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# Chunking utilities for bit and ff
# (c) 2007-2009 Jens Oehlschägel
# Licence: GPL2
# Provided 'as is', use at your own risk
# Created: 2007-09-03
# Last changed: 2007-10-25
# source("D:/mwp/eanalysis/bit/R/chunkutil.R")
#! \name{bbatch}
#! \alias{bbatch}
#! \title{ Balanced Batch sizes }
#! \description{
#! \command{bbatch} calculates batch sizes so that they have rather balanced sizes than very different sizes
#! }
#! \usage{
#! bbatch(N, B)
#! }
#! \arguments{
#! \item{N}{ total size }
#! \item{B}{ desired batch size }
#! }
#! \value{
#! a list with components
#! \item{ b }{ the batch size }
#! \item{ nb }{ the number of batches }
#! \item{ rb }{ the size of the rest }
#! }
#! \details{
#! Tries to have \code{rb==0} or \code{rb} as close to \code{b} as possible while guaranteing that \code{rb < b && (b - rb) <= min(nb, b)}
#! }
#! \author{ Jens Oehlschlägel }
#! \seealso{ \code{\link{repfromto}}, \code{\link[ff]{ffvecapply}} }
#! \examples{
#! bbatch(100, 24)
#! }
#! \keyword{ IO }
#! \keyword{ data }
# non-vectorized
#bbatch <-
#function(N,B){
# N <- as.integer(N)
# B <- as.integer(B)
# RB <- N %% B
# NB <- N %/% B
# if (RB){
# cc <- min((B - RB) %/% NB, (B - RB) %/% (NB + 1L))
# if (cc){
# rb <- RB + cc * NB
# b <- B - cc
# if (rb==b){
# return(list(b=b, nb=NB+1L, rb=0L))
# }else{
# return(list(b=b, nb=NB, rb=rb))
# }
# }else{
# return(list(b=B, nb=NB, rb=RB))
# }
# }else{
# return(list(b=B, nb=NB, rb=RB))
# }
#}
# balanced batchsizes
bbatch <- function(N,B){
if (any(B<1))
stop("B too small")
N <- as.integer(N)
B <- as.integer(B)
RB <- N %% B
NB <- N %/% B
cc <- pmin((B - RB) %/% NB, (B - RB) %/% (NB + 1L))
cc[RB==0 | NB == 0] <- 0
i <- cc > 0
RB[i] <- RB[i] + cc[i] * NB[i]
B[i] <- B[i] - cc[i]
j <- i & (RB[i] == B[i])
NB[i & j] <- NB[i & j] + 1L
RB[i & j] <- 0L
i <- (RB>0) & (NB == 0)
B[i] <- RB[i]
NB[i] <- 1L
RB[i] <- 0L
return(list(b=B, nb=NB, rb=RB))
}
#! \name{repfromto}
#! \alias{repfromto}
#! \alias{repfromto<-}
#! \title{ Virtual recycling }
#! \description{
#! \command{repfromto} virtually recylcles object \code{x} and cuts out positions \code{from .. to}
#! }
#! \usage{
#! repfromto(x, from, to)
#! repfromto(x, from, to) <- value
#! }
#! \arguments{
#! \item{x}{ an object from which to recycle }
#! \item{from}{ first position to return }
#! \item{to}{ last position to return }
#! \item{value}{ value to assign }
#! }
#! \details{
#! \code{repfromto} is a generalization of \code{\link{rep}}, where \code{rep(x, n) == repfromto(x, 1, n)}.
#! You can see this as an R-side (vector) solution of the \code{mod_iterate} macro in arithmetic.c
#! }
#! \value{
#! a vector of length \code{from - to + 1}
#! }
#! \author{ Jens Oehlschlägel }
#! \seealso{ \code{\link{rep}}, \code{\link[ff]{ffvecapply}} }
#! \examples{
#! message("a simple example")
#! repfromto(0:9, 11, 20)
#! }
#! \keyword{ IO }
#! \keyword{ data }
repfromto <- function(x, from, to){
nx <- length(x)
if (nx){
from <- as.integer(from)
to <- as.integer(to)
if (to>nx){
N <- to - from + 1L
from <- (from-1L)%%nx + 1L
to <- to%%nx
# NOTE: fetch in sequence pre-main-post in case is.ff(x)
if (from<=to && N<nx){
ret <- x[from:to]
}else{
pre <- x[from:nx]
nrep <- (N - length(pre) - to) %/%nx
main <- if (nrep) rep(x[1:nx], nrep) else NULL
post <- if (to) x[1:to] else NULL
ret <- c(pre, main, post)
}
}else{
ret <- x[from:to]
}
a <- attributes(x[1])
a$names <- NULL
attributes(ret) <- a
return(ret)
}else{
return(NA[from:to])
}
}
"repfromto<-" <- function(x, from, to, value){
x[from:to] <- value
x
}
if (FALSE){
x <- 1:10
for (n in 1:20)
for (i1 in 1:30){
i2 <- i1+n-1
cat(i1,i2,"|",repfromto(x,i1,i2), "\n")
}
}
if (FALSE){
intseq <- function(from=NULL, to=NULL, by=NULL, length.out=NULL, along.with=NULL){
