, rep(1,6))[1:6]
if(!missing(iter)) {
dim[6] <- iter
}
dimnames <- list(
quant=if(dim[1]==1){"all"}else{1:dim[1]},
year=1:dim[2],
unit=if(dim[3]==1){"unique"}else{1:dim[3]},
season=if(dim[4]==1){"all"}else{1:dim[4]},
area=if(dim[5]==1){"unique"}else{1:dim[5]},
iter=1:dim[6])
}
# both provided
else {
dim <- c(dim, rep(1,6))[1:6]
dimnames <- filldimnames(dimnames, dim=dim)
if(!missing(iter)) {
dim[6] <- iter
dimnames <- filldimnames(dimnames, dim=dim, iter=iter)
}
}
flq <- new("FLQuant", array(as.double(object), dim=dim, dimnames=dimnames),
units=units)
# Set extra iters to NA
if(dims(flq)$iter > 1 && !fill.iter)
flq[,,,,,2:dims(flq)$iter] <- as.numeric(NA)
if (!is.null(quant))
quant(flq) <- quant
return(flq)
}
) # }}}
# FLQuant(array){{{
#' @rdname FLQuant
#' @aliases FLQuant,array-method
#' @examples
#'
#' FLQuant(array(rnorm(9), dim=c(3,3,3)))
setMethod("FLQuant", signature(object="array"),
function(object, dim=rep(1,6), dimnames="missing", quant=NULL, units="NA",
iter=1, fill.iter=TRUE) {
# no dim or dimnames
if (missing(dim) && missing(dimnames)) {
# get dim from object and complete
dim <- c(dim(object), rep(1,5))[1:6]
# change dim[6] if iter is set
if(!missing(iter))
dim[6] <- iter
# if object has dimnames, use then
if(!is.null(dimnames(object))) {
dimnames <- filldimnames(dimnames(object), dim=dim)
}
# otherwise create from dim
else {
dimnames <- list(quant=1:dim[1], year=1:dim[2], unit=1:dim[3],
season=1:dim[4], area=1:dim[5], iter=1:dim[6])
dimnames[which(dim==1)] <- list(quant='all', year=1, unit='unique',
season='all', area='unique', iter='1')[which(dim==1)]
}
}
# dim missing
else if (missing(dim)) {
if(missing(iter) && length(dim(object)) == 6)
iter <- dim(object)[6]
dimnames <- filldimnames(dimnames, dim=c(dim(object), rep(1,6))[1:6], iter=iter)
# extract dim from dimnames
dim <- c(dim(object),
as.numeric(sapply(dimnames, length))[length(dim(object))+1:6])[1:6]
if(!missing(iter))
dim[6] <- iter
}
# dimnames missing
else if (missing(dimnames)) {
dim <- c(dim, rep(1,6))[1:6]
if(!missing(iter))
dim[6] <- iter
# create dimnames from dim
dimnames <- list(quant=1:dim[1], year=1:dim[2], unit=1:dim[3],
season=1:dim[4], area=1:dim[5], iter=1:iter)
dimnames[which(dim==1)] <- list(quant='all', year=1, unit='unique', season='all',
area='unique', iter='1')[which(dim==1)]
}
flq <- new("FLQuant", array(as.double(object), dim=dim, dimnames=dimnames),
units=units)
# Set extra iters to NA, unless array has 6 dimensions
if(dims(flq)$iter > 1 && !fill.iter)
flq[,,,,,2:dims(flq)$iter] <- as.numeric(NA)
if (!is.null(quant))
quant(flq) <- quant
return(flq)
}
) # }}}
# FLQuant(matrix){{{
#' @rdname FLQuant
#' @aliases FLQuant,matrix-method
#' @examples
#' FLQuant(matrix(rnorm(12), nrow=4, ncol=3))
setMethod("FLQuant", signature(object="matrix"),
function(object, dim=lapply(dimnames, length), dimnames="missing", ...) {
if(missing(dim))
dim <- c(nrow(object), ncol(object), rep(1,5))[1:6]
if(!missing(dimnames))
return(FLQuant(array(object, dim=dim, dimnames=filldimnames(dimnames, dim=dim)), ...))
if(!is.null(dimnames(object)) && missing(dimnames))
return(FLQuant(array(object, dim=dim), dimnames=filldimnames(dimnames(object),
dim=dim), ...))
return(FLQuant(array(object, dim=dim), ...))
