cohensd

Function to compute cohensd on the results provided by the aldex function

Provides scalable generalized linear and mixed effects models tailored for sequence count data analysis (e.g., analysis of 16S or RNA-seq data). Uses Dirichlet-multinomial sampling to quantify uncertainty in relative abundance or relative expression conditioned on observed count data.
Implements scale models as a generalization of normalizations which account for uncertainty in scale (e.g., total abundances) as described in Nixon et al. (2025) <doi:10.1186/s13059-025-03609-3> and McGovern et al. (2025) <doi:10.1101/2025.08.05.668734>.

Justin Silverman

ALDEx3

Linear Models for Sequence Count Data

Greg Gloor

Kyle McGovern

cohensd function

<dl><dt>m</dt>
<dd>the output of a call to <code>aldex</code></dd>
<dt>var</dt>
<dd>if aldex was called with X being a pre-computed model matrix,
this var should be an integer corresponding to a binary covariate
indicateing the desired effect size to calculate (an effect size between
two groups indicated by the binary covariate). For example, if the third
covariate in the model is an indicator denoting health (0) and disease (1)
then set <code>var=3</code>. In contrast, if X was a formula (in which case the
<code>data</code> argument should have been specified) then <code>var</code> can be set to
the unquoted name of the binary condition variable (e.g.,
<code>var=condition</code>).</dd></dl>

Arguments

Author

Cohen's D — cohensd

<dl>

<dt>m</dt>
<dd>the output of a call to <code>aldex</code></dd>


<dt>var</dt>
<dd>if aldex was called with X being a pre-computed model matrix,
this var should be an integer corresponding to a binary covariate
indicateing the desired effect size to calculate (an effect size between
two groups indicated by the binary covariate). For example, if the third
covariate in the model is an indicator denoting health (0) and disease (1)
then set <code>var=3</code>. In contrast, if X was a formula (in which case the
<code>data</code> argument should have been specified) then <code>var</code> can be set to
the unquoted name of the binary condition variable (e.g.,
<code>var=condition</code>).</dd>

</dl>

cohensd: Cohen's D

Description

Usage

Value

Arguments

Author

Details