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 and includes facilities for local prototyping and testing. Web applications are provided (via 'shiny') for the implemented methods to help in designing and deploying the computations.
Install this package the usual way in R or via:
Then, you will find a document that describes several examples installed under the R library tree. For example:
list.files(system.file("doc", package = "distcomp"))list.files(system.file("doc_src", package = "distcomp"))
The examples described in the Journal of Statistical Software paper are available as follows:
list.files(system.file("ex", package = "distcomp"))
Use of this package requires some configuration. In particular, to run
the examples on a local machine where a single
opencpu server will
be emulating several sites, a suitable R profile needs to be set
up. That profile will be something along the lines of
library(distcomp)distcompSetup(workspace = "full_path_to_workspace_directory",ssl_verifyhost = 0L, ssl_verifypeer = 0L)
where the workspace is a directory that the
opencpu server can
serialize objects to. On Unix or Mac, the above can be inserted into
.Rprofile file, but on Windows, we find that the
file needs to contain the above lines.
The effect of this is that every R process (including the
process) has access to the
distcomp library and the workspace.
In some earlier versions of Yosemite (MacOS 10.10.2 for example) there
were issues with the
opencpu package. We suspected it had more to do
with Yosemite than
httpuv---see the number of DNS
resolver issues people are having with the move to
discoveryd via a
Furthermore, even if
opencpu came up, which it did sometimes after
many tries, you were better off using the ip address
the url in place of
localhost due to those DNS problems.
We no longer see this problem in recent versions of Yosemite (10.10.5+).