kewr

Meant to make accessing data from one of Royal Botanic Gardenn Kew easier and to provide a consistent interface their public APIs.
https://github.com/barnabywalker/kewr

Category: Biosphere
Sub Category: Plants and Vegetation

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package r

Last synced: about 9 hours ago
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Repository metadata

R Package to Access Kew Data APIs

• Host: GitHub
• URL: https://github.com/barnabywalker/kewr
• Owner: barnabywalker
• License: other
• Created: 2020-11-11T14:44:21.000Z (over 4 years ago)
• Default Branch: main
• Last Pushed: 2022-06-30T11:32:44.000Z (almost 3 years ago)
• Last Synced: 2025-04-20T09:03:33.084Z (8 days ago)
• Topics: package, r
• Language: R
• Homepage: https://barnabywalker.github.io/kewr/
• Size: 2.06 MB
• Stars: 16
• Watchers: 3
• Forks: 0
• Open Issues: 5
• Releases: 0

https://github.com/barnabywalker/kewr/blob/main/

          


# kewr



[![R build
status](https://github.com/barnabywalker/kewr/workflows/R-CMD-check/badge.svg)](https://github.com/barnabywalker/kewr/actions)


An R package to access data from RGB Kew’s APIs.

## Overview

kewr is meant to make accessing data from one of RGB Kew easier and to
provide a consistent interface their public APIs.

This package should cover:

-   [x] [World Checklist of Vascular
    Plants](https://wcvp.science.kew.org/)
-   [x] [Plants of the World Online](http://powo.science.kew.org/)
-   [x] [International Plant Names Index](https://www.ipni.org/)
-   [x] [Kew Names Matching Service](http://namematch.science.kew.org/)
-   [x] [Kew’s Tree of Life](https://treeoflife.kew.org)
-   [x] [Kew Reconciliation
    Service](http://data1.kew.org/reconciliation/about/IpniName)

New sources will be added as they come up.

## Installation

kewr is not on CRAN yet but you can install the latest development
version from GitHub:

``` r
# install.packages("devtools")
devtools::install_github("barnabywalker/kewr")
```

## Usage

Functions in this package all start with a prefix specifying what action
you want to perform and a suffix referring to the resource.

Four of the resources (POWO, WCVP, IPNI, and ToL) are databases storing
flora, taxonomic, nomenclatural, or genetic information. These three
resources all have a `search_*` and `lookup_*`.

### Retrieving records

The `lookup_` functions can be used to retrieve a particular record by
its unique IPNI ID:

``` r
lookup_powo("320035-2")
lookup_wcvp("320035-2")
lookup_ipni("320035-2")
```

IPNI contains records for authors and publications, which can also be
retrieved using the `lookup_ipni` function:

``` r
lookup_ipni("20885-1", type="author")
lookup_ipni("987-2", type="publication")
```

The ToL uses its own ID system. These IDs can be found by first
searching the database.

``` r
lookup_tol("2717")
```

### Searching databases

All four of these databases can be searched as well:

``` r
search_powo("Poa annua")
search_wcvp("Poa annua")
search_ipni("Poa annua")
search_tol("Poa annua")
```

And all, except the ToL, use filters and keywords for more advanced
searches:

``` r
search_powo(list(genus="Poa", distribution="Madagascar"), 
            filters=c("accepted", "species"))
search_wcvp(list(genus="Poa"), filters=c("accepted", "species"))
search_ipni(list(genus="Poa", published=1920),
            filters=c("species"))
```

The number of search results returned are determined by the `limit`
keyword:

``` r
search_powo(list(genus="Poa"), limit=20)
search_wcvp(list(genus="Poa"), limit=20)
search_ipni(list(genus="Poa"), limit=20)
search_tol("Poa", limit=20)
```

The next page for a set of search results can be requested using the
`request_next` function:

``` r
results <- search_powo(list(genus="Poa"))
request_next(results)
```

### Loading data from ToL

Tree and gene data can be loaded directly from ToL into R.

For instance, you can load the whole Tree of Life.

``` r
load_tol()
```

Or a gene tree for a particular gene.

``` r
gene_info <- lookup_tol("51", type="gene")
load_tol(gene_info$tree_file_url)
```

Or a FASTA file for a specimen.

``` r
specimen_info <- lookup_tol("1296")
load_tol(specimen_info$fasta_file_url)
```

### Downloading from the ToL

The corresponding files can also be downloaded for use later or in other
programmes.

``` r
specimen_info <- lookup_tol("1296")
download_tol(specimen_info$fasta_file_url)
```

### Downloading the WCVP

The whole of WCVP can be download to a directory using:

``` r
download_wcvp()
```

### Matching names

The KNMS resource is only used for matching names to records in
POWO/WCVP:

``` r
match_knms(c("Poa annua", "Magnolia grandifolia", "Bulbophyllum sp."))
```

Single names can also be matched to IPNI using the KRS resources.

``` r
match_krs("Poa annua")
```

KRS is slower for matching many names, as a request needs to be made for
each one. But it has the advantage of allowing more complex matching:

``` r
match_krs(list(genus="Solanum", species="sanchez-vegae", author="S.Knapp"))
```

### Tidying results

Each function in this package returns an object that stores the original
response as well as the content of the response parsed into a list. This
is to give the user as much flexibility as possible and to make
debugging things a bit easier.

But this can be hard to use, so all the results objects can be tidied as
a `tibble`:

``` r
results <- search_powo("Poa annua")
tidy(results)
```

## Citing

You can get information about how to cite `kewr` by using:

``` r
citation("kewr")
```

You can also get the citation to use for each data service using the
different results objects:

    r <- search_wcvp("Poa")
    kew_citation(r)

        

---

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• Name:
• Login: barnabywalker
• Email:
• Kind: user
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• Repositories: 5
• Last ynced at: 2023-03-08T22:05:12.973Z
• Profile URL: https://github.com/barnabywalker

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