Tasmania

A classic dataset used in the R package mvabund. This is a study on the effects of disturbance from a soldier crab on 56 species of meiobenthos, which are small invertebrates. Eight of the sixteen observations in the data set correspond to crab disturbances. Besides the crab disturbance, there are also four different locations in the study design, where observations from each location are comprised of two disturbed and two undisturbed ones.

In fields such as ecology, microbiology, and genomics, non-Euclidean distances are widely applied to describe pairwise dissimilarity between samples. Given these pairwise distances, principal coordinates analysis (PCoA) is commonly used to construct a visualization of the data. However, confounding covariates can make patterns related to the scientific question of interest difficult to observe. We provide 'aPCoA' as an easy-to-use tool to improve data visualization in this context, enabling enhanced presentation of the effects of interest. Details are described in Yushu Shi, Liangliang Zhang, Kim-Anh Do, Christine Peterson and Robert Jenq (2020) Bioinformatics, Volume 36, Issue 13, 4099-4101.

Yushu Shi

aPCoA

Covariate Adjusted PCoA Plot

Tasmania function

<dl class="dl-horizontal">
 <dt>abund</dt><dd>The counts of 56 Meibenthos species.</dd>
 <dt>treatment</dt><dd>This observation has been disturbed by a crab or not.</dd>
 <dt>block</dt><dd>The location indicator of the observation.</dd>
</dl>

Format

Tasmania Dataset — Tasmania

<dl class='dl-horizontal'>
 <dt>abund</dt><dd>The counts of 56 Meibenthos species.</dd>
 <dt>treatment</dt><dd>This observation has been disturbed by a crab or not.</dd>
 <dt>block</dt><dd>The location indicator of the observation.</dd>
</dl>

Tasmania: Tasmania Dataset

Description

Usage

Arguments

Format

References

Examples