README_old.md

In PaulPyl/h5array: Implementation of HDF5-backed matrix and array classes

h5array

HDF5 back-end for array and matrix datastructures in R

This package desfines two datastructures with a HDF5 backend for use within R.

The h5matrix class defines objects that behave like 2D matrices and can be used in normal R code. The data itself is stored in an HDF5 file on disk and retrieved when requested.

The h5array class defines an array like object with the same properties, the main difference is that h5arrays can have arbitrary dimensions, while h5matrix objects neccessarily have exactly two dimensions. The h5array is therefore more flexible but requires a bit more boilerplate code in the accessors (e.g. the "["-operator) to work. If you know that your data is twodimensional, use the h5matrix class.

Installation

Installation from github is easiest using devtools.

install.packages("devtools") # If you do not have it yet
require(devtools)
install_github("PaulPyl/h5array")

Example of usage

require(h5array)

y <- h5arrayCreate(tempfile(), "StringData", c(10,3,2), "character", size = 10)
dimnames(y) <- list(letters[1:10], letters[1:3], c("First", "Second"))

y[,,] <- "SomeText"

y

# HDF5-backed Array
# Type: character
# Dimensions: 10, 3, 2
# File: /var/folders/sh/nzrnpqxj3ndg9fh2qcvzzpfn62qz2p/T//Rtmpq9Px1t/file48da90f2224
# Head of Data:
# , , First
# 
#   a          b          c         
# a "SomeText" "SomeText" "SomeText"
# b "SomeText" "SomeText" "SomeText"
# c "SomeText" "SomeText" "SomeText"
# d "SomeText" "SomeText" "SomeText"
# e "SomeText" "SomeText" "SomeText"
# f "SomeText" "SomeText" "SomeText"
# 
# z <- h5matrixCreate(tempfile(), "Matrix", c(1000, 120), "double")
# dimnames(z) <- list(paste0("Row", 1:1000), paste0("Column", 1:120))

z[,] <- matrix(rnorm(1000*120), ncol = 120)

z

# HDF5-backed Matrix
# Type: double
# Dimensions: 1000, 120
# File: /var/folders/sh/nzrnpqxj3ndg9fh2qcvzzpfn62qz2p/T//Rtmpq9Px1t/file48da408a6e21
# Data:
#          Column1     Column2     Column3    Column4    Column5    Column6
# Row1 -0.56270685 -1.01663856  1.82527961  1.1461153  0.7306316  0.3961885
# Row2 -0.03695803  0.91514655 -0.03043276  0.5974649  0.6352517  0.1771278
# Row3  0.31497679 -1.44066819 -2.03284089 -1.4673467 -0.7354956 -0.4922019
# Row4  1.22607774 -0.06873158  0.16690851  1.5619424 -0.3662646 -1.5805695
# Row5 -1.90615942  0.78360002  0.14870436  1.5693273  0.5804664  0.1465883
# Row6 -2.24570981  0.64120473  1.40108435 -1.6828315  0.5747368 -0.3300932

PaulPyl/h5array documentation built on May 8, 2019, 12:57 a.m.