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README.Rmd
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README.Rmd
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rvertnet
=======
```{r echo=FALSE}
knitr::opts_chunk$set(
warning = FALSE,
message = FALSE,
collapse = TRUE,
comment = "#>"
)
```
[](https://travis-ci.org/ropensci/rvertnet)
[](https://ci.appveyor.com/project/sckott/rvertnet)
[](https://codecov.io/github/ropensci/rvertnet?branch=master)
[](https://github.com/metacran/cranlogs.app)
[](https://cran.r-project.org/package=rvertnet)
`rvertnet` is a client for interacting with [VertNet.org](http://vertnet.org/).
VertNet.org API docs: [github.com/VertNet/webapp/wiki/The-API-search-function](https://github.com/VertNet/webapp/wiki/The-API-search-function)
## Installation
Stable CRAN version
```{r eval=FALSE}
install.packages("rvertnet")
```
Or development version from GitHub
```{r eval=FALSE}
install.packages("devtools")
devtools::install_github("ropensci/rvertnet")
```
```{r}
library('rvertnet')
```
## Search by term
Search for _Aves_ in the state of _California_, limit to 10 records
```{r}
res <- searchbyterm(class = "Aves", state = "California", lim = 10, verbose = FALSE)
```
Inspect metadata
```{r}
res$meta
```
Inspect data. A `dplyr` data.frame is given back, so you get a nice brief data summary:
```{r}
res$data[,1:5]
```
Search for _Mustela nigripes_ in the states of _Wyoming_ or _South Dakota_, limit to 20 records
```{r}
res <- searchbyterm(specificepithet = "nigripes", state = "(wyoming OR south dakota)", limit = 20, verbose = FALSE)
res$data[,1:5]
```
### dplyr downstream
You can pass the data object directly on to `dplyr` functions. Here, we get a table of record counts by species in descending order.
```{r}
library("dplyr")
out <- searchbyterm(genus = "Ochotona", limit = 800)
out$data %>%
group_by(scientificname) %>%
summarise(count = length(scientificname)) %>%
arrange(desc(count))
```
## Big data
Specifies a termwise search (like `searchbyterm()`), but requests that all available records be made available for download as a tab-delimited text file.
```{r eval=FALSE}
bigsearch(genus = "ochotona", rf = "pikaRecords", email = "big@@search.luv")
#> Processing request...
#>
#> Download of records file 'mydata' requested for 'you@gmail.com'
#>
#> Query/URL: "http://api.vertnet-portal.appspot.com/api/download?q=%7B%22q%22:%22genus:ochotona%22,%22n%22:%22mydata%22,%22e%22:%22you@gmail.com%22%7D"
#>
#> Thank you! Download instructions will be sent by email.
```
## Spatial search
```{r}
res <- spatialsearch(lat = 33.529, lon = -105.694, radius = 2000, limit = 10, verbose = FALSE)
res$data[,1:5]
```
## Contributors
* Scott Chamberlain [@sckott](https://github.com/sckott)
* Chris Ray [@Pika8tona](https://github.com/Pika8tona)
* Vijay Barve [@vijaybarve](https://github.com/vijaybarve)
## Meta
* Please [report any issues or bugs](https://github.com/ropensci/rvertnet/issues).
* License: MIT
* Get citation information for `rvertnet` in R doing `citation(package = 'rvertnet')`
[](http://ropensci.org)