distcomp: Computations over Distributed Data without Aggregation

Implementing algorithms and fitting models when sites (possibly remote) share computation summaries rather than actual data over HTTP with a master R process (using 'opencpu', for example). A stratified Cox model and a singular value decomposition are provided. The former makes direct use of code from the R 'survival' package. (That is, the underlying Cox model code is derived from that in the R 'survival' package.) Sites may provide data via several means: CSV files, Redcap API, etc. An extensible design allows for new methods to be added in the future. Web applications are provided (via 'shiny') for the implemented methods to help in designing and deploying the computations.

AuthorBalasubramanian Narasimhan [aut, cre], Marina Bendersky [aut], Sam Gross [aut], Terry M. Therneau [ctb], Thomas Lumley [ctb]
Date of publication2017-02-23 08:31:06
MaintainerBalasubramanian Narasimhan <naras@stat.Stanford.EDU>
LicenseLGPL (>= 2)
Version0.25.6
http://arxiv.org/abs/1412.6890

View on CRAN

Man pages

availableComputations: Return the currently available (implemented) computations

availableDataSources: Return currently implemented data sources

coxMaster: Create a master object to control worker objects generated by...

CoxWorker: Create a worker object for use as a worker with master...

createInstanceObject: Given the definition identifier of an object, instantiate and...

dccoxph: Functions copied and modified from survival package

defineNewComputation: Define a new computation

destroyInstanceObject: Destroy an instance object given its identifier

distcomp: Distributed Computing with R

distcomp-internal: Make an appropriate opencpu URL for a specified function and...

distcompSetup: Setup a workspace and configuration for a distributed...

executeMethod: Given the id of a serialized object, invoke a method on the...

generateId: Generate an identifier for an object

getComputationInfo: Get the value of a variable from the global store

getConfig: Return the workspace and configuration setup values

makeDefinition: Make a computation definition given the computation type

makeMaster: Make a master object given a definition

makeWorker: Make a worker object given a definition and data

resetComputationInfo: Clear the contents of the global store

runDistcompApp: Run a specified distcomp web application

saveNewComputation: Save a computation instance, given the computation...

setComputationInfo: Set a name to a value in a global variable

setupMaster: Setup a computation master

setupWorker: Setup a worker site

svdMaster: Create a master object to control worker objects generated by...

SVDWorker: Create a worker object for use as a worker with master...

uploadNewComputation: Upload a new computation and data to an opencpu server

writeCode: Write the code necessary to run a master process

Functions

availableComputations Man page
availableDataSources Man page
CoxMaster Man page
CoxWorker Man page
createInstanceObject Man page
dccoxph Man page
dccoxph.fit Man page
defineNewComputation Man page
.defnOK Man page
.deSerialize Man page
destroyInstanceObject Man page
distcomp Man page
distcomp-package Man page
distcompSetup Man page
executeMethod Man page
generateId Man page
getComputationInfo Man page
getConfig Man page
makeDefinition Man page
makeMaster Man page
.makeOpencpuURL Man page
makeWorker Man page
resetComputationInfo Man page
runDistcompApp Man page
saveNewComputation Man page
setComputationInfo Man page
setupMaster Man page
setupWorker Man page
SVDMaster Man page
SVDWorker Man page
uploadNewComputation Man page
writeCode Man page

