calc_shannon_index

The Shannon diversity index is calculated to quantify the diversity of molecular formulas based on
their relative abundances. This index considers both the richness (number of unique formulas)
and the evenness (distribution of abundances). Higher values indicate greater diversity.
The Shannon index is defined as:
$$H = -\sum (p_i \cdot \ln(p_i))$$
where:<ul>
<li>$p_i$ is the relative abundance of the $i$-th molecular formula.</li>
</ul>Zero-abundance formulas are excluded from the calculation.

Provides tools for assigning molecular formulas from exact masses
obtained by ultrahigh-resolution mass spectrometry. The methodology follows
the workflow described in Leefmann et al. (2019) <doi:10.1002/rcm.8315>.
The package supports the inspection, filtering and visualization of
molecular formula data and includes utilities for calculating common
molecular parameters (e.g., double bond equivalents, DBE). A graphical
user interface is available via the 'shiny'-based 'ume' application.

Boris Koch

Ultrahigh-Resolution Mass Spectrometry Data Evaluation for
Complex Organic Matter

calc_shannon_index function

<dl><dt>mf</dt>
<dd>Character vector. A list of unique molecular formulas.</dd>
<dt>magnitude</dt>
<dd>Numeric vector. A list of respective abundances (intensities) for each molecular formula.
Must be non-negative and have the same length as <code>mf</code>.</dd></dl>

Arguments

The Shannon diversity index is calculated to quantify the diversity of molecular formulas based on
their relative abundances. This index considers both the richness (number of unique formulas)
and the evenness (distribution of abundances). Higher values indicate greater diversity.
The Shannon index is defined as:
$$H = -\sum (p_i \cdot \ln(p_i))$$
where:<ul>
<li>$p_i$ is the relative abundance of the $i$-th molecular formula.</li>
</ul>

Zero-abundance formulas are excluded from the calculation.

Calculate the Shannon Diversity Index — calc_shannon_index

<dl>

<dt>mf</dt>
<dd>Character vector. A list of unique molecular formulas.</dd>


<dt>magnitude</dt>
<dd>Numeric vector. A list of respective abundances (intensities) for each molecular formula.
Must be non-negative and have the same length as <code>mf</code>.</dd>

</dl>

calc_shannon_index: Calculate the Shannon Diversity Index

Description

Usage

Value

Arguments

Examples