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<a href="background_functions.html">Background_functions</a>
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<a href="https://github.com/grunwaldlab/Population_Genetics_in_R/">Source Code</a>
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<h1 class="title toc-ignore">A2: Function glossary</h1>
</div>
<!---To quit R you can either use the Rstudio>Quit Rstudio pulldown menu command or execute ⌘+Q (OS X) or CTRL+Q (PC).
Navigation in R
----
---->
<!--```{r, eval=FALSE}
getwd() # this command will print the current working directory
ls() # list objects in the current workspace
help(options) # learn about available options
history() # viewing your command history
data(*dsname*) # access builtin database *dsname*; must have pacakge loaded containing it
q() # quit your R session
# default for saving history is ".Rhistory"
savehistory(file="myfile") # save your command history for whole session
loadhistory(file= "myfile") # recall command history save
# Package specific information
installed.packages()[,c("Package","Version")] #list packages & versions installed
browseVignettes() # see vignettes from all packages
#Help on functions
help(functionname) # Display documentation for a function
args(functionname) # What are the arguments for a given function
example(functionname) # see examples of function calls
```
-->
<div id="navigation-in-r" class="section level2">
<h2>Navigation in R</h2>
<p>Our primer is heavily based on the <em>poppr</em> and <em>adegenet</em> packages. To get help on any of their functions type a question mark before the empty function call as in:</p>
<div class="sourceCode" id="cb1"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb1-1"><a href="#cb1-1"></a>?mlg <span class="co"># open the R documentiaon of the function mlg</span></span></code></pre></div>
<p>Other information can be obtained with the following commands.</p>
<div class="sourceCode" id="cb2"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb2-1"><a href="#cb2-1"></a><span class="kw">browseVignettes</span>(<span class="dt">package =</span> <span class="st">'poppr'</span>) <span class="co"># see vignettes for poppr</span></span>
<span id="cb2-2"><a href="#cb2-2"></a><span class="kw">vignette</span>(<span class="st">'poppr_manual'</span>) <span class="co"># see manual for poppr</span></span>
<span id="cb2-3"><a href="#cb2-3"></a><span class="kw">help</span>(<span class="dt">package=</span><span class="st">"poppr"</span>) <span class="co"># shows all functions contained in poppr package</span></span></code></pre></div>
</div>
<div id="poppr-functions" class="section level2">
<h2><em>Poppr</em> functions</h2>
<div id="importexport" class="section level3">
<h3>Import/Export</h3>
<table>
<thead>
<tr class="header">
<th>Function</th>
<th>Description</th>
</tr>
</thead>
<tbody>
<tr class="odd">
<td><code>getfile</code></td>
<td>Provides a quick GUI to grab files for import</td>
</tr>
<tr class="even">
<td><code>read.genalex</code></td>
<td>Read <em>GenAlEx</em> formatted csv files to a genind object</td>
</tr>
<tr class="odd">
<td><code>genind2genalex</code></td>
<td>Converts genind objects to <em>GenAlEx</em> formatted csv files</td>
</tr>
</tbody>
</table>
</div>
<div id="manipulation" class="section level3">
<h3>Manipulation</h3>
<table>
<colgroup>
<col width="50%" />
<col width="50%" />
</colgroup>
<thead>
<tr class="header">
<th>Function</th>
<th>Description</th>
</tr>
</thead>
<tbody>
<tr class="odd">
<td><code>as.genclone</code></td>
<td>Converts genind objects to genclone objects</td>
</tr>
<tr class="even">
<td><code>setPop</code></td>
<td>Set the population using defined strata</td>
</tr>
<tr class="odd">
<td><code>splitStrata</code></td>
<td>Split concatenated strata imported as a population</td>
</tr>
<tr class="even">
<td><code>strata</code></td>
<td>Define or extract population strata of a genind object</td>
</tr>
<tr class="odd">
<td><code>addStrata</code></td>
<td>Add a vector or data frame to an existing strata</td>
</tr>
<tr class="even">
<td><code>nameStrata</code></td>
<td>Rename a population strata</td>
</tr>
<tr class="odd">
<td><code>missingno</code></td>
<td>Handles missing data</td>
</tr>
<tr class="even">
<td><code>clonecorrect</code></td>
<td>Clone censor at a specified population stratum</td>
</tr>
<tr class="odd">
<td><code>informloci</code></td>
<td>Detects and removes phylogenetically uninformative loci</td>
</tr>
<tr class="even">
<td><code>popsub</code></td>