}
) # }}}
# FLQuant(FLQuant){{{
#' @rdname FLQuant
#' @aliases FLQuant,FLQuant-method
#' @examples
#'
#' FLQuant(FLQuant(array(rnorm(9), dim=c(3,3,3)), units='kg'), units='t')
setMethod("FLQuant", signature(object="FLQuant"),
function(object, quant=attributes(object)[['quant']], units=attributes(object)[['units']],
dimnames=attributes(object)[['dimnames']], iter=dim(object)[6], fill.iter=TRUE,
dim=attributes(object)[['dim']])
{
# generate dimnames
dnames <- dimnames(object)
dnames[names(dimnames)] <- lapply(dimnames, as.character)
# dim
if(!missing(dim))
{
dims <- dim(object)
if(any(dim > dims[1:length(dim)]))
stop("resizing an object using 'dim' only allowed for trimming: use dimnames")
dims[1:length(dim)] <- dim
for(i in seq(length(dnames)))
{
dnames[[i]] <- dnames[[i]][1:dims[i]]
}
}
# change iter
if(!missing(iter))
dnames['iter'] <- list(as.character(seq(length=iter)))
# create empty FLQuant
res <- FLQuant(dimnames=dnames, quant=quant, units=units)
odnames <- dimnames(object)
if(!missing(iter))
odnames$iter <- seq(1, length(odnames$iter))
if(fill.iter==TRUE)
res[odnames[[1]][odnames[[1]]%in%dnames[[1]]],
odnames[[2]][odnames[[2]]%in%dnames[[2]]],
odnames[[3]][odnames[[3]]%in%dnames[[3]]],
odnames[[4]][odnames[[4]]%in%dnames[[4]]],
odnames[[5]][odnames[[5]]%in%dnames[[5]]],] <-
object[odnames[[1]][odnames[[1]]%in%dnames[[1]]],
odnames[[2]][odnames[[2]]%in%dnames[[2]]],
odnames[[3]][odnames[[3]]%in%dnames[[3]]],
odnames[[4]][odnames[[4]]%in%dnames[[4]]],
odnames[[5]][odnames[[5]]%in%dnames[[5]]],]
else
res[odnames[[1]][odnames[[1]]%in%dnames[[1]]],
odnames[[2]][odnames[[2]]%in%dnames[[2]]],
odnames[[3]][odnames[[3]]%in%dnames[[3]]],
odnames[[4]][odnames[[4]]%in%dnames[[4]]],
odnames[[5]][odnames[[5]]%in%dnames[[5]]],
odnames[[6]][odnames[[6]]%in%dnames[[6]]]] <-
object[odnames[[1]][odnames[[1]]%in%dnames[[1]]],
odnames[[2]][odnames[[2]]%in%dnames[[2]]],
odnames[[3]][odnames[[3]]%in%dnames[[3]]],
odnames[[4]][odnames[[4]]%in%dnames[[4]]],
odnames[[5]][odnames[[5]]%in%dnames[[5]]],
odnames[[6]][odnames[[6]]%in%dnames[[6]]]]
# listo!
return(res)
}
)# }}}
# as.FLQuant(array){{{
setMethod("as.FLQuant", signature(x="array"),
function(x, ...) {
return(FLQuant(x, ...))
}
)
setAs("array", "FLQuant", function(from)
return(FLQuant(from)))
# }}}
# as.FLQuant(matrix){{{
setMethod("as.FLQuant", signature(x="matrix"),
function(x, ...) {
return(FLQuant(x, ...))
}
)
setAs("matrix", "FLQuant", function(from)
return(FLQuant(from)))
# }}}
# as.FLQuant(FLQuant){{{
setMethod("as.FLQuant", signature(x="FLQuant"),
function(x, ...) {
return(FLQuant(x, ...))
