sd.HDF5Matrix

Equivalent to <code>sd(as.vector(X))</code> — uses Bessel's correction (N-1).

A framework for 'scalable' statistical computing on large on-disk
matrices stored in 'HDF5' files. It provides efficient block-wise
implementations of core linear-algebra operations (matrix multiplication,
SVD, PCA, and QR decomposition) written in C++ and R, along with building
blocks from which higher-level multivariate methods such as canonical
correlation analysis can be constructed. These building blocks are designed
not only for direct use, but also as foundational components for developing
new statistical methods that must operate on datasets too large to fit in
memory. The package supports data provided either as 'HDF5' files or
standard R objects, and is intended for high-dimensional applications such
as 'omics' and precision-medicine research.

Dolors Pelegri-Siso

BigDataStatMeth

Scalable Statistical Computing with HDF5-Backed Matrices

Juan R. Gonzalez

sd function

<dl><dt>x</dt>
<dd>An <code>HDF5Matrix</code> object.</dd>
<dt>na.rm</dt>
<dd>Ignored (included for generic compatibility).</dd>
<dt>...</dt>
<dd>For <code>Summary</code> methods: additional objects (currently
not supported; raises an error if supplied).</dd>
<dt>paral</dt>
<dd>Logical or NULL. Enable OpenMP parallelisation.</dd>
<dt>wsize</dt>
<dd>Integer or NULL. Block size (NULL = auto).</dd>
<dt>threads</dt>
<dd>Integer or NULL. Number of threads (NULL = auto).</dd>
<dt>save_to</dt>
<dd>Optional persistence target (same format as
<code>colSums.HDF5Matrix</code>).</dd>
<dt>overwrite</dt>
<dd>Logical. Overwrite existing dataset when saving.</dd></dl>

Arguments

Standard deviation of all elements of an HDF5Matrix — sd

<dl>

<dt>x</dt>
<dd>An <code>HDF5Matrix</code> object.</dd>


<dt>na.rm</dt>
<dd>Ignored (included for generic compatibility).</dd>


<dt>...</dt>
<dd>For <code>Summary</code> methods: additional objects (currently
not supported; raises an error if supplied).</dd>


<dt>paral</dt>
<dd>Logical or NULL. Enable OpenMP parallelisation.</dd>


<dt>wsize</dt>
<dd>Integer or NULL. Block size (NULL = auto).</dd>


<dt>threads</dt>
<dd>Integer or NULL. Number of threads (NULL = auto).</dd>


<dt>save_to</dt>
<dd>Optional persistence target (same format as
<code>colSums.HDF5Matrix</code>).</dd>


<dt>overwrite</dt>
<dd>Logical. Overwrite existing dataset when saving.</dd>

</dl>

sd: Standard deviation of all elements of an HDF5Matrix

Description

Usage

Value

Arguments