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update readme, fix URLs that were broken
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@sckott
sckott committed Jul 23, 2018
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4 changes: 2 additions & 2 deletions README.Rmd
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Expand Up @@ -84,7 +84,7 @@ Note that a few data sources require SOAP web services, which are difficult to s
<tr>
<td style="text-align:left;">IUCN Red List</td>
<td style="text-align:left;"><code>iucn</code></td>
<td style="text-align:left;"><a href="https://www.assembla.com/spaces/sis/wiki/Red_List_API?version=3">link</a></td>
<td style="text-align:left;"><a href="http://apiv3.iucnredlist.org/api/v3/docs">link</a></td>
<td style="text-align:left;"><a href="http://apiv3.iucnredlist.org/api/v3/token">link</a></td>
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<td style="text-align:left;">Open Tree of Life (TOL)</td>
<td style="text-align:left;"><code>tol</code></td>
<td style="text-align:left;"><a href="https://opentreeoflife.org">link</a></td>
<td style="text-align:left;"><a href="https://github.com/OpenTreeOfLife/germinator/wiki/Open-Tree-of-Life-Web-APIs">link</a></td>
<td style="text-align:left;">none</td>
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78 changes: 40 additions & 38 deletions README.md
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Expand Up @@ -3,6 +3,7 @@ taxize




[![cran checks](https://cranchecks.info/badges/worst/taxize)](https://cranchecks.info/pkgs/taxize)
[![Build Status](https://travis-ci.org/ropensci/taxize.svg?branch=master)](https://travis-ci.org/ropensci/taxize)
[![Build status](https://ci.appveyor.com/api/projects/status/6mgc02mkd8j4sq3g/branch/master)](https://ci.appveyor.com/project/sckott/taxize-175/branch/master)
Expand Down Expand Up @@ -76,7 +77,7 @@ Note that a few data sources require SOAP web services, which are difficult to s
<tr>
<td style="text-align:left;">IUCN Red List</td>
<td style="text-align:left;"><code>iucn</code></td>
<td style="text-align:left;"><a href="https://www.assembla.com/spaces/sis/wiki/Red_List_API?version=3">link</a></td>
<td style="text-align:left;"><a href="http://apiv3.iucnredlist.org/api/v3/docs">link</a></td>
<td style="text-align:left;"><a href="http://apiv3.iucnredlist.org/api/v3/token">link</a></td>
</tr>
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Expand Down Expand Up @@ -148,7 +149,7 @@ Note that a few data sources require SOAP web services, which are difficult to s
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<td style="text-align:left;">Open Tree of Life (TOL)</td>
<td style="text-align:left;"><code>tol</code></td>
<td style="text-align:left;"><a href="https://opentreeoflife.org">link</a></td>
<td style="text-align:left;"><a href="https://github.com/OpenTreeOfLife/germinator/wiki/Open-Tree-of-Life-Web-APIs">link</a></td>
<td style="text-align:left;">none</td>
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Expand Down Expand Up @@ -253,34 +254,35 @@ Get immediate children of _Salmo_. In this case, _Salmo_ is a genus, so this giv
children("Salmo", db = 'ncbi')
#> $Salmo
#> childtaxa_id childtaxa_name childtaxa_rank
#> 1 1509524 Salmo marmoratus x Salmo trutta species
#> 2 1484545 Salmo cf. cenerinus BOLD:AAB3872 species
#> 3 1483130 Salmo zrmanjaensis species
#> 4 1483129 Salmo visovacensis species
