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Package 'future.apply"

May 21, 2023

Version1.11.0

TitleApply Function to Elements in Parallel using Futures

DependsR (>= 3.2.0), future (>= 1.28.0)

Importsglobals (>= 0.16.1), parallel, utils

Suggestsdatasets, stats, tools, listenv (>= 0.8.0), R.rsp, markdown

VignetteBuilderR.rsp

Description

Implementations of apply(), by(), eapply(), lapply(), Map(), .mapply(), mapply(), replicate(), sap- ply(), tapply(), and vapply() that can be resolved using any future-supported backend, e.g. paral- lel on the local machine or distributed on a compute cluster. These future_*apply() func- tions come with the same pros and cons as the corresponding base-R *apply() func- tions but with the additional feature of being able to be processed via the future framework.

LicenseGPL (>= 2)

LazyLoadTRUE

URLhttps://future.apply.futureverse.org,

RoxygenNote7.2.3

NeedsCompilationno

AuthorHenrik Bengtsson [aut, cre, cph],

R Core Team [cph, ctb]

MaintainerHenrik Bengtsson

RepositoryCRAN

Date/Publication2023-05-21 04:10:02 UTC

Rtopics documented:

future.apply . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2 future_apply . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4 1

2future.apply

future_by . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6 future_eapply . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8 future_Map . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13 Index17future.applyfuture.apply: Apply Function to Elements in Parallel using FuturesDescription Thefuture.applypackages provides parallel implementations of common "apply" functions pro- vided by baseR. The parallel processing is performed via thefutureecosystem, which provides a large number of parallel backends, e.g. on the local machine, a remote cluster, and a high- performance compute cluster.

Details

Currently implemented functions are:

•future_apply(): a parallel version ofapply() •future_by(): a parallel version ofby() •future_eapply(): a parallel version ofeapply() •future_lapply(): a parallel version oflapply() •future_mapply(): a parallel version ofmapply() •future_sapply(): a parallel version ofsapply() •future_tapply(): a parallel version oftapply() •future_vapply(): a parallel version ofv apply() •future_Map(): a parallel version ofMap() •future_replicate(): a parallel version ofreplicate() •future_.mapply(): a parallel version of.mapply() Reproducibility is part of the core design, which means that perfect, parallel random number gener- ation (RNG) is supported regardless of the amount of chunking, type of load balancing, and future backend being used. Since thesefuture_*()functions have the same arguments as the corresponding baseRfunction,

start using them is often as simple as renaming the function in the code. For example, after attaching

the package: library(future.apply) code such as: x <- list(a = 1:10, beta = exp(-3:3), logic = c(TRUE,FALSE,FALSE,TRUE)) y <- lapply(x, quantile, probs = 1:3/4) future.apply3 can be updated to: y <- future_lapply(x, quantile, probs = 1:3/4) The default settings in thefutureframework is to process codesequentially. To run the above in parallel on the local machine (on any operating system), use: plan(multisession) first. That"s it! To go back to sequential processing, useplan(sequential). If you have access to multiple ma- chines on your local network, use: plan(cluster, workers = c("n1", "n2", "n2", "n3")) This will set up four workers, one onn1andn3, and two onn2. If you have SSH access to some remote machines, use: plan(cluster, workers = c("m1.myserver.org", "m2.myserver.org)) See thefuturepackage andfuture::plan()for more examples. Thefuture.batchtoolspackage provides support for high-performance compute (HPC) cluster schedulers such as SGE, Slurm, and TORQUE / PBS. For example, •plan(batchtools_slurm): Process via a Slurm scheduler job queue. •plan(batchtools_torque): Process via a TORQUE / PBS scheduler job queue. This builds on top of the queuing framework that thebatchtoolspackage provides. For more details on backend configuration, please see thefuture.batchtoolsandbatchtoolspackages. These are just a few examples of parallel/distributed backend for the future ecosystem. For more alternatives, see the "Reverse dependencies" section on the future CRAN package page

Author(s)

HenrikBengtsson, exceptfortheimplementationsoffuture_apply(),future_Map(),future_replicate(), future_sapply(), andfuture_tapply(), which are adopted from the source code of the corre- sponding baseRfunctions, which are licensed under GPL (>= 2) with "The R Core Team" as the copyright holder. Because of these dependencies, the license of this package is GPL (>= 2).

4future_applyfuture_applyApply Functions Over Array Margins via FuturesDescription

future_apply()implementsbase::apply()using future with perfect replication of results, re-

gardless of future backend used. It returns a vector or array or list of values obtained by applying a

function to margins of an array or matrix. Usage future_apply( X,

MARGIN,

FUN, simplify = TRUE, future.envir = parent.frame(), future.stdout = TRUE, future.conditions = "condition", future.globals = TRUE, future.packages = NULL, future.seed = FALSE, future.scheduling = 1, future.chunk.size = NULL, future.label = "future_apply-%d"

Arguments

Xan array, including a matrix.