if (is.null(from)){
if (is.null(to))
stop("need 'from' or 'to'")
else
to <- as.integer(to)
if (is.null(by))
by <- 1L
else
by <- as.integer(by)
}else{
from <- as.integer(from)
if (is.null(to)){
if (is.null(by))
by <- 1L
else
by <- as.integer(by)
}else{
to <- as.integer(to)
n <- to - from
if (is.null(by)){
if (to<from)
by = -1L
else
by = 1L
}else{
by <- as.integer(by)
if (n){
if (sign(n) != sign(by))
stop("wrong sign of by")
}else
return(from) # to == from
}
}
}
if (is.null(length.out)){
if (is.null(along.with)){
if (is.null(to) || is.null(from))
stop("not enough info to guess the length.out")
else{
length.out <- n %/% by + 1L
}
}else{
length.out <- length(along.with)
}
}else{
length.out <- as.integer(length.out)
}
if (length.out){
if (length.out==1L)
from
else
cumsum(c(from, rep(by, length.out-1L)))
}else
integer()
}
}
#! \name{chunk}
#! \alias{chunk}
#! \alias{chunk.default}
#! \title{ Chunked range index }
#! \description{
#! creates a sequence of range indexes using a syntax not completely unlike 'seq'
#! }
#! \usage{
#! chunk(\dots)
#! \method{chunk}{default}(from = NULL, to = NULL, by = NULL, length.out = NULL, along.with = NULL
#! , overlap = 0L, method = c("bbatch", "seq"), maxindex = NA, \dots)
#! }
#! \arguments{
#! \item{from}{ the starting value of the sequence. }
#! \item{to}{ the (maximal) end value of the sequence. }
#! \item{by}{ increment of the sequence }
#! \item{length.out}{ desired length of the sequence. }
#! \item{along.with}{ take the length from the length of this argument. }
#! \item{overlap}{ number of values to overlap (will lower the starting value of the sequence, the first range becomes smaller }
#! \item{method}{ default 'bbatch' will try to balance the chunk size, see \code{\link{bbatch}}, 'seq' will create chunks like \code{\link[base]{seq}} }
#! \item{maxindex}{ passed to \code{\link{ri}} }
#! \item{\dots}{ ignored }
#! }
#! \details{
#! \code{chunk} is generic, the default method is described here, other methods that automatically consider RAM needs are provided with package 'ff', see for example \code{\link[ff]{chunk.ffdf}}
#! }
#! \section{available methods}{
#! \code{chunk.default}, \code{\link[ff]{chunk.bit}}, \code{\link[ff]{chunk.ff_vector}}, \code{\link[ff]{chunk.ffdf}}
#! }
#! \value{
#! \code{chunk.default} returns a list of \code{\link{ri}} objects representing chunks of subscripts
#! }
#! \author{ Jens Oehlschlägel }
#! \seealso{ \code{\link{ri}}, \code{\link[base]{seq}}, \code{\link{bbatch}} }
#! \examples{
#! chunk(1, 100, by=30)
#! chunk(1, 100, by=30, method="seq")
#! \dontrun{
#! require(foreach)
#! m <- 10000
#! k <- 1000
#! n <- m*k
#! message("Four ways to loop from 1 to n. Slowest foreach to fastest chunk is 1700:1
#! on a dual core notebook with 3GB RAM\n")
#! z <- 0L;
#! print(k*system.time({it <- icount(m); foreach (i = it) \%do\% { z <- i; NULL }}))
#! z
#!
#! z <- 0L
#! print(system.time({i <- 0L; while (i<n) {i <- i + 1L; z <- i}}))
#! z
#!
#! z <- 0L
#! print(system.time(for (i in 1:n) z <- i))
#! z
#!
#! z <- 0L; n <- m*k;
#! print(system.time(for (ch in chunk(1, n, by=m)){for (i in ch[1]:ch[2])z <- i}))
#! z
#!
#! message("Seven ways to calculate sum(1:n).
#! Slowest foreach to fastest chunk is 61000:1 on a dual core notebook with 3GB RAM\n")
#! print(k*system.time({it <- icount(m); foreach (i = it, .combine="+") \%do\% { i }}))
#!
#! z <- 0;
#! print(k*system.time({it <- icount(m); foreach (i = it) \%do\% { z <- z + i; NULL }}))
#! z
#!
#! z <- 0; print(system.time({i <- 0L;while (i<n) {i <- i + 1L; z <- z + i}})); z
#!
#! z <- 0; print(system.time(for (i in 1:n) z <- z + i)); z
#!
#! print(system.time(sum(as.double(1:n))))
#!
#! z <- 0; n <- m*k
#! print(system.time(for (ch in chunk(1, n, by=m)){for (i in ch[1]:ch[2])z <- z + i}))
#! z
#!