#> 5 1483128 Salmo rhodanensis species
#> 6 1483127 Salmo pellegrini species
#> 7 1483126 Salmo opimus species
#> 8 1483125 Salmo macedonicus species
#> 9 1483124 Salmo lourosensis species
#> 10 1483123 Salmo labecula species
#> 11 1483122 Salmo farioides species
#> 12 1483121 Salmo chilo species
#> 13 1483120 Salmo cettii species
#> 14 1483119 Salmo cenerinus species
#> 15 1483118 Salmo aphelios species
#> 16 1483117 Salmo akairos species
#> 17 1201173 Salmo peristericus species
#> 18 1035833 Salmo ischchan species
#> 19 700588 Salmo labrax species
#> 20 237411 Salmo obtusirostris species
#> 21 235141 Salmo platycephalus species
#> 22 234793 Salmo letnica species
#> 23 62065 Salmo ohridanus species
#> 24 33518 Salmo marmoratus species
#> 25 33516 Salmo fibreni species
#> 26 33515 Salmo carpio species
#> 27 8032 Salmo trutta species
#> 28 8030 Salmo salar species
#> 1 2126688 Salmo ciscaucasicus species
#> 2 1509524 Salmo marmoratus x Salmo trutta species
#> 3 1484545 Salmo cf. cenerinus BOLD:AAB3872 species
#> 4 1483130 Salmo zrmanjaensis species
#> 5 1483129 Salmo visovacensis species
#> 6 1483128 Salmo rhodanensis species
#> 7 1483127 Salmo pellegrini species
#> 8 1483126 Salmo opimus species
#> 9 1483125 Salmo macedonicus species
#> 10 1483124 Salmo lourosensis species
#> 11 1483123 Salmo labecula species
#> 12 1483122 Salmo farioides species
#> 13 1483121 Salmo chilo species
#> 14 1483120 Salmo cettii species
#> 15 1483119 Salmo cenerinus species
#> 16 1483118 Salmo aphelios species
#> 17 1483117 Salmo akairos species
#> 18 1201173 Salmo peristericus species
#> 19 1035833 Salmo ischchan species
#> 20 700588 Salmo labrax species
#> 21 237411 Salmo obtusirostris species
#> 22 235141 Salmo platycephalus species
#> 23 234793 Salmo letnica species
#> 24 62065 Salmo ohridanus species
#> 25 33518 Salmo marmoratus species
#> 26 33516 Salmo fibreni species
#> 27 33515 Salmo carpio species
#> 28 8032 Salmo trutta species
#> 29 8030 Salmo salar species
#>
#> attr(,"class")
#> [1] "children"
Expand Down Expand Up @@ -440,10 +442,10 @@ Furthermore, you can just back all ids if that's your jam with the `get_*_()` fu
get_ids_(c("Chironomus riparius", "Pinus contorta"), db = 'nbn', rows=1:3)
#> $nbn
#> $nbn$`Chironomus riparius`
#> guid scientificName rank taxonomicStatus
#> 1 NBNSYS0000027573 Chironomus riparius species accepted
#> 2 NHMSYS0000864966 Damaeus (Damaeus) riparius species accepted
#> 3 NHMSYS0021059238 Rhizoclonium riparium species accepted
#> guid scientificName rank taxonomicStatus
#> 1 NBNSYS0000027573 Chironomus riparius species accepted
#> 2 NHMSYS0001718585 Hypnoidus riparius species accepted
#> 3 NBNSYS0000023345 Paederus riparius species accepted
#>
#> $nbn$`Pinus contorta`
#> guid scientificName rank taxonomicStatus
Expand Down Expand Up @@ -487,10 +489,10 @@ sci2comm('Helianthus annuus', db = 'itis')
```r
comm2sci("black bear", db = "itis")
#> $`black bear`
#> [1] "Ursus thibetanus" "Ursus thibetanus"
#> [3] "Ursus americanus luteolus" "Ursus americanus americanus"
#> [5] "Ursus americanus" "Ursus americanus"
#> [7] "Chiropotes satanas"
#> [1] "Ursus americanus luteolus" "Ursus americanus"
#> [3] "Ursus americanus" "Ursus americanus americanus"
#> [5] "Chiropotes satanas" "Ursus thibetanus"
#> [7] "Ursus thibetanus"
```

## Lowest common rank among taxa
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