| Title: | File-Backed Array for Out-of-Memory Computation |
|---|---|
| Description: | Stores large arrays in files to avoid occupying large memories. Implemented with super fast gigabyte-level multi-threaded reading/writing via 'OpenMP'. Supports multiple non-character data types (double, float, complex, integer, logical, and raw). |
| Authors: | Zhengjia Wang [aut, cre, cph] |
| Maintainer: | Zhengjia Wang <[email protected]> |
| License: | LGPL-3 |
| Version: | 0.1.9 |
| Built: | 2024-12-08 06:33:46 UTC |
| Source: | https://github.com/dipterix/filearray |
Apply functions over file array margins (extended)
apply(X, MARGIN, FUN, ..., simplify = TRUE) ## S4 method for signature 'FileArray' apply(X, MARGIN, FUN, ..., simplify = TRUE) ## S4 method for signature 'FileArrayProxy' apply(X, MARGIN, FUN, ..., simplify = TRUE)apply(X, MARGIN, FUN, ..., simplify = TRUE) ## S4 method for signature 'FileArray' apply(X, MARGIN, FUN, ..., simplify = TRUE) ## S4 method for signature 'FileArrayProxy' apply(X, MARGIN, FUN, ..., simplify = TRUE)
X |
a file array |
MARGIN |
scalar giving the subscripts which the function will be applied over. Current implementation only allows margin size to be one |
FUN |
the function to be applied |
... |
optional arguments to |
simplify |
a logical indicating whether results should be simplified if possible |
See Section 'Value' in apply;
Create or load existing file arrays
as_filearray(x, ...) as_filearrayproxy(x, ...) filearray_create( filebase, dimension, type = c("double", "float", "integer", "logical", "raw", "complex"), partition_size = NA, initialize = FALSE, ... ) filearray_load(filebase, mode = c("readwrite", "readonly")) filearray_checkload( filebase, mode = c("readonly", "readwrite"), ..., symlink_ok = TRUE ) filearray_load_or_create( filebase, dimension, on_missing = NULL, type = NA, ..., mode = c("readonly", "readwrite"), symlink_ok = TRUE, initialize = FALSE, partition_size = NA, verbose = FALSE )as_filearray(x, ...) as_filearrayproxy(x, ...) filearray_create( filebase, dimension, type = c("double", "float", "integer", "logical", "raw", "complex"), partition_size = NA, initialize = FALSE, ... ) filearray_load(filebase, mode = c("readwrite", "readonly")) filearray_checkload( filebase, mode = c("readonly", "readwrite"), ..., symlink_ok = TRUE ) filearray_load_or_create( filebase, dimension, on_missing = NULL, type = NA, ..., mode = c("readonly", "readwrite"), symlink_ok = TRUE, initialize = FALSE, partition_size = NA, verbose = FALSE )
x |
R object such as array, file array proxy, or character that can be transformed into file array |
... |
additional headers to check used by |
filebase |
a directory path to store arrays in the local file system. When creating an array, the path must not exist. |
dimension |
dimension of the array, at least length of 2 |
type |
storage type of the array; default is |
partition_size |
positive partition size for the last margin, or
|
initialize |
whether to initialize partition files; default is false for performance considerations. However, if the array is dense, it is recommended to set to true |
mode |
whether allows writing to the file; choices are
|
symlink_ok |
whether arrays with symbolic-link partitions can pass
the test; this is usually used on bound arrays with symbolic-links; see
|
on_missing |
function to handle file array (such as initialization) when a new array is created; must take only one argument, the array object |
verbose |
whether to print out some debug messages |
The file arrays partition out-of-memory array objects and store them
separately in local file systems. Since R stores matrices/arrays
in column-major style, file array uses the slowest margin (the
last margin) to slice the partitions. This helps to align the elements
within the files with the corresponding memory order. An array with
dimension 100x200x300x400 has 4 margins. The length of the
last margin is 400, which is also the maximum number of potential
partitions. The number of partitions are determined by the last margin
size divided by partition_size. For example, if the partition
size is 1, then there will be 400 partitions. If the partition size
if 3, there will be 134 partitions. The default partition sizes
are determined internally following these priorities:
the file size of each partition does not exceed 1GB
the number of partitions do not exceed 100
These two rules are not hard requirements. The goal is to reduce the numbers of partitions as much as possible.
The arguments ... in filearray_checkload should be named
arguments that provide additional checks for the header information.
The check will fail if at least one header is not identical. For example,
if an array contains header key-signature pair, one can use
filearray_checkload(..., key = signature) to validate the signature.
Note the comparison will be rigid, meaning the storage type of the headers
will be considered as well. If the signature stored in the array is an
integer while provided is a double, then the check will result in failure.
A FileArray-class instance.
Zhengjia Wang
# Prepare library(filearray) filebase <- tempfile() if(file.exists(filebase)){ unlink(filebase, TRUE) } # create array x <- filearray_create(filebase, dimension = c(200, 30, 8)) print(x) # Assign values x[] <- rnorm(48000) # Subset x[1,2,] # load existing array filearray_load(filebase) x$set_header("signature", "tom") filearray_checkload(filebase, signature = "tom") ## Not run: # Trying to load with wrong signature filearray_checkload(filebase, signature = "jerry") ## End(Not run) # check-load, and create a new array if fail x <- filearray_load_or_create( filebase = filebase, dimension = c(200, 30, 8), verbose = FALSE, signature = "henry" ) x$get_header("signature") # check-load with initialization x <- filearray_load_or_create( filebase = filebase, dimension = c(3, 4, 5), verbose = FALSE, mode = "readonly", on_missing = function(array) { array[] <- seq_len(60) } ) x[1:3,1,1] # Clean up unlink(filebase, recursive = TRUE)# Prepare library(filearray) filebase <- tempfile() if(file.exists(filebase)){ unlink(filebase, TRUE) } # create array x <- filearray_create(filebase, dimension = c(200, 30, 8)) print(x) # Assign values x[] <- rnorm(48000) # Subset x[1,2,] # load existing array filearray_load(filebase) x$set_header("signature", "tom") filearray_checkload(filebase, signature = "tom") ## Not run: # Trying to load with wrong signature filearray_checkload(filebase, signature = "jerry") ## End(Not run) # check-load, and create a new array if fail x <- filearray_load_or_create( filebase = filebase, dimension = c(200, 30, 8), verbose = FALSE, signature = "henry" ) x$get_header("signature") # check-load with initialization x <- filearray_load_or_create( filebase = filebase, dimension = c(3, 4, 5), verbose = FALSE, mode = "readonly", on_missing = function(array) { array[] <- seq_len(60) } ) x[1:3,1,1] # Clean up unlink(filebase, recursive = TRUE)
The file arrays to be merged must be homogeneous: same data type, partition size, and partition length
filearray_bind( ..., .list = list(), filebase = tempfile(), symlink = FALSE, overwrite = FALSE, cache_ok = FALSE )filearray_bind( ..., .list = list(), filebase = tempfile(), symlink = FALSE, overwrite = FALSE, cache_ok = FALSE )
..., .list
|
file array instances |
filebase |
where to create merged array |
symlink |
whether to use |
overwrite |
whether to overwrite when |
cache_ok |
see 'Details', only used if |
The input arrays must share the same data type and partition size.
