web_data.Rmd

# Acquiring data from the web 

For this tutorial we will combine data from three separate data repositories. 
* Open Fisheries - contains landings data.
* Taxize - 
* Global Biodiversity Information Facility (gbif)


First install some packages

```{r, eval = FALSE}
install.packages("rgbif")
install.packages("taxize_")
install.packages("rfisheries")
```

```{r, loading, warning = FALSE}
library(rgbif)
library(taxize)

```

```{r, fisheries_data, eval = FALSE}
library(rfisheries)
# first we acquire a list of species in the database
species <- species_codes()
```

```{r, fisheries_data2, eval = TRUE, echo = FALSE}
library(rfisheries)
# first we acquire a list of species in the database
species <- species_codes()
```


```{r, examine_data}
head(species)
# Rather than look up data for every single one in this dataset, we'll pick a random sample of 10
species <- species[sample(nrow(species), 10), ]
```

# Taxize

#
```{r, taxize}
# look up code
taxon_identifiers <- get_tsn(species[,1])
# then taxonomic info
classification_data <- classification(taxon_identifiers)
```
# gbif
```{r, gbif}
# then locations
locations <- llply(species[, 1], occurrencelist_many, .progress="text")
```