<td>Subsets genind objects by population</td>
</tr>
<tr class="odd">
<td><code>shufflepop</code></td>
<td>Shuffles genotypes at each locus using four different shuffling algorithms</td>
</tr>
<tr class="even">
<td><code>recode_polyploids</code></td>
<td>Recodes an imported polyploid data set to observed allelic frequencies</td>
</tr>
</tbody>
</table>
</div>
<div id="distances" class="section level3">
<h3>Distances</h3>
<table>
<thead>
<tr class="header">
<th>Function</th>
<th>Description</th>
</tr>
</thead>
<tbody>
<tr class="odd">
<td><code>bruvo.dist</code></td>
<td>Bruvo’s distance</td>
</tr>
<tr class="even">
<td><code>diss.dist</code></td>
<td>Absolute genetic distance (see <code>provesti.dist</code>)</td>
</tr>
<tr class="odd">
<td><code>nei.dist</code></td>
<td>Nei’s 1978 genetic distance</td>
</tr>
<tr class="even">
<td><code>rogers.dist</code></td>
<td>Rogers’ euclidean distance</td>
</tr>
<tr class="odd">
<td><code>reynolds.dist</code></td>
<td>Reynolds’ coancestry distance</td>
</tr>
<tr class="even">
<td><code>edwards.dist</code></td>
<td>Edwards’ angular distance</td>
</tr>
<tr class="odd">
<td><code>provesti.dist</code></td>
<td>Provesti’s absolute genetic distance</td>
</tr>
</tbody>
</table>
</div>
<div id="bootstrapping" class="section level3">
<h3>Bootstrapping</h3>
<table>
<colgroup>
<col width="50%" />
<col width="50%" />
</colgroup>
<thead>
<tr class="header">
<th>Function</th>
<th>Description</th>
</tr>
</thead>
<tbody>
<tr class="odd">
<td><code>aboot</code></td>
<td>Creates a bootstrapped dendrogram for any distance measure</td>
</tr>
<tr class="even">
<td><code>bruvo.boot</code></td>
<td>Produces dendrograms with bootstrap support based on Bruvo’s distance</td>
</tr>
</tbody>
</table>
</div>
<div id="analysis" class="section level3">
<h3>Analysis</h3>
<table>
<colgroup>
<col width="50%" />
<col width="50%" />
</colgroup>
<thead>
<tr class="header">
<th>Function</th>
<th>Description</th>
</tr>
</thead>
<tbody>
<tr class="odd">
<td><code>poppr.amova</code></td>
<td>Analysis of Molecular Variance (as implemented in ade4)</td>
</tr>
<tr class="even">
<td><code>ia</code></td>
<td>Calculates the index of association</td>
</tr>
<tr class="odd">
<td><code>mlg</code></td>
<td>Calculates the number of multilocus genotypes</td>
</tr>
<tr class="even">
<td><code>mlg.crosspop</code></td>
<td>Finds all multilocus genotypes that cross populations</td>
</tr>
<tr class="odd">
<td><code>mlg.table</code></td>
<td>Returns a table of populations by multilocus genotypes</td>
</tr>
<tr class="even">
<td><code>mlg.vector</code></td>
<td>Returns a vector of a numeric multilocus genotype assignment for each individual</td>
</tr>
<tr class="odd">
<td><code>mlg.id</code></td>
<td>Finds all individuals associated with each multilocus genotype</td>
</tr>
<tr class="even">
<td><code>poppr</code></td>
<td>Returns a diversity table by population</td>
</tr>
<tr class="odd">
<td><code>poppr.all</code></td>
<td>Returns a diversity table by population for all compatible files specified</td>
</tr>
<tr class="even">
<td><code>private_alleles</code></td>
<td>Tabulates the occurences of alleles that only occur in one population</td>
</tr>
<tr class="odd">
<td><code>locus_table</code></td>
<td>Create a table of summary statistics per locus</td>
</tr>
</tbody>
</table>
</div>
<div id="visualization" class="section level3">
<h3>Visualization</h3>
<table>
<colgroup>
<col width="50%" />
<col width="50%" />
</colgroup>
<thead>
<tr class="header">
<th>Function</th>
<th>Description</th>
</tr>
</thead>
<tbody>
<tr class="odd">
<td><code>plot_poppr_msn</code></td>
<td>Plots minimum spanning networks produced in poppr with scale bar and legend</td>
</tr>
<tr class="even">
<td><code>greycurve</code></td>
<td>Helper to determine the appropriate parameters for adjusting the grey level for msn functions</td>
</tr>
<tr class="odd">
<td><code>bruvo.msn</code></td>
<td>Produces minimum spanning networks based off Bruvo’s distance colored by population</td>
</tr>
<tr class="even">
<td><code>poppr.msn</code></td>
<td>Produces a minimum spanning network for any pairwise distance matrix related to the data</td>
</tr>
<tr class="odd">
<td><code>info_table</code></td>
<td>Creates a heatmap representing missing data or observed ploidy</td>
</tr>
<tr class="even">
<td><code>genotype_curve</code></td>
<td>Creates a series of boxplots to demonstrate how many markers are needed to represent the diversity of your data</td>
</tr>
</tbody>
</table>
</div>
</div>
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