The dimension for each partition should also be the same. For example
an array x1 has dimension with partition size
1, then each partition dimension is , and there are
30 partitions. x1 can bind with another array of the same
partition size. This means if x2 has dimension
and each partition size is 1, then x1 and
x2 can be merged.
If filebase exists and overwrite is FALSE, an error will
always raise. If overwrite=TRUE and cache_ok=FALSE, then
the existing filebase will be erased and any data stored within will
be lost.
If both overwrite and cache_ok are TRUE, then
, before erasing filebase, the function validates the existing
array header and compare the header signatures. If the existing header
signature is the same as the array to be created, then the existing array
will be returned. This cache_ok could be extremely useful when
binding large arrays with symlink=FALSE as the cache might avoid
moving files around. However, cache_ok should be enabled with caution.
This is because only the header information will be compared, but the
partition data will not be compared. If the existing array was generated from
an old versions of the source arrays, but the data from the source arrays
has been altered, then the cache_ok=TRUE is rarely proper as the cache
is outdated.
The symlink option should be used with extra caution. Creating
symbolic links is definitely faster than copying partition files. However,
since the partition files are simply linked to the original partition files,
changing to the input arrays will also affect the merged arrays, and
vice versa; see 'Examples'. Also for arrays created from symbolic links, if
the original
arrays are deleted, while the merged arrays will not be invalidated,
the corresponding partitions will no longer be accessible. Attempts to
set deleted partitions will likely result in failure. Therefore
symlink should be set to true when creating merged arrays are
temporary for read-only purpose, and when speed and disk space is in
consideration. For extended reading, please check files
for details.
A bound array in 'FileArray' class.
partition_size <- 1 type <- "double" x1 <- filearray_create( tempfile(), c(2,2), type = type, partition_size = partition_size) x1[] <- 1:4 x2 <- filearray_create( tempfile(), c(2,1), type = type, partition_size = partition_size) x2[] <- 5:6 y1 <- filearray_bind(x1, x2, symlink = FALSE) y2 <- filearray_bind(x1, x2) # y1 copies partition files, and y2 simply creates links # if symlink is supported y1[] - y2[] # change x1 x1[1,1] <- NA # y1 is not affected y1[] # y2 changes y2[]partition_size <- 1 type <- "double" x1 <- filearray_create( tempfile(), c(2,2), type = type, partition_size = partition_size) x1[] <- 1:4 x2 <- filearray_create( tempfile(), c(2,1), type = type, partition_size = partition_size) x2[] <- 5:6 y1 <- filearray_bind(x1, x2, symlink = FALSE) y2 <- filearray_bind(x1, x2) # y1 copies partition files, and y2 simply creates links # if symlink is supported y1[] - y2[] # change x1 x1[1,1] <- NA # y1 is not affected y1[] # y2 changes y2[]
Will enable/disable multi-threaded reading or writing
at C++ level.
filearray_threads(n, ...)filearray_threads(n, ...)
n |
number of threads to set. If |
... |
internally used |
An integer of current number of threads
S4 class definition of FileArray. Please
use filearray_create and filearray_load
to create instances.
get_header(key, default = NULL)Get header information; returns default if key is missing
set_header(key, value)Set header information; the extra headers will be stored in meta file. Please do not store large headers as they will be loaded into memory frequently.
can_write()Whether the array data can be altered
create(filebase, dimension, type = "double", partition_size = 1)Create a file array instance
delete(force = FALSE)Remove array from local file system and reset
dimension()Get dimension vector
dimnames(v)Set/get dimension names
element_size()Internal storage: bytes per element
fill_partition(part, value)Fill a partition with given scalar
get_partition(part, reshape = NULL)Get partition data, and reshape (if not null) to desired dimension
expand(n)Expand array along the last margin; returns true if expanded; if the dimnames have been assigned prior to expansion, the last dimension names will be filled with NA
initialize_partition()Make sure a partition file exists; if not, create one and fill with NAs or 0 (type='raw')
load(filebase, mode = c("readwrite", "readonly"))Load file array from existing directory
partition_path(part)Get partition file path
partition_size()Get partition size; see filearray
set_partition(part, value, ..., strict = TRUE)Set partition value
sexp_type()Get data SEXP type; see R internal manuals
show()Print information
type()Get data type
valid()Check if the array is valid.
Advanced mapping function for multiple file arrays. fmap
runs the mapping functions and stores the results in file arrays.
fmap2 stores results in memory. This
feature is experimental. There are several constraints to the input.
Failure to meet these constraints may result in undefined results, or
even crashes. Please read Section 'Details' carefully before using
this function.
fmap( x, fun, .y = NULL, .buffer_count = NA_integer_, .output_size = NA_integer_, ... ) fmap2(x, fun, .buffer_count = NA, .simplify = TRUE, ...) fmap_element_wise(x, fun, .y, ..., .input_size = NA)fmap( x, fun, .y = NULL, .buffer_count = NA_integer_, .output_size = NA_integer_, ... ) fmap2(x, fun, .buffer_count = NA, .simplify = TRUE, ...) fmap_element_wise(x, fun, .y, ..., .input_size = NA)
x |
a list of file arrays to map; each element of |
fun |
function that takes one list |
.y |
a file array object, used to save results |
.buffer_count |
number of total buffers (chunks) to run |
.output_size |
|
... |
other arguments passing to |
.simplify |
whether to apply |
.input_size |
number of elements to read from each array of |
Denote the first argument of fun as input, The length
of input equals the length of x. The size of each
element of input is defined by .input_size, except for the
last loop. For example, given dimension of each input array as
, if .input_size=100, then
length(input[[1]])=100. The total number of runs equals to
length(x[[1]])/100. If .input_size=300, then
length(input[[1]]) will be 300 except for the last run.
