update vignettes

ropensci · Jun 30, 2017 · 85d4cd9 · 85d4cd9
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diff --git a/inst/vign/name_cleaning.md b/inst/vign/name_cleaning.md
@@ -104,7 +104,7 @@ has a sister method with and trailing underscore, e.g., `get_tsn()` and `get_tsn
 ```r
 get_tsn_(searchterm = "Quercus b")
 #> $`Quercus b`
-#> # A tibble: 5 × 4
+#> # A tibble: 5 x 4
 #>      tsn         scientificName                           commonNames
 #>    <chr>                  <chr>                                 <chr>
 #> 1  19300        Quercus bicolor     swamp white oak,ch<ea>ne bicolore
@@ -125,7 +125,7 @@ number of a range of numbers:
 ```r
 get_tsn_(searchterm = "Quercus b", rows = 1)
 #> $`Quercus b`
-#> # A tibble: 1 × 4
+#> # A tibble: 1 x 4
 #>     tsn  scientificName                       commonNames nameUsage
 #>   <chr>           <chr>                             <chr>     <chr>
 #> 1 19300 Quercus bicolor swamp white oak,ch<ea>ne bicolore  accepted
@@ -135,7 +135,7 @@ get_tsn_(searchterm = "Quercus b", rows = 1)
 ```r
 get_tsn_(searchterm = "Quercus b", rows = 1:2)
 #> $`Quercus b`
-#> # A tibble: 2 × 4
+#> # A tibble: 2 x 4
 #>      tsn    scientificName                           commonNames nameUsage
 #>    <chr>             <chr>                                 <chr>     <chr>
 #> 1  19300   Quercus bicolor     swamp white oak,ch<ea>ne bicolore  accepted
@@ -227,30 +227,42 @@ in a programmatic workflow straight away.
 ```r
 spp <- names_list(rank = "species", size = 10)
 gnr_resolve(names = spp, preferred_data_sources = 11)
-#>               user_supplied_name                submitted_name
-#> 1             Eucalyptus oreades            Eucalyptus oreades
-#> 2          Alloispermum insuetum         Alloispermum insuetum
-#> 3                   Thymus rudis                  Thymus rudis
-#> 4                   Thymus rudis                  Thymus rudis
-#> 5      Trichosanthes dafangensis     Trichosanthes dafangensis
-#> 6  Ectropothecium subhaplocladum Ectropothecium subhaplocladum
-#> 7           Persoonia mitchellii          Persoonia mitchellii
-#> 8                Gilia propinqua               Gilia propinqua
-#> 9            Aberemoa furfuracea           Aberemoa furfuracea
-#> 10           Myrcia australasiae           Myrcia australasiae
-#> 11                Lotus borbasii                Lotus borbasii
-#>                                                    matched_name
-#> 1                                   Eucalyptus oreades R. Baker
-#> 2  Alloispermum insuetum C.F.Fernández, Urbatsch & G.A.Sullivan
-#> 3                                          Thymus rudis A.Kern.
-#> 4                              Thymus rudis A.Kern. ex Mazzetti
-#> 5                   Trichosanthes dafangensis N.G. Ye & S.J. Li
-#> 6                 Ectropothecium subhaplocladum Brotherus, 1928
-#> 7                                  Persoonia mitchellii Meissn.
-#> 8                             Gilia propinqua (Suksd.) St. John
-#> 9                      Aberemoa furfuracea (A. St.-Hil.) Baill.
-#> 10                                 Myrcia australasiae F.Muell.
-#> 11                                       Lotus borbasii Ujhelyi
+#>          user_supplied_name           submitted_name
+#> 1     Helichrysum candollei    Helichrysum candollei
+#> 2          Haworthia retusa         Haworthia retusa
+#> 3          Crypsinus bakeri         Crypsinus bakeri
+#> 4  Mangifera philippinensis Mangifera philippinensis
+#> 5    Selaginella atirrensis   Selaginella atirrensis
+#> 6   Hymenostomum sullivanii  Hymenostomum sullivanii
+#> 7   Hymenostomum sullivanii  Hymenostomum sullivanii
+#> 8         Cytisus urumoffii        Cytisus urumoffii
+#> 9         Cytisus urumoffii        Cytisus urumoffii
+#> 10        Cytisus urumoffii        Cytisus urumoffii
