data_sets.rmd

# Included Data Sets

The content of this book includes several data sets that come with the `gstudio` and `popgraph` libraries.  Here is a brief overview of those data sets with references to the manuscripts from which they were analyzed.






## The Sonoran desert bark beetle, *Araptus attenuata*

```{r echo=FALSE}
knitr::include_graphics("media/araptus.png")
```

*Arapatus attenuatus* is a bark beetle endemic to the Sonoran desert.  It is known only from the senescing stems of the desert plant, *Euphorbia lomelii* (syn *Pedilanthus macrocarpus*).  Samples for this data set were collected from 39 populations throughout the species range.

```{r message=FALSE, echo=FALSE, warning=FALSE, fig.cap="Sampling locales for the `arapat` data set."}
library(ggplot2)
library(ggmap)
library(gstudio)
library(ggrepel)
data(arapat)
coords <- strata_coordinates(arapat)
map <- population_map(coords)
ggmap(map) + geom_point(aes(x=Longitude,y=Latitude), data=coords) + xlab("Longitude") + ylab("Latitude") + geom_text_repel(aes(x=Longitude, y=Latitude, label=Stratum), data=coords) 
```



### Nuclear Markers

The markers in the `arapat` data set consist of eight polymorphic and codominant nuclear markers. 

```{r message=FALSE}
library(gstudio)
data(arapat)
column_class( arapat, "locus") 
```

These markers span a range of allelic diversity and richness.

```{r echo=FALSE}
df <- merge( genetic_diversity(arapat,mode="A"), genetic_diversity(arapat,mode="He"))
df <- merge( df, genetic_diversity(arapat, mode="Ae"))
knitr::kable(df,align=c("l","c","c","c"),digits=3)
```



### Methylation Markers

In addition to codominant nuclear markers, an msAFLP analysis was performed on the major clade and paired sequence and $C_pG$ methylation markers were derived.



## The Flowering Dogwood *Cornus florida*

```{r echo=FALSE, fig.cap="Inflorescence for flowering dogwood with conspicuous showy bracts and many small flowers in the center."}
knitr::include_graphics("media/dogwood_flower.png",)
```


Flowering dogwood is an ubiquitous feature of eastern north american forests. 

The data set contains five microsatellite loci.

```{r}
data(cornus)
column_class( cornus, "locus") 
```

of roughly equal genetic diversity.

```{r echo=FALSE}
df <- merge( genetic_diversity(cornus,mode="A"), genetic_diversity(cornus,mode="He"))
df <- merge( df, genetic_diversity(cornus, mode="Ae"))
knitr::kable(df,align=c("l","c","c","c"),digits=3)
```