betta_pic

A simple plotting interface for comparing total diversity across samples or
a covariate gradient.

diversity

Understanding the drivers of microbial diversity is an important frontier of microbial ecology, and investigating the diversity of samples from microbial ecosystems is a common step in any microbiome analysis. 'breakaway' is the premier package for statistical analysis of microbial diversity. 'breakaway' implements the latest and greatest estimates of species richness, described in Willis and Bunge (2015) <doi:10.1111/biom.12332>, Willis et al. (2017) <doi:10.1111/rssc.12206>, and Willis (2016) <arXiv:1604.02598>, as well as the most commonly used estimates, including the objective Bayes approach described in Barger and Bunge (2010) <doi:10.1214/10-BA527>.

Amy D Willis

breakaway

Species Richness Estimation and Modeling

Bryan D Martin

Pauline Trinh

Sarah Teichman

David Clausen

Kathryn Barger

John Bunge

betta_pic function

<dl><dt>y</dt>
<dd>A vector of estimates of total diversity. Other parameter estimates
are accessible; this method may be used for plotting any parameter
estimates..</dd>
<dt>se</dt>
<dd>The standard errors in <samp>y</samp>, the diversity (or other
parameter's) estimates.</dd>
<dt>x</dt>
<dd>A vector of covariates to form the x-coordinates of the intervals.
If no argument is given, defaults to the order.</dd>
<dt>ylimu</dt>
<dd>The upper endpoint of the y-axis.</dd>
<dt>myy</dt>
<dd>Deprecated, for backwards compatibility</dd>
<dt>mymain</dt>
<dd>Deprecated, for backwards compatibility</dd>
<dt>mycol</dt>
<dd>Deprecated, for backwards compatibility</dd>
<dt>labs</dt>
<dd>Deprecated, for backwards compatibility</dd>
<dt>mypch</dt>
<dd>Deprecated, for backwards compatibility</dd>
<dt>myxlim</dt>
<dd>Deprecated, for backwards compatibility</dd></dl>

Arguments

Author

function for plotting total diversity — betta_pic

<dl>

<dt>y</dt>
<dd>A vector of estimates of total diversity. Other parameter estimates
are accessible; this method may be used for plotting any parameter
estimates..</dd>


<dt>se</dt>
<dd>The standard errors in <samp>y</samp>, the diversity (or other
parameter's) estimates.</dd>


<dt>x</dt>
<dd>A vector of covariates to form the x-coordinates of the intervals.
If no argument is given, defaults to the order.</dd>


<dt>ylimu</dt>
<dd>The upper endpoint of the y-axis.</dd>


<dt>myy</dt>
<dd>Deprecated, for backwards compatibility</dd>


<dt>mymain</dt>
<dd>Deprecated, for backwards compatibility</dd>


<dt>mycol</dt>
<dd>Deprecated, for backwards compatibility</dd>


<dt>labs</dt>
<dd>Deprecated, for backwards compatibility</dd>


<dt>mypch</dt>
<dd>Deprecated, for backwards compatibility</dd>


<dt>myxlim</dt>
<dd>Deprecated, for backwards compatibility</dd>

</dl>

function for plotting total diversity

betta_pic: function for plotting total diversity

Description

Usage

Value

Arguments

Author

References

See Also

Examples