}
)# }}}
# as.FLQuant(vector){{{
setMethod("as.FLQuant", signature(x="vector"),
function(x, ...) {
return(FLQuant(x, ...))
}
)
setAs("vector", "FLQuant", function(from)
return(FLQuant(from)))
# }}}
# as.FLQuant(data.frame){{{
setMethod("as.FLQuant", signature(x="data.frame"),
function(x, units="NA", ...) {
# get data.frame names and compare
names(x) <- tolower(names(x))
# extract units if set
if("units" %in% names(x)) {
if(missing(units)) {
units <- unique(as.character(x$units))
}
if(length(units) > 1)
stop("Two or more units of measurement set in 'units' column")
x$units <- NULL
}
validnames <-c("year", "unit", "season", "area", "iter", "data")
indices <- match(validnames, names(x))
indices <- indices[!is.na(indices)]
# get quant
qname <- names(x)
qname[indices] <- NA
qname <- qname[!is.na(qname)]
if (length(qname) > 1)
stop("too many columns in data.frame")
if(length(qname) == 0)
qname <- "quant"
# sort years if present
if('year' %in% names(x))
x <- x[order(x$year),]
# check and fill up missing dimensions
n <- dim(x)[1]
# TODO conversion to/x factor messes up dimnames order
em <- data.frame(quant=rep('all', n), year=rep(1,n), unit=rep('unique',n),
season=rep('all',n), area=rep('unique',n), iter=rep(1,n),
stringsAsFactors=FALSE)
names(em)[names(em)=="quant"] <- qname
x[, !names(x) %in% c("data")] <- as.data.frame(x[,!names(x) %in% c("data")],
stringsAsFactors=FALSE)
em[names(x)] <- x
# create array
flq <- tapply(em[,"data"],
list(factor(x = em[,qname], levels = unique(em[,qname])),
factor(x = em[,"year"], levels = unique(em[,"year"])),
factor(x = em[,"unit"], levels = unique(em[,"unit"])),
factor(x = em[,"season"], levels = unique(em[,"season"])),
factor(x = em[,"area"], levels = unique(em[,"area"])),
factor(x = em[,"iter"], levels = unique(em[,"iter"]))),
sum)
# fix dimnames names
names(dimnames(flq)) <- c(qname, 'year', 'unit', 'season', 'area', 'iter')
# create FLQuant
flq <- FLQuant(flq, units=units, ...)
# units
if(exists("units"))
units(flq) <- units
else if(!is.null(attr(x, 'units')))
units(flq) <- attr(x, 'units')
# fill up missing years
if(length(dimnames(flq)[['year']]) != length(as.character(seq(dims(flq)$minyear,
dims(flq)$maxyear))))
{
res <- FLQuant(dimnames=c(dimnames(flq)[1], list(year=seq(dims(flq)$minyear,
dims(flq)$maxyear)), dimnames(flq)[3:6]), units=units, ...)
res[,dimnames(flq)[['year']],] <- flq
flq <- res
}
return(flq)
}
) # }}}
# dimnames<- {{{
setMethod("dimnames<-", signature(x="FLQuant", value='list'),
function(x, value) {
if(length(names(value)[!names(value)%in%c("year","unit","season","area","iter")]) > 1)
stop("more than one vector of names given for the first dimension")
xnames <- dimnames(x)
for(i in 1:length(value)) {
if(any(names(value)[i]==c("year","unit","season","area","iter")))
xnames[[names(value)[i]]] <- value[[i]]
else {
xnames[[1]] <- value[[i]]
names(xnames)[1] <- names(value)[i]
}
}
attributes(x)$dimnames <- xnames
return(x)
}
) # }}}
# dims {{{
#' @rdname dims
#' @aliases dims,FLQuant-method
#' @examples
#'
#' flq <- FLQuant(rnorm(96), dim=c(3,8,1,4), quant='age')
#' dims(flq)
#'
#' # Number of seasons