This is because cannot be divided by 300.
The element length of the last run will be 100.
The returned variable length of fun will be checked by
.output_size. If the output length exceed .output_size,
an error will be raised.
Please make sure that length(.y)/length(x[[1]]) equals to
.output_size/.input_size.
For fmap_element_wise, the input[[1]] and output length
must be the consistent.
File array instance .y
set.seed(1) x1 <- filearray_create(tempfile(), dimension = c(100,20,3)) x1[] <- rnorm(6000) x2 <- filearray_create(tempfile(), dimension = c(100,20,3)) x2[] <- rnorm(6000) # Add two arrays output <- filearray_create(tempfile(), dimension = c(100,20,3)) fmap(list(x1, x2), function(input){ input[[1]] + input[[2]] }, output) # check range(output[] - (x1[] + x2[])) output$delete() # Calculate the maximum of x1/x2 for every 100 elements # total 60 batches/loops (`.buffer_count`) output <- filearray_create(tempfile(), dimension = c(20,3)) fmap(list(x1, x2), function(input){ max(input[[1]] / input[[2]]) }, .y = output, .buffer_count = 60) # check range(output[] - apply(x1[] / x2[], c(2,3), max)) output$delete() # A large array example if(interactive()){ x <- filearray_create(tempfile(), dimension = c(287, 100, 301, 4)) dimnames(x) <- list( Trial = 1:287, Marker = 1:100, Time = 1:301, Location = 1:4 ) for(i in 1:4){ x[,,,i] <- runif(8638700) } # Step 1: # for each location, trial, and marker, calibrate (baseline) # according to first 50 time-points output <- filearray_create(tempfile(), dimension = dim(x)) # baseline-percentage change fmap( list(x), function(input){ # get locational data location_data <- input[[1]] dim(location_data) <- c(287, 100, 301) # collapse over first 50 time points for # each trial, and marker baseline <- apply(location_data[,,1:50], c(1,2), mean) # calibrate calibrated <- sweep(location_data, c(1,2), baseline, FUN = function(data, bl){ (data / bl - 1) * 100 }) return(calibrated) }, .y = output, # input dimension is 287 x 100 x 301 for each location # hence 4 loops in total .buffer_count = 4 ) # cleanup x$delete() } # cleanup x1$delete() x2$delete() output$delete()set.seed(1) x1 <- filearray_create(tempfile(), dimension = c(100,20,3)) x1[] <- rnorm(6000) x2 <- filearray_create(tempfile(), dimension = c(100,20,3)) x2[] <- rnorm(6000) # Add two arrays output <- filearray_create(tempfile(), dimension = c(100,20,3)) fmap(list(x1, x2), function(input){ input[[1]] + input[[2]] }, output) # check range(output[] - (x1[] + x2[])) output$delete() # Calculate the maximum of x1/x2 for every 100 elements # total 60 batches/loops (`.buffer_count`) output <- filearray_create(tempfile(), dimension = c(20,3)) fmap(list(x1, x2), function(input){ max(input[[1]] / input[[2]]) }, .y = output, .buffer_count = 60) # check range(output[] - apply(x1[] / x2[], c(2,3), max)) output$delete() # A large array example if(interactive()){ x <- filearray_create(tempfile(), dimension = c(287, 100, 301, 4)) dimnames(x) <- list( Trial = 1:287, Marker = 1:100, Time = 1:301, Location = 1:4 ) for(i in 1:4){ x[,,,i] <- runif(8638700) } # Step 1: # for each location, trial, and marker, calibrate (baseline) # according to first 50 time-points output <- filearray_create(tempfile(), dimension = dim(x)) # baseline-percentage change fmap( list(x), function(input){ # get locational data location_data <- input[[1]] dim(location_data) <- c(287, 100, 301) # collapse over first 50 time points for # each trial, and marker baseline <- apply(location_data[,,1:50], c(1,2), mean) # calibrate calibrated <- sweep(location_data, c(1,2), baseline, FUN = function(data, bl){ (data / bl - 1) * 100 }) return(calibrated) }, .y = output, # input dimension is 287 x 100 x 301 for each location # hence 4 loops in total .buffer_count = 4 ) # cleanup x$delete() } # cleanup x1$delete() x2$delete() output$delete()
which that is 'FileArray' compatibleA generic function of which that is 'FileArray' compatible
fwhich(x, val, arr.ind = FALSE, ret.values = FALSE, ...) ## Default S3 method: fwhich(x, val, arr.ind = FALSE, ret.values = FALSE, ...) ## S3 method for class 'FileArray' fwhich(x, val, arr.ind = FALSE, ret.values = FALSE, ...)fwhich(x, val, arr.ind = FALSE, ret.values = FALSE, ...) ## Default S3 method: fwhich(x, val, arr.ind = FALSE, ret.values = FALSE, ...) ## S3 method for class 'FileArray' fwhich(x, val, arr.ind = FALSE, ret.values = FALSE, ...)
x |
any R vector, matrix, array or file-array |
val |
values to find, or a function taking one argument (a slice of data vector) and returns either logical vector with the same length as the slice or index of the slice; see 'Examples' |
arr.ind |
logical; should array indices be
returned when |
ret.values |
whether to return the values of corresponding indices as an attributes; default is false |
... |
passed to |
The indices of x elements that are listed in val.
