sprint: Simple Parallel R INTerface

SPRINT (Simple Parallel R INTerface) is a parallel framework for R. It provides a High Performance Computing (HPC) harness which allows R scripts to run on HPC clusters. SPRINT contains a library of selected R functions that have been parallelized. Functions are named after the original R function with the added prefix 'p', i.e. the parallel version of cor() in SPRINT is called pcor(). Call to the parallel R functions are included directly in standard R scripts. SPRINT contains functions for correlation (pcor), partitioning around medoids (ppam), apply (papply), permutation testing (pmaxT), bootstrapping (pboot), random forest (prandomForest), rank product (pRP) and hamming distance (pstringdistmatrix).

AuthorUniversity of Edinburgh SPRINT Team <sprint@ed.ac.uk>
Date of publication2014-09-29 18:03:02
MaintainerEilidh Troup <e.troup@epcc.ed.ac.uk>
LicenseGPL (>= 3)
Version1.0.7
http://www.r-sprint.org

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Files

sprint
sprint/inst
sprint/inst/CITATION
sprint/inst/test_suite
sprint/inst/test_suite/all_test_suite.R
sprint/inst/test_suite/pcor_test_suite.R
sprint/inst/test_suite/all_results_2014-09-24_Darwin_.log
sprint/inst/test_suite/All-unit-test-log.html
sprint/inst/test_suite/cor_test.R
sprint/inst/test_suite/pcor_test.R
sprint/inst/test_suite/ppam_test_suite.R
sprint/inst/test_suite/ptest_test_suite.R
sprint/inst/test_suite/README
sprint/inst/test_suite/papply_test_suite.R
sprint/inst/test_suite/install_test.R
sprint/inst/test_suite/smallPcorTest.R
sprint/inst/test_suite/batch_ppam_once_test_suite.R
sprint/inst/test_suite/pstringdistmatrix_test_suite.R
sprint/inst/test_suite/pmaxT_test_suite.R
sprint/inst/test_suite/pboot_test_suite.R
sprint/inst/test_suite/all_results_2014-09-04_Darwin_.log
sprint/inst/test_suite/batchRunTests.sh
sprint/inst/test_suite/small_pmaxT_test_suite.R
sprint/inst/test_suite/batch_ppam_loop_test_suite.R
sprint/inst/test_suite/all_results_2014-09-03_Darwin_.log
sprint/inst/systemTest
sprint/inst/systemTest/pstringDist
sprint/inst/systemTest/pstringDist/large_test.R
sprint/inst/systemTest/pstringDist/pstringDist_sys_test.pbs
sprint/inst/systemTest/pstringDist/large_test.sh
sprint/inst/systemTest/pstringDist/pstringDist_sys_test.R
sprint/inst/systemTest/pcor
sprint/inst/systemTest/pcor/pcor.sh
sprint/inst/systemTest/pcor/pcor_sys_test.R
sprint/inst/systemTest/pcor/pcor_sys_test.pbs
sprint/inst/systemTest/papply
sprint/inst/systemTest/papply/large_test.R
sprint/inst/systemTest/batch
sprint/inst/systemTest/batch/ppam_loop_test.R
sprint/inst/systemTest/batch/ppam_once_test.R
sprint/inst/doc
sprint/inst/doc/External_User_Guide_1.0.7.docx
sprint/inst/doc/External_Release_Notes_1.0.7.pdf
sprint/inst/doc/External_User_Guide_1.0.7.pdf
sprint/inst/doc/External_Release_Notes_1.0.7.docx
sprint/inst/unitTests
sprint/inst/unitTests/pboot
sprint/inst/unitTests/pboot/runnit_weight.R
sprint/inst/unitTests/pboot/runnit_simple.R
sprint/inst/unitTests/pboot/runnit_dotdotdot.R
sprint/inst/unitTests/pboot/runnit_boot_example.R
sprint/inst/unitTests/pboot/runnit_standard_datacol.R
sprint/inst/unitTests/pboot/runnit_scene3.R
sprint/inst/unitTests/pboot/runnit_standard_tn.R
sprint/inst/unitTests/pboot/runnit_standard.R
sprint/inst/unitTests/pboot/runnit_m.R
sprint/inst/unitTests/pcor
sprint/inst/unitTests/pcor/runit_correct_args.R
sprint/inst/unitTests/pcor/runit_dimnames.R