+#> 11        Baptisia uniflora        Baptisia uniflora
+#> 12        Baptisia uniflora        Baptisia uniflora
+#> 13        Baptisia uniflora        Baptisia uniflora
+#> 14        Baptisia uniflora        Baptisia uniflora
+#> 15     Nephelium xerocarpum     Nephelium xerocarpum
+#> 16  Baccharis gnaphalioides  Baccharis gnaphalioides
+#> 17  Baccharis gnaphalioides  Baccharis gnaphalioides
+#>                                             matched_name
+#> 1  Helichrysum candollei (Bojer ex DC.) R.Vig. & Humbert
+#> 2                            Haworthia retusa (L.) Duval
+#> 3                        Crypsinus bakeri (Luerss.) Tag.
+#> 4                      Mangifera philippinensis Mukherji
+#> 5                         Selaginella atirrensis Hieron.
+#> 6      Hymenostomum sullivanii C. Müller ex Geheeb, 1897
+#> 7                      Hymenostomum sullivanii C. Müller
+#> 8                     Cytisus urumoffii Davidov ex Stoj.
+#> 9                Cytisus urumoffii Davidoff ex Stoyanoff
+#> 10                            Cytisus urumoffii Davidoff
+#> 11                               Baptisia uniflora Hook.
+#> 12                      Baptisia uniflora (Michx.) Nutt.
+#> 13                        Baptisia uniflora (Michx.) Sm.
+#> 14                             Baptisia uniflora Spreng.
+#> 15                   Nephelium xerocarpum (Bl.) Cambess.
+#> 16                       Baccharis gnaphalioides Spreng.
+#> 17                           Baccharis gnaphalioides DC.
 #>         data_source_title score
 #> 1  GBIF Backbone Taxonomy 0.988
 #> 2  GBIF Backbone Taxonomy 0.988
@@ -263,6 +275,12 @@ gnr_resolve(names = spp, preferred_data_sources = 11)
 #> 9  GBIF Backbone Taxonomy 0.988
 #> 10 GBIF Backbone Taxonomy 0.988
 #> 11 GBIF Backbone Taxonomy 0.988
+#> 12 GBIF Backbone Taxonomy 0.988
+#> 13 GBIF Backbone Taxonomy 0.988
+#> 14 GBIF Backbone Taxonomy 0.988
+#> 15 GBIF Backbone Taxonomy 0.988
+#> 16 GBIF Backbone Taxonomy 0.988
+#> 17 GBIF Backbone Taxonomy 0.988
 ```
 
 ## Other functions

diff --git a/inst/vign/taxize_infotable.Rmd b/inst/vign/taxize_infotable.Rmd
@@ -9,15 +9,24 @@ Some key functions in taxize, what they do, and their data sources.
 
 Function name | What it does | Source |
 ----------- | ----------- | ----------- |
-children | Get direct children | COL, NCBI, ITIS |
-classification | Upstream classification | COL, NCBI, ITIS, Tropicos, EOL, GBIF, NBN |
-comm2sci | Get scientific from common names | EOL, NCBI, ITIS, Tropicos |
-downstream | Downstream taxa to specified rank | COL, ITIS, GBIF |
-get_ids | Get taxonomic identifiers | COL, NCBI, ITIS, Tropicos, EOL, GBIF, NBN |
-resolve | Resolve names using any resolver | GNR, TNRS, iPlant |
-sci2comm | Get common from scientific names | EOL, NCBI, ITIS |
-synonyms | Retrieve synonyms given input names/identifiers | COL, NCBI, ITIS, Tropicos |
-upstream | Retrieve upstream taxa given names/identifiers | COL, ITIS |
+`children` | Get direct children | COL, NCBI, ITIS |
+`classification` | Upstream classification | COL, NCBI, ITIS, Tropicos, EOL, GBIF, NBN |
+`comm2sci` | Get scientific from common names | EOL, NCBI, ITIS, Tropicos |
+`downstream` | Downstream taxa to specified rank | COL, ITIS, GBIF |
+`get_ids` | Get taxonomic identifiers | COL, NCBI, ITIS, Tropicos, EOL, GBIF, NBN |
+`resolve` | Resolve names using many resolvers | GNR, TNRS, iPlant |
+`gnr_resolve` | Resolve names using Global Names Resolver | GNR |
+`tnrs` | Phylotastic Taxonomic Name Resolution Service | NCBI, iPlant, MSW3 |
+`tol_resolve` | Resolve names using any resolver | TOL |
+`iplant_resolve` | iPlant name resolution| iPlant |
+`sci2comm` | Get common from scientific names | EOL, NCBI, ITIS |
+`synonyms` | Retrieve synonyms given input names/identifiers | COL, NCBI, ITIS, Tropicos |