# ---- Default case ------------------------------------ x <- array(1:27 + 2, rep(3,3)) # find index of `x` equal to either 4 or 5 fwhich(x, c(4,5)) res <- fwhich(x, c(4,5), ret.values = TRUE) res attr(res, "values") # ---- file-array case -------------------------------- arr <- filearray_create(tempfile(), dim(x)) arr[] <- x fwhich(arr, c(4,5)) fwhich(arr, c(4,5), arr.ind = TRUE, ret.values = TRUE) arr[2:3, 1, 1] # Clean up this example arr$delete() # ---- `val` is a function ---------------------------- x <- as_filearray(c(sample(15), 15), dimension = c(4,4)) ret <- fwhich(x, val = which.max, ret.values = TRUE, arr.ind = FALSE) # ret is the index ret == which.max(x[]) # attr(ret, "values") is the max value max(x[]) == attr(ret, "values") # customize `val` fwhich(x, ret.values = TRUE, arr.ind = FALSE, val = function( slice ) { slice > 10 # or which(slice > 10) })# ---- Default case ------------------------------------ x <- array(1:27 + 2, rep(3,3)) # find index of `x` equal to either 4 or 5 fwhich(x, c(4,5)) res <- fwhich(x, c(4,5), ret.values = TRUE) res attr(res, "values") # ---- file-array case -------------------------------- arr <- filearray_create(tempfile(), dim(x)) arr[] <- x fwhich(arr, c(4,5)) fwhich(arr, c(4,5), arr.ind = TRUE, ret.values = TRUE) arr[2:3, 1, 1] # Clean up this example arr$delete() # ---- `val` is a function ---------------------------- x <- as_filearray(c(sample(15), 15), dimension = c(4,4)) ret <- fwhich(x, val = which.max, ret.values = TRUE, arr.ind = FALSE) # ret is the index ret == which.max(x[]) # attr(ret, "values") is the max value max(x[]) == attr(ret, "values") # customize `val` fwhich(x, ret.values = TRUE, arr.ind = FALSE, val = function( slice ) { slice > 10 # or which(slice > 10) })
A map-reduce method to iterate blocks of file-array data with little memory usage
mapreduce(x, map, reduce, ...) ## S4 method for signature 'FileArray,ANY,function' mapreduce(x, map, reduce, buffer_size = NA, ...) ## S4 method for signature 'FileArray,ANY,NULL' mapreduce(x, map, reduce, buffer_size = NA, ...) ## S4 method for signature 'FileArray,ANY,missing' mapreduce(x, map, reduce, buffer_size = NA, ...)mapreduce(x, map, reduce, ...) ## S4 method for signature 'FileArray,ANY,function' mapreduce(x, map, reduce, buffer_size = NA, ...) ## S4 method for signature 'FileArray,ANY,NULL' mapreduce(x, map, reduce, buffer_size = NA, ...) ## S4 method for signature 'FileArray,ANY,missing' mapreduce(x, map, reduce, buffer_size = NA, ...)
x |
a file array object |
map |
mapping function that receives 3 arguments; see 'Details' |
reduce |
|
... |
passed to other methods |
buffer_size |
control how we split the array; see 'Details' |
When handling out-of-memory arrays, it is recommended to load
a block of array at a time and execute on block level. See
apply for a implementation. When an array is too large,
and when there are too many blocks, this operation will become
very slow if computer memory is low.
This is because the R will perform garbage collection frequently.
Implemented in C++, mapreduce creates a buffer to store
the block data. By reusing the memory over and over again, it is possible
to iterate through the array with minimal garbage collections. Many
statistics, including min, max, sum,
mean, ... These statistics can be calculated in this
way efficiently.
The function map contains three arguments: data (mandate),
size (optional), and first_index (optional).
The data is the buffer,
whose length is consistent across iterations. size indicates
the effective size of the buffer. If the partition size
is not divisible by the buffer size, only first size elements of
the data are from array, and the rest elements will be NA.
This situation could only occurs when buffer_size is manually
specified. By default, all of data should belong to arrays.
The last argument first_index is the index of the first element
data[1] in the whole array. It is useful when positional data
is needed.
The buffer size, specified by buffer_size is an
additional optional argument in .... Its default is NA,
and will be calculated automatically. If manually specified, a
large buffer size would be desired to speed up the calculation.
The default buffer size will not exceed , where
nThreads is the number of threads set by filearray_threads.
When partition length cannot be divided by the buffer size, instead of
trimming the buffer, NAs will be filled to the buffer,
passed to map function; see previous paragraph for treatments.
The function mapreduce ignores the missing partitions. That means
if a partition is missing, its data will not be read nor passed to
map function. Please run x$initialize_partition() to make sure
partition files exist.
If reduce is NULL, return mapped results, otherwise
return reduced results from reduce function
x <- filearray_create(tempfile(), c(100, 100, 10)) x[] <- rnorm(1e5) ## calculate summation # identical to sum(x[]), but is more feasible in large cases mapreduce(x, map = function(data, size){ # make sure `data` is all from array if(length(data) != size){ data <- data[1:size] } sum(data) }, reduce = function(mapped_list){ do.call(sum, mapped_list) }) ## Find elements are less than -3 positions <- mapreduce( x, map = function(data, size, first_index) { if (length(data) != size) { data <- data[1:size] } which(data < -3) + (first_index - 1) }, reduce = function(mapped_list) { do.call(c, mapped_list) } ) if(length(positions)){ x[[positions[1]]] }x <- filearray_create(tempfile(), c(100, 100, 10)) x[] <- rnorm(1e5) ## calculate summation # identical to sum(x[]), but is more feasible in large cases mapreduce(x, map = function(data, size){ # make sure `data` is all from array if(length(data) != size){ data <- data[1:size] } sum(data) }, reduce = function(mapped_list){ do.call(sum, mapped_list) }) ## Find elements are less than -3 positions <- mapreduce( x, map = function(data, size, first_index) { if (length(data) != size) { data <- data[1:size] } which(data < -3) + (first_index - 1) }, reduce = function(mapped_list) { do.call(c, mapped_list) } ) if(length(positions)){ x[[positions[1]]] }
These are 'S3' methods for 'FileArray'
## S3 method for class 'FileArray' x[ i, ..., drop = TRUE, reshape = NULL, strict = TRUE, dimnames = TRUE, split_dim = 0 ] ## S3 replacement method for class 'FileArray' x[i, ..., lazy = FALSE] <- value ## S3 method for class 'FileArray' x[[i]] ## S3 method for class 'FileArray' as.array(x, reshape = NULL, drop = FALSE, ...) ## S3 method for class 'FileArray' dim(x) ## S3 method for class 'FileArray' dimnames(x) ## S3 replacement method for class 'FileArray' dimnames(x) <- value ## S3 method for class 'FileArray' length(x) ## S3 method for class 'FileArray' max(x, na.rm = FALSE, ...) ## S3 method for class 'FileArray' min(x, na.rm = FALSE, ...) ## S3 method for class 'FileArray' range(x, na.rm = FALSE, ...) ## S3 method for class 'FileArray' sum(x, na.rm = FALSE, ...) ## S3 method for class 'FileArray' subset(x, ..., drop = FALSE, .env = parent.frame())## S3 method for class 'FileArray' x[ i, ..., drop = TRUE, reshape = NULL, strict = TRUE, dimnames = TRUE, split_dim = 0 ] ## S3 replacement method for class 'FileArray' x[i, ..., lazy = FALSE] <- value ## S3 method for class 'FileArray' x[[i]] ## S3 method for class 'FileArray' as.array(x, reshape = NULL, drop = FALSE, ...) ## S3 method for class 'FileArray' dim(x) ## S3 method for class 'FileArray' dimnames(x) ## S3 replacement method for class 'FileArray' dimnames(x) <- value ## S3 method for class 'FileArray' length(x) ## S3 method for class 'FileArray' max(x, na.rm = FALSE, ...) ## S3 method for class 'FileArray' min(x, na.rm = FALSE, ...) ## S3 method for class 'FileArray' range(x, na.rm = FALSE, ...) ## S3 method for class 'FileArray' sum(x, na.rm = FALSE, ...) ## S3 method for class 'FileArray' subset(x, ..., drop = FALSE, .env = parent.frame())
x |
a file array |
i, ...