#! z <- 0; n <- m*k
#! print(system.time(for (ch in chunk(1, n, by=m)){z <- z+sum(as.double(ch[1]:ch[2]))}))
#! z
#! }
#! }
#! \keyword{ data }
chunk <- function(...)
UseMethod("chunk")
chunk.default <- function(
from = NULL
, to = NULL
, by = NULL
, length.out = NULL
, along.with = NULL
, overlap = 0L
, method=c("bbatch","seq")
, maxindex = NA
, ...
)
{
method <- match.arg(method)
if (!is.null(along.with)){
if (is.null(from))
from <- 1L
else{
if (length(from)==1)
from <- as.integer(from)
else
stop("'from' must be scalar")
}
if (is.null(to))
to <- length(along.with)
else{
if (length(to)==1)
to <- as.integer(to)
else
stop("'to' must be scalar")
}
}
if (length(from)==1)
from <- as.integer(from)
else
stop("'from' must be scalar")
if (length(to)==1)
to <- as.integer(to)
else
stop("'to' must be scalar")
if (to<from)
stop("to < from")
N <- to - from + 1L
if (is.null(by)){
if (is.null(length.out))
stop("need either 'by' or 'length.out'")
else{
if (length(length.out)==1){
length.out <- as.integer(length.out)
if (length.out>N)
length.out <- N
by <- N %/% length.out
}else
stop("'length.out' must be scalar")
}
}else{
if (length(by)==1){
by <- as.integer(by)
if (by<1)
stop("'by' must be > 0")
length.out <- (N - 1L) %/% by + 1L
}else
stop("'by' must be scalar")
}
if (method=="bbatch")
by <- bbatch(N, by)$b
if (length.out>1L){
from <- cumsum(c(from, rep(by, length.out - 1L)))
to <- c(from[-1], from[1] + N) - 1L # fixed by Edwin de Jonge, 18.1.2011
if (overlap>0)
from[-1] <- from[-1] - overlap
}
n <- length(from)
s <- seq_len(n)
ret <- vector("list", n)
for (i in s){
ret[[i]] <- ri(from[i], to[i], maxindex)
}
ret
}
#! \name{vecseq}
#! \alias{vecseq}
#! \title{ Vectorized Sequences }
#! \description{
#! \command{vecseq} returns concatenated multiple sequences
#! }
#! \usage{
#! vecseq(x, y=NULL, concat=TRUE, eval=TRUE)
#! }
#! \arguments{
#! \item{x}{ vector of sequence start points }
#! \item{y}{ vector of sequence end points (if \code{is.null(y)} then \code{x} are taken as endpoints, all starting at 1) }
#! \item{concat}{ vector of sequence end points (if \code{is.null(y)} then \code{x} are taken as endpoints, all starting at 1) }
#! \item{eval}{ vector of sequence end points (if \code{is.null(y)} then \code{x} are taken as endpoints, all starting at 1) }
#! }
#! \details{
#! This is a generalization of \code{\link{sequence}} in that you can choose sequence starts other than 1 and also have options to no concat and/or return a call instead of the evaluated sequence.
#! }
#! \value{
#! if \code{concat==FALSE} and \code{eval==FALSE} a list with n calls that generate sequences \cr
#! if \code{concat==FALSE} and \code{eval==TRUE } a list with n sequences \cr
#! if \code{concat==TRUE } and \code{eval==FALSE} a single call generating the concatenated sequences \cr
#! if \code{concat==TRUE } and \code{eval==TRUE } an integer vector of concatentated sequences
#! }
#! \author{ Angelo Canty, Jens Oehlschlägel }
#! \seealso{ \code{\link{:}}, \code{\link{seq}}, \code{\link{sequence}} }
#! \examples{
#! sequence(c(3,4))
#! vecseq(c(3,4))
#! vecseq(c(1,11), c(5, 15))
#! vecseq(c(1,11), c(5, 15), concat=FALSE, eval=FALSE)
#! vecseq(c(1,11), c(5, 15), concat=FALSE, eval=TRUE)
#! vecseq(c(1,11), c(5, 15), concat=TRUE, eval=FALSE)
#! vecseq(c(1,11), c(5, 15), concat=TRUE, eval=TRUE)
#! }
#! \keyword{ manip }
vecseq <- function(x, y=NULL, concat=TRUE, eval=TRUE){
if (missing(y)){
y <- x
x <- 1L
}
if (concat){
if (eval){
# pure R version was: eval(parse(text=paste("c(",paste(x,y,sep=":",collapse=","),")")))
# now calling C-code
nx <- length(x)
ny <- length(y)
if (nx<ny)
x <- rep(as.integer(x), length.out=ny)
if (ny<nx)
y <- rep(as.integer(y), length.out=nx)
.Call("R_bit_vecseq", as.integer(x), as.integer(y), PACKAGE="bit")
}else
parse(text=paste("c(",paste(x,y,sep=":",collapse=","),")"))[[1]]
}else{
if (eval)
eval(parse(text=paste("list(",paste(x,y,sep=":",collapse=","),")")))
else
as.list(parse(text=paste(x,y,sep=":")))
}
}
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