Function_Glossary.Rmd

```{r,message=FALSE,echo=FALSE}
  library("knitcitations")
  library("knitr")
  cite_options(citation_format = "pandoc", max.names = 3, style = "html", hyperlink = "to.doc")
  bib <- read.bibtex("bibtexlib.bib")
  opts_chunk$set(tidy = FALSE)
```
---
title: "A2: Function glossary"
---

<!---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
```
-->


Navigation in R
----

Our primer is heavily based on the *poppr* and *adegenet* packages. To get help
on any of their functions type a question mark before the empty function call as
in:

```{r, eval=FALSE}
?mlg # open the R documentiaon of the function mlg
```

Other information can be obtained with the following commands.

```{r, eval = FALSE}
browseVignettes(package = 'poppr') # see vignettes for poppr
vignette('poppr_manual')           # see manual for poppr
help(package="poppr")              # shows all functions contained in poppr package
```

*Poppr* functions
----

### Import/Export
Function | Description    
----|----
`getfile` | Provides a quick GUI to grab files for import
`read.genalex` | Read *GenAlEx* formatted csv files to a genind object
`genind2genalex` | Converts genind objects to *GenAlEx* formatted csv files

### Manipulation
Function | Description    
----|----
`as.genclone` | Converts genind objects to genclone objects
`setPop` | Set the population using defined strata
`splitStrata` | Split concatenated strata imported as a population
`strata` | Define or extract population strata of a genind object
`addStrata` | Add a vector or data frame to an existing strata
`nameStrata` | Rename a population strata
`missingno` | Handles missing data
`clonecorrect` | Clone censor at a specified population stratum
`informloci` | Detects and removes phylogenetically uninformative loci
`popsub` | Subsets genind objects by population
`shufflepop` | Shuffles genotypes at each locus using four different shuffling algorithms
`recode_polyploids` | Recodes an imported polyploid data set to observed allelic frequencies


### Distances
Function | Description    
----|----
`bruvo.dist` | Bruvo’s distance
`diss.dist` | Absolute genetic distance (see `provesti.dist`)
`nei.dist` | Nei’s 1978 genetic distance
`rogers.dist` | Rogers’ euclidean distance
`reynolds.dist` | Reynolds’ coancestry distance
`edwards.dist` | Edwards’ angular distance
`provesti.dist` | Provesti’s absolute genetic distance

### Bootstrapping
Function | Description    
----|----
`aboot` | Creates a bootstrapped dendrogram for any distance measure
`bruvo.boot` | Produces dendrograms with bootstrap support based on Bruvo’s distance

### Analysis
Function | Description    
----|----
`poppr.amova` | Analysis of Molecular Variance (as implemented in ade4)
`ia` | Calculates the index of association
`mlg` | Calculates the number of multilocus genotypes
`mlg.crosspop` | Finds all multilocus genotypes that cross populations
`mlg.table` | Returns a table of populations by multilocus genotypes
`mlg.vector` | Returns a vector of a numeric multilocus genotype assignment for each individual
`mlg.id` | Finds all individuals associated with each multilocus genotype
`poppr` | Returns a diversity table by population
`poppr.all` | Returns a diversity table by population for all compatible files specified
`private_alleles` | Tabulates the occurences of alleles that only occur in one population
`locus_table` | Create a table of summary statistics per locus

### Visualization
Function | Description    
----|----
`plot_poppr_msn` | Plots minimum spanning networks produced in poppr with scale bar and legend
`greycurve` | Helper to determine the appropriate parameters for adjusting the grey level for msn functions
`bruvo.msn` | Produces minimum spanning networks based off Bruvo’s distance colored by population
`poppr.msn` | Produces a minimum spanning network for any pairwise distance matrix related to the data
`info_table` | Creates a heatmap representing missing data or observed ploidy
`genotype_curve` | Creates a series of boxplots to demonstrate how many markers are needed to represent the diversity of your data