updated vignettes, bumped version, remove whitespace

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: taxize
 Title: Taxonomic Information from Around the Web
 Description: Interacts with a suite of web 'APIs' for taxonomic tasks,
-    such as verifying species names, and getting taxonomic hierarchies.
-Version: 0.6.9.9100
+    such as verifying species names, and getting taxonomic 'hierarchies'.
+Version: 0.7.0
 License: MIT + file LICENSE
 URL: https://github.com/ropensci/taxize
 BugReports: https://github.com/ropensci/taxize/issues

NEWS.md

@@ -5,28 +5,28 @@ taxize 0.7.0
 
 * Now requires `R >= 3.2.1`. Good idea to update your R installation anyway (#476)
 * New function `ion()` for obtaining data from Index of Organism Names (#345)
-* New function `eubon()` for obtaining data from EU (European Union) BON 
-taxonomy (#466) Note that you may onloy get partial results for some requests 
+* New function `eubon()` for obtaining data from EU (European Union) BON
+taxonomy (#466) Note that you may onloy get partial results for some requests
 as paging isn't implemented yet in the EU BON API (#481)
 * New suite of functions, with prefix `fg_*()` for obtaining data from Index
-Fungorum. More work has to be done yet on this data source, but these initial 
+Fungorum. More work has to be done yet on this data source, but these initial
 functions allow some Index Fungorum data access (#471)
-* New function `gbif_downstream()` for obtaining downstream names from 
-GBIF's backbone taxonomy. Also available in `downstream()`, where you can 
+* New function `gbif_downstream()` for obtaining downstream names from
+GBIF's backbone taxonomy. Also available in `downstream()`, where you can
 request downstream names from GBIF, along with other data sources (#414)
 
 ## MINOR IMPROVEMENTS
 
-* Note added in docs for all `db` parameters to warn users that if they 
-provide the wrong `db` value for the given taxon ID, they can get data 
+* Note added in docs for all `db` parameters to warn users that if they
+provide the wrong `db` value for the given taxon ID, they can get data
 back, but it would be wrong. That is, all taxonomic data sources available
 in `taxize` use their own unique IDs, so a single ID value can be in multiple
 data sources, even though the ID refers to different taxa in each data source.
 There is no way we can think of to prevent this from happening, so be cautious.
 (#465)
-* A note added to all IUCN functions to warn users that sometimes incorrect 
-data is returned. This is beyond our control, as sometimes IUCN itself gives 
-back incorrect data, and sometimes EOL/Global Names (which we use in some of 
+* A note added to all IUCN functions to warn users that sometimes incorrect
+data is returned. This is beyond our control, as sometimes IUCN itself gives
+back incorrect data, and sometimes EOL/Global Names (which we use in some of
 the IUCN functions) give back incorrect data. (#468) (#473) (#174) (472) (#475)
 
 ## BUG FIXES
@@ -36,8 +36,8 @@ passed to the function. GNR is case sensitive, so case matters (#469)
 
 ## DEFUNCT
 
-* `phylomatic_tree()` and `phylomatic_format()` are defunct. They were deprecated 
-in recent versions, but are now gone. See the new package `brranching` for 
+* `phylomatic_tree()` and `phylomatic_format()` are defunct. They were deprecated
+in recent versions, but are now gone. See the new package `brranching` for
 Phylomatic data (#479)
 
 taxize 0.6.6

inst/vign/taxize_infotable.Rmd

@@ -12,7 +12,7 @@ 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 |
+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 |

inst/vign/taxize_infotable.md

@@ -12,7 +12,7 @@ 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 |
+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 |

inst/vign/taxize_vignette.md

@@ -311,12 +311,12 @@ get_nbnid_("Poa annua", rows = 1:10)
 #> 2  NHMSYS0000461798              Poa   Genus  Recommended
 #> 3  NHMSYS0000461804         Poa laxa Species      Synonym
 #> 4  NHMSYS0021060390           Poales   Order  Recommended
-#> 5  NBNSYS0000002547       Poa alpina Species  Recommended
+#> 5  NBNSYS0000160753          Poaceae  Family  Recommended
 #> 6  NBNSYS0000002551       Poa glauca Species  Recommended
-#> 7  NBNSYS0000002551       Poa caesia Species      Synonym
-#> 8  NBNSYS0000160753          Poaceae  Family  Recommended
-#> 9  NHMSYS0000461804        Poa minor Species      Synonym
-#> 10 NBNSYS0000002545       Poa exilis Species Undetermined
+#> 7  NBNSYS0000002547       Poa alpina Species  Recommended
+#> 8  NHMSYS0000461804        Poa minor Species      Synonym
+#> 9  NBNSYS0000002545       Poa exilis Species Undetermined
+#> 10 NBNSYS0000002551       Poa caesia Species      Synonym
 ```
 
 ## Coerce numerics/alphanumerics to taxon IDs
@@ -393,7 +393,7 @@ system.time( replicate(3, as.gbifid(c("2704179","2435099","3171445"), check=TRUE
 
 ```
 #>    user  system elapsed 
-#>   0.117   0.003   1.753
+#>   0.122   0.004   1.776
 ```
 
 ```r
@@ -402,7 +402,7 @@ system.time( replicate(3, as.gbifid(c("2704179","2435099","3171445"), check=FALS
 
 ```
 #>    user  system elapsed 
-#>   0.001   0.000   0.001
+#>   0.000   0.000   0.001
 ```
 
 ## What taxa are downstream of my taxon of interest?

vignettes/taxize_infotable.Rmd

@@ -12,7 +12,7 @@ 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 |
+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 |

vignettes/taxize_vignette.Rmd

@@ -311,12 +311,12 @@ get_nbnid_("Poa annua", rows = 1:10)
 #> 2  NHMSYS0000461798              Poa   Genus  Recommended
 #> 3  NHMSYS0000461804         Poa laxa Species      Synonym
 #> 4  NHMSYS0021060390           Poales   Order  Recommended
-#> 5  NBNSYS0000002547       Poa alpina Species  Recommended
+#> 5  NBNSYS0000160753          Poaceae  Family  Recommended
 #> 6  NBNSYS0000002551       Poa glauca Species  Recommended
-#> 7  NBNSYS0000002551       Poa caesia Species      Synonym
-#> 8  NBNSYS0000160753          Poaceae  Family  Recommended
-#> 9  NHMSYS0000461804        Poa minor Species      Synonym
-#> 10 NBNSYS0000002545       Poa exilis Species Undetermined
+#> 7  NBNSYS0000002547       Poa alpina Species  Recommended
+#> 8  NHMSYS0000461804        Poa minor Species      Synonym
+#> 9  NBNSYS0000002545       Poa exilis Species Undetermined
+#> 10 NBNSYS0000002551       Poa caesia Species      Synonym
 ```
 
 ## Coerce numerics/alphanumerics to taxon IDs
@@ -393,7 +393,7 @@ system.time( replicate(3, as.gbifid(c("2704179","2435099","3171445"), check=TRUE
 
 ```
 #>    user  system elapsed 
-#>   0.117   0.003   1.753
+#>   0.122   0.004   1.776
 ```
 
 ```r
@@ -402,7 +402,7 @@ system.time( replicate(3, as.gbifid(c("2704179","2435099","3171445"), check=FALS
 
 ```
 #>    user  system elapsed 
-#>   0.001   0.000   0.001
+#>   0.000   0.000   0.001
 ```
 
 ## What taxa are downstream of my taxon of interest?