#' dims(flq)$season
#'
#' # Length of first dimension
#' dims(flq)[[quant(flq)]]
#'
setMethod("dims", signature(obj="FLQuant"),
function(obj, element, ...){
names <- names(dimnames(obj))
quant <- as.numeric(dim(obj)[names == quant(obj)])
min <- suppressWarnings(as.numeric(dimnames(obj)[[quant(obj)]][1]))
max <- suppressWarnings(as.numeric(dimnames(obj)[[quant(obj)]][length(dimnames(obj)[[quant(obj)]])]))
year<- as.numeric(dim(obj)[names == "year"])
minyear <- suppressWarnings(as.numeric(dimnames(obj)$year[1]))
maxyear <- suppressWarnings(as.numeric(dimnames(obj)$year[dim(obj)[names == "year"]]))
unit<- dim(obj)[names == "unit"]
season <- dim(obj)[names == "season"]
area <- dim(obj)[names == "area"]
iter <- dim(obj)[names == "iter"]
list <- list(quant=quant, min=min, max=max, year=year, minyear=minyear,
maxyear=maxyear, unit=unit, season=season, area=area, iter=iter)
names(list)[1] <- quant(obj)
if(!missing(element))
return(list[[element]])
return(list)
}
) # }}}
# ages {{{
#' @examples
#' ages(m(ple4))
#' # Seasonal objects get decimal ages
#' ages(expand(m(ple4), season=1:4))[,,,1]
#' ages(expand(m(ple4), season=1:4))[,,,2]
setMethod("ages", signature(object="FLQuant"),
function(object) {
res <- FLQuant(an(dimnames(object)$age), dimnames=dimnames(object),
units="")
# TODO: DEAL with (spawning) units + seasons (e.g. SKJ)
# SEASONAL object
if(dim(res)[4] > 1) {
nseas <- dim(object)[4]
seas <- do.call(expand, c(list(x=FLQuant(seq(0, length=nseas, by=1 / nseas),
dimnames=list(season=dimnames(object)$season), quant=quant(object),
units="")), dimnames(object)[-4]))
res <- res + seas
}
return(res)
}
)
# }}}
# is.FLQuant {{{
is.FLQuant <- function(x)
return(is(x, "FLQuant"))
# }}}
# show {{{
setMethod("show", signature(object="FLQuant"),
function(object){
callNextMethod()
cat("units: ", object@units, "\n")
}
) # }}}
# print {{{
setMethod("print", signature(x="FLQuant"),
function(x){
show(x)
invisible(x)
}
) # }}}
# totals {{{
setMethod('quantTotals', signature(x='FLQuant'),
function(x, na.rm=TRUE) {
sums <- x
for (i in 1:dim(x)[2])
sums[,i,,,,] <- rowSums(x, na.rm=na.rm, dims=1)
return(sums)
}
)
setMethod('yearTotals', signature(x='FLQuant'),
function(x, na.rm=TRUE) {
sums <- x
for (i in 1:dim(x)[1])
sums[i,,,,] <- colSums(x, na.rm=na.rm)[,1,1,1,1]
return(sums)
}
) # }}}
# sums {{{
#' @rdname dimSummaries
setMethod('quantSums', signature(x='FLQuant'), function(x, na.rm=TRUE) {
res <- colSums(x, na.rm=na.rm)
dim(res) <- c(1, dim(res))
# FIX all NAs
if(na.rm & any(res == 0)) {
z <- is.na(x)
y <- colSums(z) == dim(x)[1]
res[y] <- NA
}
return(FLQuant(res, dimnames= c(list(quant='all'),dimnames(x)[2:6]),
quant=quant(x), units=units(x)))
})
#' @rdname dimSummaries
setMethod('yearSums', signature(x='FLQuant'), function(x, na.rm=TRUE) {
return(apply(x,c(1,3,4,5,6), function(x, NA.RM=na.rm){
z <- x[!is.na(x)]; ifelse(length(z), sum(z, na.rm=NA.RM), as.numeric(NA))
}))
})
#' @rdname dimSummaries
setMethod('unitSums', signature(x='FLQuant'), function(x, na.rm=TRUE) {
return(FLQuant(c(rowSums(aperm(x, c(1,2,4,5,6,3)), na.rm=na.rm, dim=5)),
