bit-package {bit} | R Documentation |
Package 'bit' provides bitmapped vectors of booleans (no NAs),
coercion from and to logicals, integers and integer subscripts;
fast boolean operators and fast summary statistics.
With bit vectors you can store true binary booleans {FALSE,TRUE} at the expense
of 1 bit only, on a 32 bit architecture this means factor 32 less RAM and
factor 32 more speed on boolean operations. With this speed gain it even
pays-off to convert to bit in order to avoid a single boolean operation on
logicals or a single set operation on (longer) integer subscripts, the pay-off
is dramatic when such components are used more than once.
Reading from and writing to bit is approximately as fast as accessing standard
logicals - mostly due to R's time for memory allocation. The package allows to
work with pre-allocated memory for return values by calling .Call() directly:
when evaluating the speed of C-access with pre-allocated vector memory, coping
from bit to logical requires only 70% of the time for copying from logical to
logical; and copying from logical to bit comes at a performance penalty of 150%.
Since bit objects cannot be used as subsripts in R, a second class 'bitwhich'
allows to store selections as efficiently as possible with standard R types.
This is usefull either to represent parts of bit objects or to represent
very asymetric selections.
Class 'ri' (range index) allows to select ranges of positions for chunked processing: all three classes 'bit', 'bitwhich' and 'ri' can be used for subsetting 'ff' objects (ff-2.1.0 and higher).
bit(length) ## S3 method for class 'bit' print(x, ...)
length |
length of vector in bits |
x |
a bit vector |
... |
further arguments to print |
Package: | bit |
Type: | Package |
Version: | 1.1.0 |
Date: | 2012-06-05 |
License: | GPL-2 |
LazyLoad: | yes |
Encoding: | latin1 |
Index:
bit function | bitwhich function | ri function | see also | description |
.BITS | globalenv | variable holding number of bits on this system | ||
bit_init | .First.lib | initially allocate bit-masks (done in .First.lib) | ||
bit_done | .Last.lib | finally de-allocate bit-masks (done in .Last.lib) | ||
bit | bitwhich | ri | logical | create bit object |
print.bit | print.bitwhich | print.ri | print | print bit vector |
length.bit | length.bitwhich | length.ri | length | get length of bit vector |
length<-.bit | length<-.bitwhich | length<- | change length of bit vector | |
c.bit | c.bitwhich | c | concatenate bit vectors | |
is.bit | is.bitwhich | is.ri | is.logical | test for bit class |
as.bit | as.bitwhich | as.logical | generically coerce to bit or bitwhich | |
as.bit.logical | as.bitwhich.logical | logical | coerce logical to bit vector (FALSE => FALSE, c(NA, TRUE) => TRUE) | |
as.bit.integer | as.bitwhich.integer | integer | coerce integer to bit vector (0 => FALSE, ELSE => TRUE) | |
as.bit.double | as.bitwhich.double | double | coerce double to bit vector (0 => FALSE, ELSE => TRUE) | |
as.double.bit | as.double.bitwhich | as.double.ri | as.double | coerce bit vector to double (0/1) |
as.integer.bit | as.integer.bitwhich | as.integer.ri | as.integer | coerce bit vector to integer (0L/1L) |
as.logical.bit | as.logical.bitwhich | as.logical.ri | as.logical | coerce bit vector to logical (FALSE/TRUE) |
as.which.bit | as.which.bitwhich | as.which.ri | as.which | coerce bit vector to positive integer subscripts |
as.bit.which | as.bitwhich.which | bitwhich | coerce integer subscripts to bit vector | |
as.bit.bitwhich | as.bitwhich.bitwhich | coerce from bitwhich | ||
as.bit.bit | as.bitwhich.bit | UseMethod | coerce from bit | |
as.bit.ri | as.bitwhich.ri | coerce from range index | ||
as.bit.ff | ff | coerce ff boolean to bit vector | ||
as.ff.bit | as.ff | coerce bit vector to ff boolean | ||
as.hi.bit | as.hi.bitwhich | as.hi.ri | as.hi | coerce to hybrid index (requires package ff) |
as.bit.hi | as.bitwhich.hi | coerce from hybrid index (requires package ff) | ||
[[.bit | [[ | get single bit (index checked) | ||
[[<-.bit | [[<- | set single bit (index checked) | ||
[.bit | [ | get vector of bits (unchecked) | ||
[<-.bit | [<- | set vector of bits (unchecked) | ||
!.bit | !.bitwhich | (works as second arg in | ! | boolean NOT on bit |
&.bit | &.bitwhich | bit and bitwhich ops) | & | boolean AND on bit |
|.bit | |.bitwhich | | | boolean OR on bit | |
xor.bit | xor.bitwhich | xor | boolean XOR on bit | |
!=.bit | !=.bitwhich | != | boolean unequality (same as XOR) | |
==.bit | ==.bitwhich | == | boolean equality | |
all.bit | all.bitwhich | all.ri | all | aggregate AND |
any.bit | any.bitwhich | any.ri | any | aggregate OR |
min.bit | min.bitwhich | min.ri | min | aggregate MIN (first TRUE position) |
max.bit | max.bitwhich | max.ri | max | aggregate MAX (last TRUE position) |
range.bit | range.bitwhich | range.ri | range | aggregate [MIN,MAX] |
sum.bit | sum.bitwhich | sum.ri | sum | aggregate SUM (count of TRUE) |
summary.bit | summary.bitwhich | summary.ri | tabulate | aggregate c(nFALSE, nTRUE, minRange, maxRange) |
regtest.bit | regressiontests for the package | |||
bit
returns a vector of integer sufficiently long to store 'length' bits
(but not longer) with an attribute 'n' and class 'bit'
Currently operations on bit objects have some overhead from R-calls. Do expect speed gains for vectors
of length ~ 10000 or longer.
