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combine redundant info from readme into vignette
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@slager
slager committed Feb 12, 2024
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2 changes: 1 addition & 1 deletion Makefile
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Expand Up @@ -26,7 +26,7 @@ check: build
@rm -rf ${PACKAGE}.Rcheck

readme:
${RSCRIPT} -e "knitr::knit('README.Rmd')"
${RSCRIPT} -e "devtools::build_readme()"

check_windows:
${RSCRIPT} -e "devtools::check_win_devel(); devtools::check_win_release()"
138 changes: 15 additions & 123 deletions README.Rmd
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Expand Up @@ -16,11 +16,9 @@ knitr::opts_chunk$set(
```

<!-- badges: start -->
[![Project Status: Active – The project has reached a stable, usable state and is being actively developed.](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active)
[![R-CMD-check](https://github.com/ropensci/rvertnet/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/ropensci/rvertnet/actions/workflows/R-CMD-check.yaml)
[![Codecov test coverage](https://codecov.io/gh/ropensci/rvertnet/branch/master/graph/badge.svg)](https://app.codecov.io/gh/ropensci/rvertnet?branch=master)
[![rstudio mirror downloads](https://cranlogs.r-pkg.org/badges/rvertnet)](https://github.com/r-hub/cranlogs.app)
[![cran version](https://www.r-pkg.org/badges/version/rvertnet)](https://cran.r-project.org/package=rvertnet)

[![Project Status: Active – The project has reached a stable, usable state and is being actively developed.](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active) [![R-CMD-check](https://github.com/ropensci/rvertnet/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/ropensci/rvertnet/actions/workflows/R-CMD-check.yaml) [![Codecov test coverage](https://codecov.io/gh/ropensci/rvertnet/branch/master/graph/badge.svg)](https://app.codecov.io/gh/ropensci/rvertnet?branch=master) [![rstudio mirror downloads](https://cranlogs.r-pkg.org/badges/rvertnet)](https://github.com/r-hub/cranlogs.app) [![cran version](https://www.r-pkg.org/badges/version/rvertnet)](https://cran.r-project.org/package=rvertnet)

<!-- badges: end -->

# rvertnet
Expand All @@ -29,138 +27,32 @@ knitr::opts_chunk$set(

VertNet.org API docs: <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}
remotes::install_github("ropensci/rvertnet")
```

```{r}
library('rvertnet')
```
## Get started

## Vignette
### [View vignette on ropensci](https://docs.ropensci.org/rvertnet/articles/rvertnet.html)

View the vignette in your web browser
### View vignette locally in your web browser

```{r eval=FALSE}
browseVignettes("rvertnet")
```

Or view the vignette in Rstudio
### View vignette in Rstudio

```{r eval=FALSE}
vignette("rvertnet")
```

## Search by term

Search for _Aves_ in the state of _California_, limit to 10 records

```{r}
res <- searchbyterm(class = "Aves", stateprovince = "California",
limit = 10, messages = 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",
stateprovince = "(wyoming OR south dakota)",
limit = 20, messages = 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 eval=FALSE}
library("dplyr")
out <- searchbyterm(genus = "Ochotona", limit = 800)
out$data %>%
group_by(scientificname) %>%
summarise(count = length(scientificname)) %>%
arrange(desc(count))
#> # A tibble: 20 x 2
#> scientificname count
#> <chr> <int>
#> 1 Ochotona princeps 450
#> 2 Ochotona pallasi 129
#> 3 Ochotona princeps saxatilis 103
#> 4 Ochotona hyperborea 30
#> 5 Ochotona dauurica 21
#> 6 Ochotona collaris 15
#> 7 Ochotona princeps figginsi 14
#> 8 Ochotona princeps taylori 8
#> 9 Ochotona princeps schisticeps 6
#> 10 Ochotona alpina 4
#> 11 Ochotona princeps muiri 4
#> 12 Ochotona hyperborea mantchurica 3
#> 13 Ochotona princeps incana 3
#> 14 Ochotona princeps princeps 3
#> 15 Ochotona princeps murri 2
#> 16 Ochotona princeps brunnescens 1
#> 17 Ochotona princeps jewetti 1
#> 18 Ochotona princeps tutelata 1
#> 19 Ochotona princeps uinta 1
#> 20 Ochotona princeps ventorum 1
```


## 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", rfile = "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, long = -105.694, radius = 2000,
limit = 10, messages = FALSE)
res$data[,1:5]
```

## Contributors

* Dave Slager [@slager](https://github.com/slager)
* Scott Chamberlain [@sckott](https://github.com/sckott)
* Chris Ray [@Pika8tona](https://github.com/Pika8tona)
* Vijay Barve [@vijaybarve](https://github.com/vijaybarve)
- Dave Slager [\@slager](https://github.com/slager)
- 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')`
* Please note that this package is released with a [Contributor Code of Conduct](https://ropensci.org/code-of-conduct/). By contributing to this project, you agree to abide by its terms.
- 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')`
- Please note that this package is released with a [Contributor Code of Conduct](https://ropensci.org/code-of-conduct/). By contributing to this project, you agree to abide by its terms.
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