dimnames=c(dimnames(x)[-3], unit='unique'), units=units(x)))
})
#' @rdname dimSummaries
setMethod('seasonSums', signature(x='FLQuant'), function(x, na.rm=TRUE) {
# output, 1 season
res <- x[,,,1]
dimnames(res)$season <- "all"
# DROP dimnames
dimnames(x) <- NULL
# PERMUTATE to season first
x <- aperm(x, c(4,1,2,3,5,6))
# SUM across dim 1
res[] <- colSums(x, dims=1, na.rm=TRUE)
idx <- colSums(is.na(x), dims=1) == dim(x)[1]
res[idx] <- as.numeric(NA)
return(res)
})
#' @rdname dimSummaries
setMethod('areaSums', signature(x='FLQuant'), function(x, na.rm=TRUE) {
return(apply(x,c(1,2,3,4,6), function(x, NA.RM=na.rm){
z <- x[!is.na(x)]; ifelse(length(z), sum(z, na.rm=NA.RM), as.numeric(NA))
}))
})
#' @rdname dimSummaries
setMethod('iterSums', signature(x='FLQuant'), function(x, na.rm=TRUE) {
return(apply(x,1:5, function(x, NA.RM=na.rm){
z <- x[!is.na(x)]; ifelse(length(z), sum(z, na.rm=NA.RM), as.numeric(NA))
}))
})
# }}}
# means {{{
#' @rdname dimSummaries
setMethod('quantMeans', signature(x='FLQuant'), function(x, na.rm=TRUE) {
return(FLQuant(c(colMeans(x, na.rm=na.rm, dims=1)),
dimnames=c(dimnames(x)[-1], quant='all'), quant=quant(x), units=units(x)))
})
#' @rdname dimSummaries
setMethod('yearMeans', signature(x='FLQuant'), function(x, na.rm=TRUE) {
return(FLQuant(c(rowMeans(aperm(x, c(1,3,4,5,6,2)), na.rm=na.rm, dims=5)),
dimnames=c(dimnames(x)[-2], year='1'), units=units(x)))
})
#' @rdname dimSummaries
setMethod('unitMeans', signature(x='FLQuant'), function(x, na.rm=TRUE) {
return(FLQuant(c(rowMeans(aperm(x, c(1,2,4,5,6,3)), na.rm=na.rm, dims=5)),
dimnames=c(dimnames(x)[-3], unit='unique'), units=units(x)))
})
#' @rdname dimSummaries
setMethod('seasonMeans', signature(x='FLQuant'), function(x, na.rm=TRUE) {
return(FLQuant(c(rowMeans(aperm(x, c(1,2,3,5,6,4)), na.rm=na.rm, dims=5)),
dimnames=c(dimnames(x)[-4], season='all'), units=units(x)))
})
#' @rdname dimSummaries
setMethod('areaMeans', signature(x='FLQuant'), function(x, na.rm=TRUE) {
return(FLQuant(c(rowMeans(aperm(x, c(1,2,3,4,6,5)), na.rm=na.rm, dims=5)),
dimnames=c(dimnames(x)[-5], area='unique'), units=units(x)))
})
#' @rdname dimSummaries
setMethod('iterMeans', signature(x='FLQuant'), function(x, na.rm=TRUE) {
return(FLQuant(c(rowMeans(x, na.rm=na.rm, dims=5)),
dimnames=c(dimnames(x)[-6], iter='1'), units=units(x)))
})
# }}}
# medians {{{
#' @rdname dimSummaries
setMethod('yearMedians', signature(x='FLQuant'), function(x, na.rm=TRUE) {
return(apply(x, c(1, 3:6), median, na.rm=na.rm))
})
#' @rdname dimSummaries
setMethod('iterMedians', signature(x='FLQuant'), function(x, na.rm=TRUE) {
return(apply(x, c(1:5), median, na.rm=na.rm))
})
# }}}
# vars {{{
#' @rdname dimSummaries
setMethod('quantVars', signature(x='FLQuant'), function(x, na.rm=TRUE) {
return(apply(x, 2:6, var, na.rm=na.rm))
})
#' @rdname dimSummaries
setMethod('yearVars', signature(x='FLQuant'), function(x, na.rm=TRUE) {
return(apply(x, c(1,3:6), var, na.rm=na.rm))
})
#' @rdname dimSummaries
setMethod('unitVars', signature(x='FLQuant'), function(x, na.rm=TRUE) {
return(apply(x, c(1:2,4:6), var, na.rm=na.rm))
})
#' @rdname dimSummaries