+`upstream` | Retrieve upstream taxa given names/identifiers | COL, ITIS |
+`lowest_common` | Retrieve the lowest common taxon and rank for a given taxon name or ID | COL, ITIS, GBIF, TOL, NCBI |
+`genbank2uid` | Get NCBI taxonomy UID from GenBankID | NCBI |
+`tax_name` | Get taxonomic names for a given rank | NCBI, ITIS |
+`tax_rank` | Get rank for a given taxonomic name | BOLD, COL, EOL, GBIF, NATSERV, NBN, TOL, TROPICOS, ITIS, NCBI, WORMS |
+`tpl_get` | Get The Plant List csv files | TPL |
 
 ### Acronyms
 
@@ -30,3 +39,10 @@ upstream | Retrieve upstream taxa given names/identifiers | COL, ITIS |
 * iPlant: iPlant Name Resolution Service
 * GNR: Global Names Resolver
 * TNRS: Taxonomic Name Resolution Service
+* TOL: Open Tree of Life
+* MSW3: Mammal Species of the World, 3rd Edition
+* TPL: The Plant List
+* BOLD: Barcode of Life
+* NATSERV: Natureserve
+* TROPICOS: Tropicos plant database
+* WORMS: World Register of Marine Species
diff --git a/inst/vign/taxize_infotable.md b/inst/vign/taxize_infotable.md
@@ -9,15 +9,24 @@ Some key functions in taxize, what they do, and their data sources.
 
 Function name | What it does | Source |
 ----------- | ----------- | ----------- |
-children | Get direct children | COL, NCBI, ITIS |
-classification | Upstream classification | COL, NCBI, ITIS, Tropicos, EOL, GBIF, NBN |
-comm2sci | Get scientific from common names | EOL, NCBI, ITIS, Tropicos |
-downstream | Downstream taxa to specified rank | COL, ITIS, GBIF |
-get_ids | Get taxonomic identifiers | COL, NCBI, ITIS, Tropicos, EOL, GBIF, NBN |
-resolve | Resolve names using any resolver | GNR, TNRS, iPlant |
-sci2comm | Get common from scientific names | EOL, NCBI, ITIS |
-synonyms | Retrieve synonyms given input names/identifiers | COL, NCBI, ITIS, Tropicos |
-upstream | Retrieve upstream taxa given names/identifiers | COL, ITIS |
+`children` | Get direct children | COL, NCBI, ITIS |
+`classification` | Upstream classification | COL, NCBI, ITIS, Tropicos, EOL, GBIF, NBN |
+`comm2sci` | Get scientific from common names | EOL, NCBI, ITIS, Tropicos |
+`downstream` | Downstream taxa to specified rank | COL, ITIS, GBIF |
+`get_ids` | Get taxonomic identifiers | COL, NCBI, ITIS, Tropicos, EOL, GBIF, NBN |
+`resolve` | Resolve names using many resolvers | GNR, TNRS, iPlant |
+`gnr_resolve` | Resolve names using Global Names Resolver | GNR |
+`tnrs` | Phylotastic Taxonomic Name Resolution Service | NCBI, iPlant, MSW3 |
+`tol_resolve` | Resolve names using any resolver | TOL |
+`iplant_resolve` | iPlant name resolution| iPlant |
+`sci2comm` | Get common from scientific names | EOL, NCBI, ITIS |
+`synonyms` | Retrieve synonyms given input names/identifiers | COL, NCBI, ITIS, Tropicos |
+`upstream` | Retrieve upstream taxa given names/identifiers | COL, ITIS |
+`lowest_common` | Retrieve the lowest common taxon and rank for a given taxon name or ID | COL, ITIS, GBIF, TOL, NCBI |
+`genbank2uid` | Get NCBI taxonomy UID from GenBankID | NCBI |
+`tax_name` | Get taxonomic names for a given rank | NCBI, ITIS |
+`tax_rank` | Get rank for a given taxonomic name | BOLD, COL, EOL, GBIF, NATSERV, NBN, TOL, TROPICOS, ITIS, NCBI, WORMS |
+`tpl_get` | Get The Plant List csv files | TPL |
 
 ### Acronyms
 
@@ -30,3 +39,10 @@ upstream | Retrieve upstream taxa given names/identifiers | COL, ITIS |
 * iPlant: iPlant Name Resolution Service
 * GNR: Global Names Resolver
 * TNRS: Taxonomic Name Resolution Service
+* TOL: Open Tree of Life
+* MSW3: Mammal Species of the World, 3rd Edition
+* TPL: The Plant List
+* BOLD: Barcode of Life
+* NATSERV: Natureserve
+* TROPICOS: Tropicos plant database
+* WORMS: World Register of Marine Species
diff --git a/inst/vign/taxize_vignette.md b/inst/vign/taxize_vignette.md
@@ -135,9 +135,7 @@ classification(specieslist, db = 'itis')
 