|
index set, or passed to other methods |
drop |
whether to drop dimensions; see topic |
reshape |
a new dimension to set before returning subset results; default is |
strict |
whether to allow indices to exceed bound; currently only accept |
dimnames |
whether to preserve |
split_dim |
internally used; split dimension and calculate indices to manually speed up the subset; value ranged from 0 to size of dimension minus one. |
lazy |
whether to lazy-evaluate the method, only works when assigning arrays with logical array index |
value |
value to substitute or set |
na.rm |
whether to remove |
.env |
environment to evaluate formula when evaluating subset margin indices. |
[: subset array
`[`(FileArray) <- value: subset assign array
[[: get element by index
as.array(FileArray): converts file array to native array in R
dim(FileArray): get dimensions
dimnames(FileArray): get dimension names
dimnames(FileArray) <- value: set dimension names
length(FileArray): get array length
max(FileArray): get max value
min(FileArray): get min value
range(FileArray): get value range
sum(FileArray): get summation
subset(FileArray): get subset file array with formulae
FileArray
'S4' methods for FileArray
## S4 method for signature 'FileArray,FileArray' e1 + e2 ## S4 method for signature 'FileArray,numeric' e1 + e2 ## S4 method for signature 'numeric,FileArray' e1 + e2 ## S4 method for signature 'FileArray,complex' e1 + e2 ## S4 method for signature 'complex,FileArray' e1 + e2 ## S4 method for signature 'FileArray,logical' e1 + e2 ## S4 method for signature 'logical,FileArray' e1 + e2 ## S4 method for signature 'FileArray,array' e1 + e2 ## S4 method for signature 'array,FileArray' e1 + e2 ## S4 method for signature 'FileArray,FileArray' e1 - e2 ## S4 method for signature 'FileArray,numeric' e1 - e2 ## S4 method for signature 'numeric,FileArray' e1 - e2 ## S4 method for signature 'FileArray,complex' e1 - e2 ## S4 method for signature 'complex,FileArray' e1 - e2 ## S4 method for signature 'FileArray,logical' e1 - e2 ## S4 method for signature 'logical,FileArray' e1 - e2 ## S4 method for signature 'FileArray,array' e1 - e2 ## S4 method for signature 'array,FileArray' e1 - e2 ## S4 method for signature 'FileArray,FileArray' e1 * e2 ## S4 method for signature 'FileArray,numeric' e1 * e2 ## S4 method for signature 'numeric,FileArray' e1 * e2 ## S4 method for signature 'FileArray,complex' e1 * e2 ## S4 method for signature 'complex,FileArray' e1 * e2 ## S4 method for signature 'FileArray,logical' e1 * e2 ## S4 method for signature 'logical,FileArray' e1 * e2 ## S4 method for signature 'FileArray,array' e1 * e2 ## S4 method for signature 'array,FileArray' e1 * e2 ## S4 method for signature 'FileArray,FileArray' e1 / e2 ## S4 method for signature 'FileArray,numeric' e1 / e2 ## S4 method for signature 'numeric,FileArray' e1 / e2 ## S4 method for signature 'FileArray,complex' e1 / e2 ## S4 method for signature 'complex,FileArray' e1 / e2 ## S4 method for signature 'FileArray,logical' e1 / e2 ## S4 method for signature 'logical,FileArray' e1 / e2 ## S4 method for signature 'FileArray,array' e1 / e2 ## S4 method for signature 'array,FileArray' e1 / e2 ## S4 method for signature 'FileArray,FileArray' e1 ^ e2 ## S4 method for signature 'FileArray,numeric' e1 ^ e2 ## S4 method for signature 'numeric,FileArray' e1 ^ e2 ## S4 method for signature 'FileArray,complex' e1 ^ e2 ## S4 method for signature 'complex,FileArray' e1 ^ e2 ## S4 method for signature 'FileArray,logical' e1 ^ e2 ## S4 method for signature 'logical,FileArray' e1 ^ e2 ## S4 method for signature 'FileArray,array' e1 ^ e2 ## S4 method for signature 'array,FileArray' e1 ^ e2 ## S4 method for signature 'FileArray,FileArray' e1 %% e2 ## S4 method for signature 'FileArray,numeric' e1 %% e2 ## S4 method for signature 'numeric,FileArray' e1 %% e2 ## S4 method for signature 'FileArray,complex' e1 %% e2 ## S4 method for signature 'complex,FileArray' e1 %% e2 ## S4 method for signature 'FileArray,logical' e1 %% e2 ## S4 method for signature 'logical,FileArray' e1 %% e2 ## S4 method for signature 'FileArray,array' e1 %% e2 ## S4 method for signature 'array,FileArray' e1 %% e2 ## S4 method for signature 'FileArray,FileArray' e1 %/% e2 ## S4 method for signature 'FileArray,numeric' e1 %/% e2 ## S4 method for signature 'numeric,FileArray' e1 %/% e2 ## S4 method for signature 'FileArray,complex' e1 %/% e2 ## S4 method for signature 'complex,FileArray' e1 %/% e2 ## S4 method for signature 'FileArray,logical' e1 %/% e2 ## S4 method for signature 'logical,FileArray' e1 %/% e2 ## S4 method for signature 'FileArray,array' e1 %/% e2 ## S4 method for signature 'array,FileArray' e1 %/% e2 ## S4 method for signature 'FileArray,FileArray' e1 == e2 ## S4 method for signature 'FileArray,numeric' e1 == e2 ## S4 method for signature 'numeric,FileArray' e1 == e2 ## S4 method for signature 'FileArray,complex' e1 == e2 ## S4 method for signature 'complex,FileArray' e1 == e2 ## S4 method for signature 'FileArray,logical' e1 == e2 ## S4 method for signature 'logical,FileArray' e1 == e2 ## S4 method for signature 