setMethod('seasonVars', signature(x='FLQuant'), function(x, na.rm=TRUE) {
return(apply(x, c(1:3,5:6), var, na.rm=na.rm))
})
#' @rdname dimSummaries
setMethod('areaVars', signature(x='FLQuant'), function(x, na.rm=TRUE) {
return(apply(x, c(1:4,6), var, na.rm=na.rm))
})
#' @rdname dimSummaries
setMethod('iterVars', signature(x='FLQuant'), function(x, na.rm=TRUE) {
return(apply(x, c(1:5), var, na.rm=na.rm))
}) # }}}
# CVs {{{
#' @rdname dimSummaries
setMethod('iterCVs', signature(x='FLQuant'), function(x, na.rm=TRUE) {
return(sqrt(iterVars(x))/iterMeans(x))
}) # }}}
# prob {{{
#' @rdname dimSummaries
setMethod('iterProb', signature(x='FLQuant'), function(x, na.rm=TRUE) {
return(apply(x, c(1:5), sum, na.rm=na.rm) / dim(x)[6])
}) # }}}
# yearSample {{{
#' Samples along the year dimension
#'
#' A resample from an FLQuant object along the 'year' dimension is returned. The
#' 'year' dimnames of the output object can be specified, although that is not
#' needed if the resample is to be assigned in a slot.
#'
#' @param x An FLQuant object.
#' @param size Number of samples (years), non-negative integer.
#' @param years Optional vector to set as 'year' dimnames in output.
#' @param replace should sampling be with replacement? Defaults to TRUE.
#' @param prob a vector of probability weights.
#'
#' @return RETURN Description, class
#'
#' @author Iago Mosqueira (WMR)
#' @seealso [FLQuant-class] [sample()]
#' @keywords classes
#' @examples
#' data(ple4)
#' # Take 20 samples of recent recruitment
#' yearSample(rec(ple4)[, ac(2013:2017)], 20)
#' # Providing 'years' sets the output object dimnames
#' yearSample(rec(ple4)[, ac(2013:2017)], 20, year=2000:2019)
yearSample <- function(x, size=length(years), years, replace=TRUE, prob=NULL) {
# STOP if !FLQuant
if(!is(x, "FLQuant"))
stop("'yearSample' expects an 'FLQuant' with year as 2nd dimension")
# SAMPLE along 2nd (year) dimension
res <- x[, sample(seq(dim(x)[2]), size, replace=replace, prob=prob)]
# ASSIGn year dimnames if provided
if(!missing(years))
dimnames(res)$year <- years
return(res)
}
# }}}
# quantile {{{
setMethod("quantile", signature(x="FLQuant"),
function(x, probs=seq(0, 1, 0.25), na.rm=FALSE, ...) {
res <- FLQuant(NA, dimnames=c(dimnames(x)[-6],
list(iter=paste(probs*100, "%", sep=""))), units=units(x))
res[,,,,,] <- aperm(apply(x@.Data, 1:5, quantile, c(0, probs), na.rm=na.rm),
c(2:6,1))[,,,,,-1,drop=FALSE]
return(res)
}
) # }}}
# iters {{{
setGeneric("iters", function(object, ...) {
value <- standardGeneric("iters")
value
}
)
setMethod("iters", signature(object="FLQuant"),
function(object) {
for (i in dimnames(object)$iter) {
cat("-- iter: ", i,"\n")
print(object@.Data[,,,,,i])
}
cat("\nunits: ", object@units, "\n")
}
) # }}}
# iter<- {{{
setMethod("iter<-", signature(object="FLQuant", value="FLQuant"),
function(object, iter, value) {
object[,,,,,iter] <- value
return(object)
}
)
setMethod("iter<-", signature(object="FLQuant", value="numeric"),
function(object, iter, value) {
object[,,,,,iter] <- c(value)
return(object)
}
)
# }}}
# propagate {{{
#' @rdname propagate
#' @param object Object to be propagated.