 ```
 #> $`Abies procera`
-#> # A tibble: 12 × 3
 #>               name          rank     id
-#>              <chr>         <chr>  <chr>
 #> 1          Plantae       kingdom 202422
 #> 2    Viridiplantae    subkingdom 954898
 #> 3     Streptophyta  infrakingdom 846494
@@ -152,9 +150,7 @@ classification(specieslist, db = 'itis')
 #> 12   Abies procera       species 181835
 #> 
 #> $`Pinus contorta`
-#> # A tibble: 12 × 3
 #>               name          rank     id
-#>              <chr>         <chr>  <chr>
 #> 1          Plantae       kingdom 202422
 #> 2    Viridiplantae    subkingdom 954898
 #> 3     Streptophyta  infrakingdom 846494
@@ -265,7 +261,7 @@ get_nbnid(c("Zootoca vivipara","Pinus contorta"), rows = 1)
 ```
 
 ```
-#> [1] "NHMSYS0001706186" "NHMSYS0000494848"
+#> [1] "NHMSYS0001706186" "NBNSYS0000004786"
 #> attr(,"class")
 #> [1] "nbnid"
 #> attr(,"match")
@@ -276,7 +272,7 @@ get_nbnid(c("Zootoca vivipara","Pinus contorta"), rows = 1)
 #> [1] FALSE FALSE
 #> attr(,"uri")
 #> [1] "https://data.nbn.org.uk/Taxa/NHMSYS0001706186"
-#> [2] "https://data.nbn.org.uk/Taxa/NHMSYS0000494848"
+#> [2] "https://data.nbn.org.uk/Taxa/NBNSYS0000004786"
 ```
 
 Or you can select a range of rows
@@ -287,22 +283,26 @@ get_nbnid(c("Zootoca vivipara","Pinus contorta"), rows = 1:3)
 ```
 
 ```
-#>              nbnid                  searchmatchtitle       rank
+#>              nbnid                    scientificName       rank
 #> 1 NHMSYS0001706186                  Zootoca vivipara    species
 #> 2 NHMSYS0020784960 Zootoca vivipara subsp. pannonica subspecies
-#> 3 NHMSYS0001706185                           Zootoca      genus
-#>    namestatus
-#> 1 Recommended
-#> 2 Recommended
-#> 3 Recommended
-#>              nbnid               searchmatchtitle       rank  namestatus
-#> 1 NHMSYS0000494848   Pinus contorta var. contorta    variety Recommended
-#> 2 NBNSYS0000004786                 Pinus contorta    species Recommended
-#> 3 NHMSYS0000494848 Pinus contorta subsp. contorta subspecies Recommended
-```
-
-```
-#> [1] "NHMSYS0001706186" "NHMSYS0000494848"
+#> 3 NHMSYS0000461615                 Bistorta vivipara    species
+#>   taxonomicStatus
+#> 1        accepted
+#> 2        accepted
+#> 3         synonym
+#>              nbnid                  scientificName       rank
+#> 1 NBNSYS0000004786                  Pinus contorta    species
+#> 2 NHMSYS0000494848  Pinus contorta subsp. contorta subspecies
+#> 3 NHMSYS0000494858 Pinus contorta subsp. murreyana subspecies
+#>   taxonomicStatus
+#> 1        accepted
+#> 2         synonym
+#> 3         synonym
+```
+
+```
+#> [1] "NHMSYS0001706186" "NBNSYS0000004786"
 #> attr(,"class")
 #> [1] "nbnid"
 #> attr(,"match")
@@ -313,7 +313,7 @@ get_nbnid(c("Zootoca vivipara","Pinus contorta"), rows = 1:3)
 #> [1] FALSE FALSE
 #> attr(,"uri")
 #> [1] "https://data.nbn.org.uk/Taxa/NHMSYS0001706186"
-#> [2] "https://data.nbn.org.uk/Taxa/NHMSYS0000494848"
+#> [2] "https://data.nbn.org.uk/Taxa/NBNSYS0000004786"
 ```
 
