scidb package - RDocumentation

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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")  # development branch

# or

devtools::install_github("Paradigm4/SciDBR", ref="laboratory")  # experimental branch

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.

GitHub branch policy: the "devel" branch is for new ideas that have a good chance of making it into the CRAN package, but all tests might not yet pass. The "master" branch should pass all R CMD check tests against the current R-devel version of R on all platforms, tested against the current SciDB release.

Getting Started Documentation

https://Paradigm4.github.io/SciDBR

Changes in package version 2.0.0

This is a major release that breaks API compatibility with previous package releases. Array objects have been removed. All SciDB arrays are now presented as virtual data frames in R. This change was informed by the most common uses we've seen.

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Version

Install

install.packages('scidb')

Monthly Downloads

87

Version

3.0.0

License

AGPL-3

Maintainer

Kriti Sen Sharma

Last Published

August 12th, 2020

Functions in scidb (3.0.0)

Internal function for processing SciDB dimension schema

Returns TRUE if version string x is greater than or equal to than version y

cov,scidb-method

Covariance matrix This function is more limited than R's default cov function. It can only compute a covariance matrix from a data matrix without any missing value handling by the procedure (in R notation) S0 <- sweep(x, 2, colMeans(x)), crossprod(S0)/(nrow(S0) - 1) # (covariance matrix result)

Names of array dimensions

Download SciDB data to R

Run a SciDB query, optionally returning the result.

help,operator-method

AFL operator help

print,afl-method

Print a summary of a afl SciDB database connection object

print,scidb-method

Print a summary of a scidb object

AFL array aliasing

Simple utility to interactively enter a password without showing it on the screen

Substitute scalar-valued R expressions into an AFL expression R expressions are marked with R(expression)

Print a summary of a afl SciDB database connection object

scidb_unpack_to_dataframe

Unpack and return a SciDB query expression as a data frame

List contents of a SciDB database

Connect to a SciDB database

%as%,scidb-method

AFL arrary aliasing

Update available AFL operators

Evaluate an expression to scidb or scidb objects

Internal function to upload an R data frame to SciDB

An important internal convenience function that returns a scidb object. If eval=TRUE, a new SciDB array is created the returned scidb object refers to that. Otherwise, the returned scidb object represents a SciDB array promise.

Fast write.table/textConnection substitute

SciDB dimension and attribute names

SciDB/R Interface

SciDB array schema

Base SciDB operators

Register an AFL prefix expression

Create an R reference to a SciDB array or expression.

show,afl-method

Print a summary of a afl object

show,scidb-method

Print a summary of a scidb object

Internal function for processing SciDB attribute schema

Upload R data to SciDB

Display SciDB AFL operator documentation

Convenience function for digest authentication.