#' @param iters No. of iterations in output.
#' @param fill.iter Should first array be copied to others? Defaults to FALSE.
#' @examples
#'
#' # An FLQuant with one iter (dim(flq)[6] == 1)
#' flq <- FLQuant(rnorm(80), dim=c(4,20), quant='age')
#'
#' # can now be extended along the `iter` dimension, with
#' #' copies of the first
#' propagate(flq, 100)
#'
#' # or without
#' iter(propagate(flq, 100, fill.iter=FALSE), 2)
setMethod("propagate", signature(object="FLQuant"),
function(object, iter, fill.iter=TRUE) {
# RETURN object if iter == iters
dob <- dim(object)
if(iter == dob[6])
return(object)
# CHECK no iters in object
if(dob[6] > 1)
stop("propagate can only extend objects with no iters")
# fill.iter
if(fill.iter) {
return(new('FLQuant', array(rep(c(object), iter), dim=c(dob[-6], iter),
dimnames=c(dimnames(object)[-6], list(iter=seq(iter)))),
units=units(object)))
# or NAs
} else {
return(new('FLQuant', array(c(object, rep(NA, prod(dob)*(iter-1))),
dim=c(dim(object)[-6], iter),
dimnames=c(dimnames(object)[-6], list(iter=seq(iter)))), units=units(object)))
}
}
) # }}}
# rnorm{{{
setMethod("rnorm", signature(n="numeric", mean="FLQuant", sd="FLQuant"),
function(n=1, mean, sd) {
if(!dim(mean)[6] %in% c(1, n) | !dim(sd)[6] %in% c(1, n))
stop("mean or sd can only have iter=1")
if(any(dim(mean) != dim(sd)))
stop("dims of mean and sd must be equal")
FLQuant(array(rnorm(prod(dim(mean)[-6]) * n, rep(iter(mean, 1)[drop=TRUE], n),
rep(iter(sd, 1)[drop=TRUE], n)), dim=c(dim(mean)[-6], n)),
dimnames=c(dimnames(mean)[-6], list(iter=seq(n))), units=units(mean))
}
)
setMethod("rnorm", signature(n="numeric", mean="FLQuant", sd="numeric"),
function(n=1, mean, sd) {
rnorm(n, mean, FLQuant(sd, dimnames=dimnames(mean)))
}
)
setMethod("rnorm", signature(n="numeric", mean="numeric", sd="FLQuant"),
function(n=1, mean, sd) {
rnorm(n, FLQuant(mean, dimnames=dimnames(sd)), sd)
}
)
setMethod("rnorm", signature(n="numeric", mean="FLQuant", sd="missing"),
function(n=1, mean) {
rnorm(n, mean, 1)
}
)
setMethod("rnorm", signature(n="numeric", mean="missing", sd="FLQuant"),
function(n=1, sd) {
rnorm(n, 0, sd)
}
)
setMethod("rnorm", signature(n="missing", mean="FLQuant", sd="numeric"),
function(mean, sd=1) {
mean[] <- rnorm(length(mean), c(mean), sd)
return(mean)
}
)
setMethod("rnorm", signature(n="missing", mean="numeric", sd="FLQuant"),
function(mean=0, sd) {
sd[] <- rnorm(length(sd), mean, c(sd))
return(sd)
}
)
setMethod("rnorm", signature(n="missing", mean="FLQuant", sd="FLQuant"),
function(mean, sd) {
if(!all(dim(mean) == dim(sd)))
stop("dimensions of 'mean' and 'sd' must be the same")
mean[] <- rnorm(length(mean), c(mean), c(sd))
return(mean)
}
)
# }}}
# rlnorm {{{
setMethod("rlnorm", signature(n="numeric", meanlog="FLQuant", sdlog="FLQuant"),
function(n=1, meanlog, sdlog) {
# CHECK iters match
if(!all(dim(meanlog)[6] %in% c(1, n), dim(sdlog)[6] %in% c(1, n)))