MARGINA vector giving the subscripts which the function will be applied over. For example, for a matrix1indicates rows,2indicates columns,c(1, 2)indicates rows and columns. WhereXhas named dimnames, it can be a character vector selecting dimension names.

FUNA function taking at least one argument.

simplifya logical indicating whether results should be simplified if possible. future.envirAnen vironmentpassed as ar gumentenvirtofuture::future()as-is. future.stdoutIfTRUE(default), then the standard output of the underlying futures is captured, and re-outputted as soon as possible. IfFALSE, any output is silenced (by sinking it to the null device as it is outputted). IfNA(not recommended), output isnot intercepted. future.conditions A character string of conditions classes to be captured and relayed. The default is the same as theconditionargument offuture::Future(). To not intercept conditions, useconditions = character(0L). Errors are always relayed. future_apply5 future.globalsA logical, a character vector, or a named list for controlling how globals are handled. For details, see below section. future.packages (optional) a character vector specifying packages to be attached in the R envi- ronment evaluating the future. future.seedA logical or an integer (of length one or seven), or a list oflength(X)with pre-generated random seeds. For details, see below section. future.scheduling Average number of futures ("chunks") per worker. If0.0, then a single future is used to process all elements ofX. If1.0orTRUE, then one future per worker is used. If2.0, then each worker will process two futures (if there are enough elements inX). IfInforFALSE, then one future per element ofXis used. Only used iffuture.chunk.sizeisNULL. future.chunk.size The average number of elements per future ("chunk"). IfInf, then all elements are processed in a single future. IfNULL, then argumentfuture.schedulingis used. future.labelIfacharacterstring, theneachfutureisassignedalabelsprintf(future.label, chunk_idx). IfTRUE,thenthesameasfuture.label = "future_lapply-%d".

If FALSE, no labels are assigned.

...(optional) Additional arguments passed toFUN(), exceptfuture.*arguments, which are passed on tofuture_lapply()used internally. Value

Returns a vector or array or list of values obtained by applying a function to margins of an array or

matrix. Seebase::apply()for details.

Author(s)

The implementations offuture_apply()is adopted from the source code of the corresponding baseRfunction, which is licensed under GPL (>= 2) with "The R Core Team" as the copyright holder.

Examples

## apply()

X <- matrix(c(1:4, 1, 6:8), nrow = 2L)

Y0 <- apply(X, MARGIN = 1L, FUN = table)

Y1 <- future_apply(X, MARGIN = 1L, FUN = table)

print(Y1) stopifnot(all.equal(Y1, Y0, check.attributes = FALSE)) ## FIXME Y0 <- apply(X, MARGIN = 1L, FUN = stats::quantile) Y1 <- future_apply(X, MARGIN = 1L, FUN = stats::quantile) print(Y1)

6future_by

stopifnot(all.equal(Y1, Y0)) ## Parallel Random Number Generation ## Regardless of the future plan, the number of workers, and ## where they are, the random numbers produced are identical

X <- matrix(c(1:4, 1, 6:8), nrow = 2L)

plan(multisession) set.seed(0xBEEF) Y1 <- future_apply(X, MARGIN = 1L, FUN = sample, future.seed = TRUE) print(Y1) plan(sequential) set.seed(0xBEEF) Y2 <- future_apply(X, MARGIN = 1L, FUN = sample, future.seed = TRUE) print(Y2)

stopifnot(all.equal(Y1, Y2))future_byApply a Function to a Data Frame Split by Factors via FuturesDescription

Apply a Function to a Data Frame Split by Factors via Futures Usage future_by( data,

INDICES,

FUN, simplify = TRUE, future.envir = parent.frame()

Arguments

dataAnRobject, normally a data frame, possibly a matrix. INDICESA factor or a list of factors, each of lengthnrow(data). future_by7 FUNa function to be applied to (usually data-frame) subsets ofdata. simplifylogical: seebase::tapply . future.envirAnen vironmentpassed as ar gumentenvirtofuture::future()as-is. ...Additional arguments pass tofuture_lapply()and then toFUN().

Details

Internally,datais grouped byINDICESinto a list ofdatasubset elements which is then processed byfuture_lapply(). When the groups differ significantly in size, the processing time may differ significantly between the groups. To correct for processing-time imbalances, adjust the amount of chunking via argumentsfuture.schedulingandfuture.chunk.size. Value

An object of class "by", giving the results for each subset. This is always a list if simplify is false,

otherwise a list or array (see base::tapply ). See alsobase::by()for details.

Note on "stringsAsFactors"

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