Since this package was created for high performance purposes, only positive integer subscripts are allowed:
All R-functions behave as expected - i.e. they do not change their arguments and create new return values.
If you want to save the time for return value memory allocation, you must use .Call
directly
(see the dontrun example in sum.bit
).
Jens Oehlschlägel <Jens.Oehlschlaegel@truecluster.com>
Maintainer: Jens Oehlschlägel <Jens.Oehlschlaegel@truecluster.com>
logical
in base R and vmode
in package 'ff'
x <- bit(12) # create bit vector x # autoprint bit vector length(x) <- 16 # change length length(x) # get length x[[2]] # extract single element x[[2]] <- TRUE # replace single element x[1:2] # extract parts of bit vector x[1:2] <- TRUE # replace parts of bit vector as.which(x) # coerce bit to subscripts x <- as.bit.which(3:4, 4) # coerce subscripts to bit as.logical(x) # coerce bit to logical y <- as.bit(c(FALSE, TRUE, FALSE, TRUE)) # coerce logical to bit is.bit(y) # test for bit !x # boolean NOT x & y # boolean AND x | y # boolean OR xor(x, y) # boolean Exclusive OR x != y # boolean unequality (same as xor) x == y # boolean equality all(x) # aggregate AND any(x) # aggregate OR min(x) # aggregate MIN (integer version of ALL) max(x) # aggregate MAX (integer version of ANY) range(x) # aggregate [MIN,MAX] sum(x) # aggregate SUM (count of TRUE) summary(x) # aggregate count of FALSE and TRUE ## Not run: message("\nEven for a single boolean operation transforming logical to bit pays off") n <- 10000000 x <- sample(c(FALSE, TRUE), n, TRUE) y <- sample(c(FALSE, TRUE), n, TRUE) system.time(x|y) system.time({ x <- as.bit(x) y <- as.bit(y) }) system.time( z <- x | y ) system.time( as.logical(z) ) message("Even more so if multiple operations are needed :-)") message("\nEven for a single set operation transforming subscripts to bit pays off\n") n <- 10000000 x <- sample(n, n/2) y <- sample(n, n/2) system.time( union(x,y) ) system.time({ x <- as.bit.which(x, n) y <- as.bit.which(y, n) }) system.time( as.which.bit( x | y ) ) message("Even more so if multiple operations are needed :-)") message("\nSome timings WITH memory allocation") n <- 2000000 l <- sample(c(FALSE, TRUE), n, TRUE) # copy logical to logical system.time(for(i in 1:100){ # 0.0112 l2 <- l l2[1] <- TRUE # force new memory allocation (copy on modify) rm(l2) })/100 # copy logical to bit system.time(for(i in 1:100){ # 0.0123 b <- as.bit(l) rm(b) })/100 # copy bit to logical b <- as.bit(l) system.time(for(i in 1:100){ # 0.009 l2 <- as.logical(b) rm(l2) })/100 # copy bit to bit b <- as.bit(l) system.time(for(i in 1:100){ # 0.009 b2 <- b b2[1] <- TRUE # force new memory allocation (copy on modify) rm(b2) })/100 l2 <- l # replace logical by TRUE system.time(for(i in 1:100){ l[] <- TRUE })/100 # replace bit by TRUE (NOTE that we recycle the assignment # value on R side == memory allocation and assignment first) system.time(for(i in 1:100){ b[] <- TRUE })/100 # THUS the following is faster system.time(for(i in 1:100){ b <- !bit(n) })/100 # replace logical by logical system.time(for(i in 1:100){ l[] <- l2 })/100 # replace bit by logical system.time(for(i in 1:100){ b[] <- l2 })/100 # extract logical system.time(for(i in 1:100){ l2[] })/100 # extract bit system.time(for(i in 1:100){ b[] })/100 message("\nSome timings WITHOUT memory allocation (Serge, that's for you)") n <- 2000000L l <- sample(c(FALSE, TRUE), n, TRUE) b <- as.bit(l) # read from logical, write to logical l2 <- logical(n) system.time(for(i in 1:100).Call("R_filter_getset", l, l2, PACKAGE="bit")) / 100 # read from bit, write to logical l2 <- logical(n) system.time(for(i in 1:100).Call("R_bit_get", b, l2, c(1L, n), PACKAGE="bit")) / 100 # read from logical, write to bit system.time(for(i in 1:100).Call("R_bit_set", b, l2, c(1L, n), PACKAGE="bit")) / 100 ## End(Not run)