stop("meanlog or sdlog can only have iter=1 or n")
# CHECK dims match
if(any(dim(meanlog)[-6] != dim(sdlog)[-6]))
stop("dims of mean and sd, except iter, must be equal")
mlog <- rep(c(meanlog), n / dim(meanlog)[6])
slog <- rep(c(sdlog), n / dim(sdlog)[6])
ns <- prod(dim(meanlog)[-6]) * n
return(FLQuant(array(rlnorm(ns, mlog, slog)), dim=c(dim(meanlog)[-6], n),
dimnames=c(dimnames(meanlog)[-6], list(iter=seq(n))),
units=units(meanlog)))
}
)
setMethod("rlnorm", signature(n='numeric', meanlog="FLQuant", sdlog="numeric"),
function(n=1, meanlog, sdlog) {
rlnorm(n, meanlog, FLQuant(sdlog, dimnames=dimnames(meanlog)))
}
)
setMethod("rlnorm", signature(n='numeric', meanlog="numeric", sdlog="FLQuant"),
function(n=1, meanlog, sdlog)
rlnorm(n, FLQuant(meanlog, dimnames=dimnames(sdlog)), sdlog)
)
setMethod("rlnorm", signature(n='numeric', meanlog="FLQuant", sdlog="missing"),
function(n=1, meanlog, sdlog)
rlnorm(n, meanlog, 1)
)
setMethod("rlnorm", signature(n='numeric', meanlog="missing", sdlog="FLQuant"),
function(n=1, meanlog, sdlog)
rlnorm(n, 0, sdlog)
)
setMethod("rlnorm", signature(n='FLQuant', meanlog="ANY", sdlog="ANY"),
function(n, meanlog=0, sdlog=1) {
FLQuant(rlnorm(length(n), meanlog, sdlog), dimnames=dimnames(n), units=units(n))
}
)
setMethod("rlnorm", signature(n="missing", meanlog="FLQuant", sdlog="ANY"),
function(meanlog, sdlog=1) {
meanlog[] <- rlnorm(length(meanlog), c(meanlog), sdlog)
return(meanlog)
}
)
setMethod("rlnorm", signature(n="missing", meanlog="FLQuant", sdlog="FLQuant"),
function(meanlog, sdlog) {
if(!all(dim(meanlog)[-6] == dim(sdlog)[-6]))
stop("dimensions of 'meanlog' and 'sdlog' must be the same")
meanlog[] <- rlnorm(length(meanlog), c(meanlog), c(sdlog))
return(meanlog)
}
)
# }}}
# rpois{{{
setMethod("rpois", signature(n='numeric', lambda="FLQuant"),
function(n=1, lambda) {
if(dim(lambda)[6] > 1)
stop("lambda can only have iter=1")
FLQuant(array(rnorm(prod(dim(lambda)[-6])*n, rep(iter(lambda, 1)[drop=TRUE], n)),
dim=c(dim(lambda)[-6], n)),
dimnames=c(dimnames(lambda)[-6], list(iter=seq(n))), fill.iter=TRUE, units=units(lambda))
}
) # }}}
# mvrnorm {{{
setMethod("mvrnorm",
signature(n="numeric", mu="FLQuant", Sigma="matrix"),
function(n=1, mu, Sigma) {
dmu <- dim(mu)
# input checks
if(any(dmu[3:6] > 1))
stop("mvrnorm can only work on 'quant' by 'year' FLQuant objects")
if (!isSymmetric(Sigma, tol = sqrt(.Machine$double.eps),
check.attributes = FALSE)) {
stop("Sigma must be a symmetric matrix")
}
if (dmu[1] != nrow(sigma)) {
stop("mu and Sigma have non-conforming size")
}
# "chol" method, from mvtnorm pkg
retval <- chol(Sigma, pivot = TRUE)
o <- order(attr(retval, "pivot"))
retval <- retval[, o]
retval <- matrix(rnorm(n * prod(dmu)), nrow = n * dmu[2]) %*% retval
# iter, year, age, unit, season, area
dim(retval)<-c(n, dmu[2], dmu[1], 1, 1, 1)
# aperm into FLQ
retval <- mu + FLQuant(aperm(retval, c(3,2,4,5,6,1)))
return(retval)
}