sprint/inst/unitTests/pmaxT
sprint/inst/unitTests/pmaxT/runit_correct_args.R
sprint/inst/unitTests/pmaxT/runit_test_B.R
sprint/inst/unitTests/pmaxT/runit_small_test.R
sprint/inst/unitTests/pmaxT/runit_wrong_args.R
sprint/inst/unitTests/papply
sprint/inst/unitTests/papply/runit_test.R
sprint/inst/unitTests/ppam
sprint/inst/unitTests/ppam/runit_exercise1.R
sprint/inst/unitTests/ppam/runit_correct_args.R
sprint/inst/unitTests/ppam/runit_dimnames.R
sprint/inst/unitTests/ppam/runit_correct_args_ff.R
sprint/inst/unitTests/ptest
sprint/inst/unitTests/ptest/runit_ptest.R
sprint/inst/unitTests/pstringdistmatrix
sprint/inst/unitTests/pstringdistmatrix/runit_simple.R
sprint/configure.ac
sprint/src
sprint/src/Makefile
sprint/src/sprint.c
sprint/src/algorithms
sprint/src/algorithms/pboot
sprint/src/algorithms/pboot/implementation
sprint/src/algorithms/pboot/implementation/boot.c
sprint/src/algorithms/pboot/interface
sprint/src/algorithms/pboot/interface/pboot.c
sprint/src/algorithms/prandomForest
sprint/src/algorithms/prandomForest/implementation
sprint/src/algorithms/prandomForest/implementation/random_forest_driver.c
sprint/src/algorithms/prandomForest/interface
sprint/src/algorithms/prandomForest/interface/random_forest.c
sprint/src/algorithms/pcor
sprint/src/algorithms/pcor/implementation
sprint/src/algorithms/pcor/implementation/kernel.c
sprint/src/algorithms/pcor/implementation/kernel.h
sprint/src/algorithms/pcor/implementation/correlation.c
sprint/src/algorithms/pcor/interface
sprint/src/algorithms/pcor/interface/pcor.c
sprint/src/algorithms/rng
sprint/src/algorithms/rng/implementation
sprint/src/algorithms/rng/implementation/sprint-rng-worker.c
sprint/src/algorithms/rng/interface
sprint/src/algorithms/rng/interface/sprint-rng.c
sprint/src/algorithms/pmaxT
sprint/src/algorithms/pmaxT/implementation
sprint/src/algorithms/pmaxT/implementation/mt.h
sprint/src/algorithms/pmaxT/implementation/mt.c
sprint/src/algorithms/pmaxT/implementation/pairt_sampling_fixed.c
sprint/src/algorithms/pmaxT/implementation/stat_order.c
sprint/src/algorithms/pmaxT/implementation/random.c
sprint/src/algorithms/pmaxT/implementation/pairt_sampling.c
sprint/src/algorithms/pmaxT/implementation/permutation.c
sprint/src/algorithms/pmaxT/implementation/bootloop.c
sprint/src/algorithms/pmaxT/implementation/Rpack.c
sprint/src/algorithms/pmaxT/implementation/block_sampling_fixed.c
sprint/src/algorithms/pmaxT/implementation/stat_func.c
sprint/src/algorithms/pmaxT/implementation/sampling_fixed.c
sprint/src/algorithms/pmaxT/implementation/sampling.c
sprint/src/algorithms/pmaxT/interface
sprint/src/algorithms/pmaxT/interface/pmaxT.c
sprint/src/algorithms/papply
sprint/src/algorithms/papply/implementation
sprint/src/algorithms/papply/implementation/apply.c
sprint/src/algorithms/papply/implementation/ffapply.c
sprint/src/algorithms/papply/implementation/ffapply.h
sprint/src/algorithms/papply/implementation/main.c
sprint/src/algorithms/papply/implementation/lapply.c
sprint/src/algorithms/papply/implementation/comms.c
sprint/src/algorithms/papply/implementation/main.h
sprint/src/algorithms/papply/implementation/apply.h
sprint/src/algorithms/papply/implementation/comms.h
sprint/src/algorithms/papply/implementation/lapply.h
sprint/src/algorithms/papply/interface
sprint/src/algorithms/papply/interface/papply.c
sprint/src/algorithms/ppam
sprint/src/algorithms/ppam/implementation
sprint/src/algorithms/ppam/implementation/bswap.c