'FileArray,array' e1 == e2 ## S4 method for signature 'array,FileArray' e1 == e2 ## S4 method for signature 'FileArray,FileArray' e1 > e2 ## S4 method for signature 'FileArray,numeric' e1 > e2 ## S4 method for signature 'numeric,FileArray' e1 > e2 ## S4 method for signature 'FileArray,complex' e1 > e2 ## S4 method for signature 'complex,FileArray' e1 > e2 ## S4 method for signature 'FileArray,logical' e1 > e2 ## S4 method for signature 'logical,FileArray' e1 > e2 ## S4 method for signature 'FileArray,array' e1 > e2 ## S4 method for signature 'array,FileArray' e1 > e2 ## S4 method for signature 'FileArray,FileArray' e1 < e2 ## S4 method for signature 'FileArray,numeric' e1 < e2 ## S4 method for signature 'numeric,FileArray' e1 < e2 ## S4 method for signature 'FileArray,complex' e1 < e2 ## S4 method for signature 'complex,FileArray' e1 < e2 ## S4 method for signature 'FileArray,logical' e1 < e2 ## S4 method for signature 'logical,FileArray' e1 < e2 ## S4 method for signature 'FileArray,array' e1 < e2 ## S4 method for signature 'array,FileArray' e1 < e2 ## S4 method for signature 'FileArray,FileArray' e1 != e2 ## S4 method for signature 'FileArray,numeric' e1 != e2 ## S4 method for signature 'numeric,FileArray' e1 != e2 ## S4 method for signature 'FileArray,complex' e1 != e2 ## S4 method for signature 'complex,FileArray' e1 != e2 ## S4 method for signature 'FileArray,logical' e1 != e2 ## S4 method for signature 'logical,FileArray' e1 != e2 ## S4 method for signature 'FileArray,array' e1 != e2 ## S4 method for signature 'array,FileArray' e1 != e2 ## S4 method for signature 'FileArray,FileArray' e1 >= e2 ## S4 method for signature 'FileArray,numeric' e1 >= e2 ## S4 method for signature 'numeric,FileArray' e1 >= e2 ## S4 method for signature 'FileArray,complex' e1 >= e2 ## S4 method for signature 'complex,FileArray' e1 >= e2 ## S4 method for signature 'FileArray,logical' e1 >= e2 ## S4 method for signature 'logical,FileArray' e1 >= e2 ## S4 method for signature 'FileArray,array' e1 >= e2 ## S4 method for signature 'array,FileArray' e1 >= e2 ## S4 method for signature 'FileArray,FileArray' e1 <= e2 ## S4 method for signature 'FileArray,numeric' e1 <= e2 ## S4 method for signature 'numeric,FileArray' e1 <= e2 ## S4 method for signature 'FileArray,complex' e1 <= e2 ## S4 method for signature 'complex,FileArray' e1 <= e2 ## S4 method for signature 'FileArray,logical' e1 <= e2 ## S4 method for signature 'logical,FileArray' e1 <= e2 ## S4 method for signature 'FileArray,array' e1 <= e2 ## S4 method for signature 'array,FileArray' e1 <= e2 ## S4 method for signature 'FileArray,FileArray' e1 & e2 ## S4 method for signature 'FileArray,numeric' e1 & e2 ## S4 method for signature 'numeric,FileArray' e1 & e2 ## S4 method for signature 'FileArray,complex' e1 & e2 ## S4 method for signature 'complex,FileArray' e1 & e2 ## S4 method for signature 'FileArray,logical' e1 & e2 ## S4 method for signature 'logical,FileArray' e1 & e2 ## S4 method for signature 'FileArray,array' e1 & e2 ## S4 method for signature 'array,FileArray' e1 & e2 ## S4 method for signature 'FileArray,FileArray' e1 | e2 ## S4 method for signature 'FileArray,numeric' e1 | e2 ## S4 method for signature 'numeric,FileArray' e1 | e2 ## S4 method for signature 'FileArray,complex' e1 | e2 ## S4 method for signature 'complex,FileArray' e1 | e2 ## S4 method for signature 'FileArray,logical' e1 | e2 ## S4 method for signature 'logical,FileArray' e1 | e2 ## S4 method for signature 'FileArray,array' e1 | e2 ## S4 method for signature 'array,FileArray' e1 | e2 ## S4 method for signature 'FileArray' !x ## S4 method for signature 'FileArray' exp(x) ## S4 method for signature 'FileArray' expm1(x) ## S4 method for signature 'FileArray' log(x, base = exp(1)) ## S4 method for signature 'FileArray' log10(x) ## S4 method for signature 'FileArray' log2(x) ## S4 method for signature 'FileArray' log1p(x) ## S4 method for signature 'FileArray' abs(x) ## S4 method for signature 'FileArray' sqrt(x) ## S4 method for signature 'FileArray' sign(x) ## S4 method for signature 'FileArray' signif(x, digits = 6) ## S4 method for signature 'FileArray' trunc(x, ...) ## S4 method for signature 'FileArray' floor(x) ## S4 method for signature 'FileArray' ceiling(x) ## S4 method for signature 'FileArray' round(x, digits = 0) ## S4 method for signature 'FileArray' acos(x) ## S4 method for signature 'FileArray' acosh(x) ## S4 method for signature 'FileArray' asin(x) ## S4 method for signature 'FileArray' asinh(x) ## S4 method for signature 'FileArray' atan(x) ## S4 method for signature 'FileArray' atanh(x) ## S4 method for signature 'FileArray' cos(x) ## S4 method for signature 'FileArray' cosh(x) ## S4 method for signature 'FileArray' cospi(x) ## S4 method for signature 'FileArray' sin(x) ## S4 method for signature 'FileArray' sinh(x) ## S4 method for signature 'FileArray' sinpi(x) ## S4 method for signature 'FileArray' tan(x) ## S4 method for signature 'FileArray' tanh(x) ## S4 method for signature 'FileArray' tanpi(x) ## S4 method for signature 'FileArray' gamma(x) ## S4 method for signature 'FileArray' lgamma(x) ## S4 