distcomp: Computations over Distributed Data without Aggregation

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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.

Author
Balasubramanian Narasimhan [aut, cre], Marina Bendersky [aut], Sam Gross [aut], Terry M. Therneau [ctb], Thomas Lumley [ctb]
Date of publication
2015-10-28 00:09:45
Maintainer
Balasubramanian Narasimhan <naras@stat.Stanford.EDU>
License
LGPL (>= 2)
Version
0.25.4
URLs

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

Files in this package

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/distcompSetup.Rd
distcomp/man/createInstanceObject.Rd
distcomp/man/CoxMaster.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/uploadNewComputation.Rd
distcomp/man/SVDWorker.Rd
distcomp/man/SVDMaster.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