jrivers96 / SciDBR

R package for SciDB

Thanks for trying out the SciDB package for R. I hope you enjoy using it.

Install the package from CRAN with

install.packages("scidb")

The current development version of the package can be installed directly from sources on GitHub using the devtools package as follows (requires an R development environment and the R devtools package):

devtools::install_github("Paradigm4/SciDBR")

Note! The SciDBR package depends on the RCurl R package, which in turn requires support for the curl library in your operating system. This might mean that you need to install a libcurl development library RPM or deb package on your OS. On RHEL and CentOS, this package is usually called libcurl-devel and on Ubuntu it's called libcurl4-gnutls-dev.

The SciDB R package requires installation of a simple open-source HTTP network service called on the computer that SciDB is installed on. This service only needs to be installed on the SciDB machine, not on client computers that connect to SciDB from R. See http://github.com/paradigm4/shim for source code and installation instructions.

Developers please note that R CMD check-style unit tests are skipped unless a system environment variable named SCIDB_TEST_HOST is set to the host name or I.P. address of SciDB. See the tests directory for test code.

Wiki

Check out (and feel free to contribute to) examples in the wiki pages for this project here:

https://github.com/Paradigm4/SciDBR/wiki/_pages

This project also has a pretty web page on Github here:

https://Paradigm4.github.io/SciDBR

Changes in package version 1.3.0

This is a major release that breaks some API compatibility with the previous package release. It's designed to support SciDB version 15.7 and also tries to maintain compatibility with previous SciDB releases.

Labeled coordinates have been removed

The package has dropped all use of rownames. Use of rownames is of marginal value and the SciDB package implementation was very inefficient. Similar functionality can be achieved with subset (data.frame-like objects), or indexing by vectors or other SciDB arrays.

The colnames and names functions still work when applied to data.frame-like objects.

Some infix operator name changes

Changed the name of the %>% and %<% functions to %gt% and %lt%, respectively to avoid conflict with the populate magrittr package.

order methods have been removed and replaced by order_scidb

...to avoid unfortunate conflicts with the base::order function.

The subset function is more powerful and efficient

It generates better-optimized SciDB queries than previous versions. See ?subset for details and examples.

Array subset indexing is more efficient

We removed use of subarray to reset array coordinate systems after subsetting. Subsets of sparse or dense arrays returned to R are labeled by their original coordinates.

If you need an array subset to start at the coordinate system origin, use the new translate function. For example:

x <- build("double(i+j)", c(5,5))
y <- x[1:2,2:3]
schema(y)          # Note the coordinate indices
# [1] "<val:double> [i=1:2,1000,0,j=2:3,1000,0]"

z <- translate(y)  # Reset origin with translate, see ?translate for details
schema(z)
# [1] "<val:double> [i=0:1,1000,0,j=0:1,1000,0]"

The merge and redimension functions are more efficient

New versions of these functions generate better-optimized SciDB queries than before.