Files

distcomp
distcomp/inst
distcomp/inst/ex
distcomp/inst/ex/SVDTestDefn.rds
distcomp/inst/ex/README.Rmd
distcomp/inst/ex/SVDMaster.Rout
distcomp/inst/ex/uis-example.Rout
distcomp/inst/ex/STCoxMaster.Rout
distcomp/inst/ex/uis-example.R
distcomp/inst/ex/STCoxMaster.R
distcomp/inst/ex/uis-site2.csv
distcomp/inst/ex/STCoxTest.rds
distcomp/inst/ex/README.md
distcomp/inst/ex/uis.RDS
distcomp/inst/ex/SVDMaster.R
distcomp/inst/ex/svd-example.R
distcomp/inst/ex/svd-site1.csv
distcomp/inst/ex/Rprofile
distcomp/inst/ex/svd-site2.csv
distcomp/inst/ex/svd-site3.csv
distcomp/inst/ex/README.html
distcomp/inst/ex/svd-example.Rout
distcomp/inst/ex/SVDSetup.Rout
distcomp/inst/ex/uis-site1.csv
distcomp/inst/ex/STCoxSetup.Rout
distcomp/inst/doc_src
distcomp/inst/doc_src/examples.md
distcomp/inst/doc_src/examples.Rmd
distcomp/inst/doc_src/prostate.RDS
distcomp/inst/COPYRIGHTS
distcomp/inst/webApps
distcomp/inst/webApps/setupWorkerApp
distcomp/inst/webApps/setupWorkerApp/ui.R
distcomp/inst/webApps/setupWorkerApp/server.R
distcomp/inst/webApps/setupWorkerApp/setupSVDWorker
distcomp/inst/webApps/setupWorkerApp/setupSVDWorker/ui.R
distcomp/inst/webApps/setupWorkerApp/setupSVDWorker/server.R
distcomp/inst/webApps/setupWorkerApp/setupCoxWorker
distcomp/inst/webApps/setupWorkerApp/setupCoxWorker/ui.R
distcomp/inst/webApps/setupWorkerApp/setupCoxWorker/server.R
distcomp/inst/webApps/setupMasterApp
distcomp/inst/webApps/setupMasterApp/ui.R
distcomp/inst/webApps/setupMasterApp/server.R
distcomp/inst/webApps/definitionApp
distcomp/inst/webApps/definitionApp/ui.R
distcomp/inst/webApps/definitionApp/server.R
distcomp/inst/webApps/definitionApp/defineNewCoxModel
distcomp/inst/webApps/definitionApp/defineNewCoxModel/ui.R
distcomp/inst/webApps/definitionApp/defineNewCoxModel/server.R
distcomp/inst/webApps/definitionApp/defineNewSVDModel
distcomp/inst/webApps/definitionApp/defineNewSVDModel/ui.R
distcomp/inst/webApps/definitionApp/defineNewSVDModel/server.R
distcomp/inst/doc
distcomp/inst/doc/examples.html
distcomp/inst/doc/examples.pdf
distcomp/src
distcomp/src/coxcount1.c
distcomp/src/chinv2.c
distcomp/src/survS.h
distcomp/src/chsolve2.c
distcomp/src/survproto.h
distcomp/src/coxmart.c
distcomp/src/coxfit6.c
distcomp/src/cholesky2.c
distcomp/src/init.c
distcomp/src/dmatrix.c
distcomp/NAMESPACE
distcomp/R
distcomp/R/coxstuff.R distcomp/R/distcomp.R distcomp/R/svdstuff.R distcomp/R/survivalstuff.R distcomp/R/firstlib.R
distcomp/README.md
distcomp/MD5
distcomp/DESCRIPTION
distcomp/man
distcomp/man/resetComputationInfo.Rd distcomp/man/writeCode.Rd distcomp/man/distcomp.Rd distcomp/man/getComputationInfo.Rd distcomp/man/makeDefinition.Rd distcomp/man/coxMaster.Rd distcomp/man/distcompSetup.Rd distcomp/man/createInstanceObject.Rd distcomp/man/setupMaster.Rd distcomp/man/CoxWorker.Rd distcomp/man/distcomp-internal.Rd distcomp/man/setupWorker.Rd distcomp/man/executeMethod.Rd distcomp/man/makeWorker.Rd distcomp/man/defineNewComputation.Rd distcomp/man/dccoxph.Rd distcomp/man/generateId.Rd distcomp/man/setComputationInfo.Rd distcomp/man/makeMaster.Rd distcomp/man/svdMaster.Rd distcomp/man/uploadNewComputation.Rd distcomp/man/SVDWorker.Rd distcomp/man/runDistcompApp.Rd distcomp/man/getConfig.Rd distcomp/man/availableComputations.Rd distcomp/man/availableDataSources.Rd distcomp/man/destroyInstanceObject.Rd distcomp/man/saveNewComputation.Rd

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.