method for signature 'FileArray' digamma(x) ## S4 method for signature 'FileArray' trigamma(x) ## S4 method for signature 'FileArray' Arg(z) ## S4 method for signature 'FileArray' Conj(z) ## S4 method for signature 'FileArray' Im(z) ## S4 method for signature 'FileArray' Mod(z) ## S4 method for signature 'FileArray' Re(z) ## S4 method for signature 'FileArray' is.na(x)## S4 method for signature 'FileArray,FileArray' e1 + e2 ## S4 method for signature 'FileArray,numeric' e1 + e2 ## S4 method for signature 'numeric,FileArray' e1 + e2 ## S4 method for signature 'FileArray,complex' e1 + e2 ## S4 method for signature 'complex,FileArray' e1 + e2 ## S4 method for signature 'FileArray,logical' e1 + e2 ## S4 method for signature 'logical,FileArray' e1 + e2 ## S4 method for signature 'FileArray,array' e1 + e2 ## S4 method for signature 'array,FileArray' e1 + e2 ## S4 method for signature 'FileArray,FileArray' e1 - e2 ## S4 method for signature 'FileArray,numeric' e1 - e2 ## S4 method for signature 'numeric,FileArray' e1 - e2 ## S4 method for signature 'FileArray,complex' e1 - e2 ## S4 method for signature 'complex,FileArray' e1 - e2 ## S4 method for signature 'FileArray,logical' e1 - e2 ## S4 method for signature 'logical,FileArray' e1 - e2 ## S4 method for signature 'FileArray,array' e1 - e2 ## S4 method for signature 'array,FileArray' e1 - e2 ## S4 method for signature 'FileArray,FileArray' e1 * e2 ## S4 method for signature 'FileArray,numeric' e1 * e2 ## S4 method for signature 'numeric,FileArray' e1 * e2 ## S4 method for signature 'FileArray,complex' e1 * e2 ## S4 method for signature 'complex,FileArray' e1 * e2 ## S4 method for signature 'FileArray,logical' e1 * e2 ## S4 method for signature 'logical,FileArray' e1 * e2 ## S4 method for signature 'FileArray,array' e1 * e2 ## S4 method for signature 'array,FileArray' e1 * e2 ## S4 method for signature 'FileArray,FileArray' e1 / e2 ## S4 method for signature 'FileArray,numeric' e1 / e2 ## S4 method for signature 'numeric,FileArray' e1 / e2 ## S4 method for signature 'FileArray,complex' e1 / e2 ## S4 method for signature 'complex,FileArray' e1 / e2 ## S4 method for signature 'FileArray,logical' e1 / e2 ## S4 method for signature 'logical,FileArray' e1 / e2 ## S4 method for signature 'FileArray,array' e1 / e2 ## S4 method for signature 'array,FileArray' e1 / e2 ## S4 method for signature 'FileArray,FileArray' e1 ^ e2 ## S4 method for signature 'FileArray,numeric' e1 ^ e2 ## S4 method for signature 'numeric,FileArray' e1 ^ e2 ## S4 method for signature 'FileArray,complex' e1 ^ e2 ## S4 method for signature 'complex,FileArray' e1 ^ e2 ## S4 method for signature 'FileArray,logical' e1 ^ e2 ## S4 method for signature 'logical,FileArray' e1 ^ e2 ## S4 method for signature 'FileArray,array' e1 ^ e2 ## S4 method for signature 'array,FileArray' e1 ^ e2 ## S4 method for signature 'FileArray,FileArray' e1 %% e2 ## S4 method for signature 'FileArray,numeric' e1 %% e2 ## S4 method for signature 'numeric,FileArray' e1 %% e2 ## S4 method for signature 'FileArray,complex' e1 %% e2 ## S4 method for signature 'complex,FileArray' e1 %% e2 ## S4 method for signature 'FileArray,logical' e1 %% e2 ## S4 method for signature 'logical,FileArray' e1 %% e2 ## S4 method for signature 'FileArray,array' e1 %% e2 ## S4 method for signature 'array,FileArray' e1 %% e2 ## S4 method for signature 'FileArray,FileArray' e1 %/% e2 ## S4 method for signature 'FileArray,numeric' e1 %/% e2 ## S4 method for signature 'numeric,FileArray' e1 %/% e2 ## S4 method for signature 'FileArray,complex' e1 %/% e2 ## S4 method for signature 'complex,FileArray' e1 %/% e2 ## S4 method for signature 'FileArray,logical' e1 %/% e2 ## S4 method for signature 'logical,FileArray' e1 %/% e2 ## S4 method for signature 'FileArray,array' e1 %/% e2 ## S4 method for signature 'array,FileArray' e1 %/% e2 ## S4 method for signature 'FileArray,FileArray' e1 == e2 ## S4 method for signature 'FileArray,numeric' e1 == e2 ## S4 method for signature 'numeric,FileArray' e1 == e2 ## S4 method for signature 'FileArray,complex' e1 == e2 ## S4 method for signature 'complex,FileArray' e1 == e2 ## S4 method for signature 'FileArray,logical' e1 == e2 ## S4 method for signature 'logical,FileArray' e1 == e2 ## S4 method for signature 'FileArray,array' e1 == e2 ## S4 method for signature 'array,FileArray' e1 == e2 ## S4 method for signature 'FileArray,FileArray' e1 > e2 ## S4 method for signature 'FileArray,numeric' e1 > e2 ## S4 method for signature 'numeric,FileArray' e1 > e2 ## S4 method for signature 'FileArray,complex' e1 > e2 ## S4 method for signature 'complex,FileArray' e1 > e2 ## S4 method for signature 'FileArray,logical' e1 > e2 ## S4 method for signature 'logical,FileArray' e1 > e2 ## S4 method for signature 'FileArray,array' e1 > e2 ## S4 method for signature 'array,FileArray' e1 > e2 ## S4 method for signature 'FileArray,FileArray' e1 < e2 ## S4 method for signature 'FileArray,numeric' e1 < e2 ## S4 method for signature 'numeric,FileArray' e1 < e2 ## S4 method for signature 'FileArray,complex' e1 < e2 ## S4 method for signature 