sprint/src/algorithms/ppam/implementation/pamedoids.h
sprint/src/algorithms/ppam/implementation/silhouette.h
sprint/src/algorithms/ppam/implementation/silhouette.c
sprint/src/algorithms/ppam/implementation/pamedoids.c
sprint/src/algorithms/ppam/implementation/bswap.h
sprint/src/algorithms/ppam/implementation/cstat.h
sprint/src/algorithms/ppam/implementation/cstat.c
sprint/src/algorithms/ppam/interface
sprint/src/algorithms/ppam/interface/ppam.c
sprint/src/algorithms/ppam/interface/ppam.h
sprint/src/algorithms/common
sprint/src/algorithms/common/serialize.c
sprint/src/algorithms/common/utils.c
sprint/src/algorithms/common/functions.c
sprint/src/algorithms/common/mmap.h
sprint/src/algorithms/common/utils.h
sprint/src/algorithms/common/mmap.c
sprint/src/algorithms/common/serialize.h
sprint/src/algorithms/pRP
sprint/src/algorithms/pRP/implementation
sprint/src/algorithms/pRP/implementation/rank-product.h
sprint/src/algorithms/pRP/implementation/boot-rank-product.c
sprint/src/algorithms/pRP/implementation/rp-generic.c
sprint/src/algorithms/pRP/implementation/rank-product.c
sprint/src/algorithms/pRP/interface
sprint/src/algorithms/pRP/interface/rp.c
sprint/src/algorithms/pRP/interface/boot-rp.c
sprint/src/algorithms/psvm
sprint/src/algorithms/psvm/implementation
sprint/src/algorithms/psvm/implementation/Rsvm.h
sprint/src/algorithms/psvm/implementation/svm.h
sprint/src/algorithms/psvm/implementation/svm_call.c
sprint/src/algorithms/psvm/implementation/Rsvm.c
sprint/src/algorithms/psvm/implementation/svm.cpp
sprint/src/algorithms/psvm/interface
sprint/src/algorithms/psvm/interface/psvm.c
sprint/src/algorithms/psvm/interface/psvm.h
sprint/src/algorithms/ptest
sprint/src/algorithms/ptest/implementation
sprint/src/algorithms/ptest/implementation/test.c
sprint/src/algorithms/ptest/interface
sprint/src/algorithms/ptest/interface/ptest.c
sprint/src/algorithms/pstringdistmatrix
sprint/src/algorithms/pstringdistmatrix/implementation
sprint/src/algorithms/pstringdistmatrix/implementation/stringDist.c
sprint/src/algorithms/pstringdistmatrix/implementation/stringDist_kernel.h
sprint/src/algorithms/pstringdistmatrix/implementation/stringDist_kernel.c
sprint/src/algorithms/pstringdistmatrix/interface
sprint/src/algorithms/pstringdistmatrix/interface/pstringDist.c
sprint/src/functions.h
sprint/src/Makevars.in
sprint/src/sprint.h
sprint/NAMESPACE
sprint/NEWS
sprint/R
sprint/R/pcombine.R sprint/R/papply.R
sprint/R/pstringdistmatrix.R
sprint/R/messages.R sprint/R/prandomForest.default.R sprint/R/prandomForest.R
sprint/R/pterminate.R
sprint/R/ptest.R
sprint/R/prandomForest.formula.R sprint/R/pRP.R sprint/R/pmaxT.R
sprint/R/pboot.R
sprint/R/pcor.R sprint/R/sprint-rng.R
sprint/R/zzz.R
sprint/R/ppam.R
sprint/MD5
sprint/README
sprint/DESCRIPTION
sprint/configure
sprint/man
sprint/man/pRSadvance.Rd sprint/man/pterminate.Rd sprint/man/sprint.Rd sprint/man/pstringdistmatrix.Rd sprint/man/pboot.Rd sprint/man/pRS.Rd sprint/man/pcor.Rd sprint/man/ppam.Rd sprint/man/prandomForest.Rd sprint/man/ptest.Rd sprint/man/pRPadvance.Rd sprint/man/pmaxT.Rd sprint/man/reset.rng.Rd sprint/man/pcombine.Rd sprint/man/papply.Rd sprint/man/init.rng.Rd sprint/man/pRP.Rd
sprint/cleanup
sprint/tools
sprint/tools/install-sh
sprint/tools/m4
sprint/tools/m4/acx_mpi.m4
sprint/tools/m4/README
sprint/tools/config.guess
sprint/tools/reconfigure.sh
sprint/tools/config.sub

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