README.Rmd

paleobiologyDB
==============

## Exploring the new R API to the paleobiologyDB.

Preliminary loading of required packages.  

```{r load, warning=FALSE,message=FALSE}
library(devtools)
library(maps)
library(raster)
if (!require(paleobioDB)) {
  install_github("ropensci/paleobioDB")
  library(paleobioDB)
                         }
```

Now we get all PaleobioDB occurrences for Quaternary bovids.  

```{r getdata, cache=TRUE}
bovidae <-  pbdb_occurrences (limit="all",
                               base_name="bovidae", 
                               interval="Quaternary",             
                               show=c("coords", "phylo", "ident"))
head(bovidae)
```

## Map the bovids

```{r map, fig.width=15}
pbdb_map(bovidae)
```

## Map the richness

```{r richness, fig.width=15}
pbdb_map_richness (bovidae, res= 3, rank="species")
```

## Map sampling effort

```{r samplingeffort, fig.width=15}
pbdb_map_occur (bovidae, res= 2)
```


## Plot the number of subtaxa in the data set 

```{r plotsubtaxa, cache=TRUE}
pbdb_subtaxa (bovidae, do.plot=TRUE)  
```

## Origins and Extinctions
```{r origextinct, fig.width = 15}
pbdb_orig_ext (bovidae, rank="species", orig_ext=1, temporal_extent=c(0,10), res=1)
pbdb_orig_ext (bovidae, rank="species", orig_ext=2, temporal_extent=c(0,10), res=1)
```

## Temporal resolution

```{r temporalres}
pbdb_temporal_resolution (bovidae)
```

## Temporal range

```{r temporalrange}
pbdb_temp_range (bovidae, rank="species")
```