'complex,FileArray' e1 < e2 ## S4 method for signature 'FileArray,logical' e1 < e2 ## S4 method for signature 'logical,FileArray' e1 < e2 ## S4 method for signature 'FileArray,array' e1 < e2 ## S4 method for signature 'array,FileArray' e1 < e2 ## S4 method for signature 'FileArray,FileArray' e1 != e2 ## S4 method for signature 'FileArray,numeric' e1 != e2 ## S4 method for signature 'numeric,FileArray' e1 != e2 ## S4 method for signature 'FileArray,complex' e1 != e2 ## S4 method for signature 'complex,FileArray' e1 != e2 ## S4 method for signature 'FileArray,logical' e1 != e2 ## S4 method for signature 'logical,FileArray' e1 != e2 ## S4 method for signature 'FileArray,array' e1 != e2 ## S4 method for signature 'array,FileArray' e1 != e2 ## S4 method for signature 'FileArray,FileArray' e1 >= e2 ## S4 method for signature 'FileArray,numeric' e1 >= e2 ## S4 method for signature 'numeric,FileArray' e1 >= e2 ## S4 method for signature 'FileArray,complex' e1 >= e2 ## S4 method for signature 'complex,FileArray' e1 >= e2 ## S4 method for signature 'FileArray,logical' e1 >= e2 ## S4 method for signature 'logical,FileArray' e1 >= e2 ## S4 method for signature 'FileArray,array' e1 >= e2 ## S4 method for signature 'array,FileArray' e1 >= e2 ## S4 method for signature 'FileArray,FileArray' e1 <= e2 ## S4 method for signature 'FileArray,numeric' e1 <= e2 ## S4 method for signature 'numeric,FileArray' e1 <= e2 ## S4 method for signature 'FileArray,complex' e1 <= e2 ## S4 method for signature 'complex,FileArray' e1 <= e2 ## S4 method for signature 'FileArray,logical' e1 <= e2 ## S4 method for signature 'logical,FileArray' e1 <= e2 ## S4 method for signature 'FileArray,array' e1 <= e2 ## S4 method for signature 'array,FileArray' e1 <= e2 ## S4 method for signature 'FileArray,FileArray' e1 & e2 ## S4 method for signature 'FileArray,numeric' e1 & e2 ## S4 method for signature 'numeric,FileArray' e1 & e2 ## S4 method for signature 'FileArray,complex' e1 & e2 ## S4 method for signature 'complex,FileArray' e1 & e2 ## S4 method for signature 'FileArray,logical' e1 & e2 ## S4 method for signature 'logical,FileArray' e1 & e2 ## S4 method for signature 'FileArray,array' e1 & e2 ## S4 method for signature 'array,FileArray' e1 & e2 ## S4 method for signature 'FileArray,FileArray' e1 | e2 ## S4 method for signature 'FileArray,numeric' e1 | e2 ## S4 method for signature 'numeric,FileArray' e1 | e2 ## S4 method for signature 'FileArray,complex' e1 | e2 ## S4 method for signature 'complex,FileArray' e1 | e2 ## S4 method for signature 'FileArray,logical' e1 | e2 ## S4 method for signature 'logical,FileArray' e1 | e2 ## S4 method for signature 'FileArray,array' e1 | e2 ## S4 method for signature 'array,FileArray' e1 | e2 ## S4 method for signature 'FileArray' !x ## S4 method for signature 'FileArray' exp(x) ## S4 method for signature 'FileArray' expm1(x) ## S4 method for signature 'FileArray' log(x, base = exp(1)) ## S4 method for signature 'FileArray' log10(x) ## S4 method for signature 'FileArray' log2(x) ## S4 method for signature 'FileArray' log1p(x) ## S4 method for signature 'FileArray' abs(x) ## S4 method for signature 'FileArray' sqrt(x) ## S4 method for signature 'FileArray' sign(x) ## S4 method for signature 'FileArray' signif(x, digits = 6) ## S4 method for signature 'FileArray' trunc(x, ...) ## S4 method for signature 'FileArray' floor(x) ## S4 method for signature 'FileArray' ceiling(x) ## S4 method for signature 'FileArray' round(x, digits = 0) ## S4 method for signature 'FileArray' acos(x) ## S4 method for signature 'FileArray' acosh(x) ## S4 method for signature 'FileArray' asin(x) ## S4 method for signature 'FileArray' asinh(x) ## S4 method for signature 'FileArray' atan(x) ## S4 method for signature 'FileArray' atanh(x) ## S4 method for signature 'FileArray' cos(x) ## S4 method for signature 'FileArray' cosh(x) ## S4 method for signature 'FileArray' cospi(x) ## S4 method for signature 'FileArray' sin(x) ## S4 method for signature 'FileArray' sinh(x) ## S4 method for signature 'FileArray' sinpi(x) ## S4 method for signature 'FileArray' tan(x) ## S4 method for signature 'FileArray' tanh(x) ## S4 method for signature 'FileArray' tanpi(x) ## S4 method for signature 'FileArray' gamma(x) ## S4 method for signature 'FileArray' lgamma(x) ## S4 method for signature 'FileArray' digamma(x) ## S4 method for signature 'FileArray' trigamma(x) ## S4 method for signature 'FileArray' Arg(z) ## S4 method for signature 'FileArray' Conj(z) ## S4 method for signature 'FileArray' Im(z) ## S4 method for signature 'FileArray' Mod(z) ## S4 method for signature 'FileArray' Re(z) ## S4 method for signature 'FileArray' is.na(x)
x, z, e1, e2
|
|
base, digits, ...
|
passed to other methods |
See S4groupGeneric
The type of a file array (extended)
typeof(x) ## S4 method for signature 'FileArray' typeof(x) ## S4 method for signature 'FileArrayProxy' typeof(x)typeof(x) ## S4 method for signature 'FileArray' typeof(x) ## S4 method for signature 'FileArrayProxy' typeof(x)
x |
any file array |
A character string. The possible values are "double",
"integer", "logical", and "raw"