From 81ef3403a2c7e70d2c622de16d029f09b7a81620 Mon Sep 17 00:00:00 2001 From: Scott Chamberlain Date: Mon, 23 Jul 2018 15:19:05 -0700 Subject: [PATCH] update readme, fix URLs that were broken --- README.Rmd | 4 +-- README.md | 78 ++++++++++++++++++++++++++++-------------------------- 2 files changed, 42 insertions(+), 40 deletions(-) diff --git a/README.Rmd b/README.Rmd index c4394826..1e349fb7 100644 --- a/README.Rmd +++ b/README.Rmd @@ -84,7 +84,7 @@ Note that a few data sources require SOAP web services, which are difficult to s IUCN Red List iucn - link + link link @@ -156,7 +156,7 @@ Note that a few data sources require SOAP web services, which are difficult to s Open Tree of Life (TOL) tol - link + link none diff --git a/README.md b/README.md index 747682e2..bda16fb7 100644 --- a/README.md +++ b/README.md @@ -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) @@ -76,7 +77,7 @@ Note that a few data sources require SOAP web services, which are difficult to s IUCN Red List iucn - link + link link @@ -148,7 +149,7 @@ Note that a few data sources require SOAP web services, which are difficult to s Open Tree of Life (TOL) tol - link + link none @@ -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" @@ -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 @@ -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