 In addition, in case you don't want to do interactive name selection in the case where there are a lot of names, you can get all data back with functions of the form, e.g., `get_tsn_()`, and likewise for other data sources. For example:
@@ -325,7 +325,7 @@ NROW(out$`Poa annua`)
 ```
 
 ```
-#> [1] 152
+#> [1] 25
 ```
 
 That's a lot of data, so we can get only certain rows back
@@ -337,17 +337,17 @@ get_nbnid_("Poa annua", rows = 1:10)
 
 ```
 #> $`Poa annua`
-#>    ptaxonversionkey searchmatchtitle    rank   namestatus
-#> 1  NBNSYS0000002544        Poa annua species  Recommended
-#> 2  NHMSYS0000461798              Poa   genus  Recommended
-#> 3  NHMSYS0000461804         Poa laxa species      Synonym
-#> 4  NHMSYS0021060390           Poales   order  Recommended
-#> 5  NBNSYS0000002551       Poa glauca species  Recommended
-#> 6  NBNSYS0000002547       Poa alpina species  Recommended
-#> 7  NHMSYS0000456981       Poa rigida species      Synonym
-#> 8  NBNSYS0000002551       Poa caesia species      Synonym
-#> 9  NBNSYS0000002545       Poa exilis species Undetermined
-#> 10 NHMSYS0000461804        Poa minor species      Synonym
+#>                guid    scientificName    rank taxonomicStatus
+#> 1  NBNSYS0000002544         Poa annua species        accepted
+#> 2  NBNSYS0000002739      Adonis annua species         synonym
+#> 3  NBNSYS0200001901      Bellis annua species        accepted
+#> 4  NHMSYS0000456951 Carrichtera annua species         synonym
+#> 5  NBNSYS0200003392  Triumfetta annua species        accepted
+#> 6  NBNSYS0000002918     Lunaria annua species        accepted
+#> 7  NBNSYS0200002555       Lonas annua species        accepted
+#> 8  NBNSYS0000033325   Artemisia annua species        accepted
+#> 9  NHMSYS0000456951 Carrichtera annua species        accepted
+#> 10 NHMSYS0000461806     Poa imbecilla species         synonym
 ```
 
 ## Coerce numerics/alphanumerics to taxon IDs
@@ -447,7 +447,7 @@ system.time( replicate(3, as.gbifid(c("2704179","2435099","3171445"), check=TRUE
 
 ```
 #>    user  system elapsed 
-#>   0.072   0.002   1.703
+#>   0.072   0.002   1.656
 ```
 
 ```r
@@ -456,7 +456,7 @@ system.time( replicate(3, as.gbifid(c("2704179","2435099","3171445"), check=FALS
 
 ```
 #>    user  system elapsed 
-#>   0.001   0.000   0.001
+#>   0.002   0.000   0.002
 ```
 
 ## What taxa are downstream of my taxon of interest?