update vignettes

.gitignore

@@ -3,3 +3,4 @@
 .Rproj.user
 plantatt.pdf
 inst/PLANTATT_19_Nov_08/*
+inst/vign/vigncache

inst/vign/betydb.md

@@ -40,20 +40,20 @@ out %>%
 ```
 
 ```
-## Source: local data frame [509 x 2]
-## 
+## # A tibble: 449 x 2
 ##       id mean_result
-## 1   1666       27.36
-## 2  16845       27.00
-## 3   1669       26.36
-## 4  16518       26.00
-## 5   1663       25.35
-## 6  16742       25.00
-## 7   1594       24.78
-## 8   1674       22.71
-## 9   1606       22.54
+##    <int>       <dbl>
+##  1  1666       27.36
+##  2 16845       27.00
+##  3  1669       26.36
+##  4 16518       26.00
+##  5  1663       25.35
+##  6 16742       25.00
+##  7  1594       24.78
+##  8  1674       22.71
+##  9  1606       22.54
 ## 10  1665       22.46
-## ..   ...         ...
+## # ... with 439 more rows
 ```
 
 Single trait
@@ -64,18 +64,12 @@ betydb_trait(id = 10)
 ```
 
 ```
-## $created_at
-## NULL
-## 
 ## $description
 ## [1] "Leaf Percent Nitrogen"
 ## 
 ## $id
 ## [1] 10
 ## 
-## $label
-## NULL
-## 
 ## $max
 ## [1] "10"
 ## 
@@ -88,12 +82,6 @@ betydb_trait(id = 10)
 ## $notes
 ## [1] ""
 ## 
-## $standard_name
-## NULL
-## 
-## $standard_units
-## NULL
-## 
 ## $units
 ## [1] "percent"
 ## 
@@ -111,15 +99,12 @@ betydb_specie(id = 10)
 ```
 
 ```
-## $AcceptedSymbol
+## $acceptedsymbol
 ## [1] "ACKA2"
 ## 
 ## $commonname
 ## [1] "karroothorn"
 ## 
-## $created_at
-## NULL
-## 
 ## $genus
 ## [1] "Acacia"
 ## 
@@ -132,9 +117,6 @@ betydb_specie(id = 10)
 ## $scientificname
 ## [1] "Acacia karroo"
 ## 
-## $spcd
-## NULL
-## 
 ## $species
 ## [1] "karroo"
 ## 
@@ -155,9 +137,6 @@ betydb_citation(10)
 ## $author
 ## [1] "Casler"
 ## 
-## $created_at
-## NULL
-## 
 ## $doi
 ## [1] "10.2135/cropsci2003.2226"
 ## 
@@ -176,15 +155,9 @@ betydb_citation(10)
 ## $title
 ## [1] "Cultivar X environment interactions in switchgrass"
 ## 
-## $updated_at
-## NULL
-## 
 ## $url
 ## [1] "http://crop.scijournals.org/cgi/content/abstract/43/6/2226"
 ## 
-## $user_id
-## NULL
-## 
 ## $vol
 ## [1] 43
 ## 
@@ -222,4 +195,7 @@ betydb_site(id = 1)
 ## 
 ## $state
 ## [1] ""
+## 
+## $time_zone
+## [1] "Europe/Athens"
 ```

inst/vign/traits_intro.Rmd

@@ -27,7 +27,7 @@ Get trait data for Willow (_Salix_ spp.)
 
 ```{r}
 (salix <- betydb_search("Salix Vcmax"))
-# equivalent: 
+# equivalent:
 # (out <- betydb_search("willow"))
 ```
 
@@ -50,7 +50,7 @@ salix %>%
 Get sequences by id
 
 ```{r}
-ncbi_byid(ids = "360040093", format = "fasta")
+ncbi_byid(ids = "360040093")
 ```
 
 Get sequences searching by taxonomic name
@@ -60,69 +60,35 @@ out <- ncbi_searcher(taxa = "Umbra limi", seqrange = "1:2000")
 head(out)
 ```
 
-## GISD invasive species data
-
-```{r}
-sp <- c("Carpobrotus edulis", "Rosmarinus officinalis")
-g_invasive(sp)
-```
-
-Or as simplified output
-
-```{r}
-g_invasive(sp, simplify = TRUE)
-```
-
-## EOL invasive species data
-
-```{r}
-eol_invasive_('Brassica oleracea', dataset = 'gisd')
-```
-
-Another example, with more species, and from 
-
-```{r}
-eol_invasive_(c('Lymantria dispar','Cygnus olor','Hydrilla verticillata','Pinus concolor'),
-              dataset = 'i3n')
-```
-
 ## EOL's traitbank trait data
 
-Searching for _Mesoplodon bidens_, page id `328566`
+Searching for _Balaenoptera musculus_ (blue whale), page id `328574`
 
-```{r cache=TRUE}
-res <- traitbank(trait = 328566)
-res$graph %>% 
-  select(dwc.measurementtype..id, dwc.measurementtype.rdfs.label.en, dwc.measurementvalue) %>% 
-  filter(!is.na(dwc.measurementvalue))
+```{r}
+res <- traitbank(328574)
+res$graph %>%
+  select(`dwc:measurementtype`) %>%
+  filter(!is.na(`dwc:measurementtype`))
 ```
 
 ## Coral
 
 Get the species list and their ids
 
-```{r cache=TRUE}
+```{r}
 coral_species()
 ```
 
 Get data by taxon
 
-```{r cache=TRUE}
+```{r}
 coral_taxa(80)
 ```
 
 Get data by trait
 
-```{r cache=TRUE}
-coral_traits(105)
-```
-
-## Flora Europaea
-
 ```{r}
-sp <- c("Lavandula stoechas", "Carpobrotus edulis", "Rhododendron ponticum",
-        "Alkanna lutea", "Anchusa arvensis")
-sapply(sp, fe_native, simplify = FALSE)
+coral_traits(105)
 ```
 
 ## Birdlife International
@@ -138,22 +104,3 @@ Threats data
 ```{r}
 birdlife_threats(22721692)
 ```
-
-## Nativity
-
-```{r}
-sp <- c("Lavandula stoechas", "Carpobrotus edulis", "Rhododendron ponticum",
-      "Alkanna lutea", "Anchusa arvensis")
-```
-
-Native in the continental USA?
-
-```{r}
-sapply(sp, is_native, where = "Continental US", region = "america")
-```
-
-Native on Islas Baleares?
-
-```{r}
-sapply(sp, is_native, where = "Islas_Baleares", region = "europe")
-```