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).

Author
University of Edinburgh SPRINT Team <sprint@ed.ac.uk>
Date of publication
2014-09-29 18:03:02
Maintainer
Eilidh Troup <e.troup@epcc.ed.ac.uk>
License
GPL (>= 3)
Version
1.0.7
URLs

View on CRAN

Man pages

init.rng
init.rng
papply
Parallel Apply
pboot
Parallel Bootstrapping
pcombine
pcombine
pcor
Parallel Correlation
pmaxT
Ajusted p-values for step down multiple testing
ppam
Parallel Partitioning Around Medoids
prandomForest
Parallel random forest generation
pRP
Parallel Rank Product
pRPadvance
pRPadvance
pRS
pRS
pRSadvance
pRSadvance
pstringdistmatrix
Parallel compute hamming distance between strings
pterminate
SPRINT close
ptest
SPRINT Installation Test
reset.rng
reset.rng
sprint
Overview of SPRINT

Files in this package

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