updated main vignette, just minimal betydb cause other vign with bety…

…, bumped to v0.1
ropensci · Jun 11, 2015 · 303d88d · 303d88d
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diff --git a/.Rbuildignore b/.Rbuildignore
@@ -11,3 +11,5 @@ inst/stuff/
 README.Rmd
 tests/testthat.R
 cran-comments.md
+inst/readmecache
+inst/vign/vigncache
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -5,7 +5,7 @@ Description: Species trait data from many different sources, including
     data from the Global Invasive Species Database and 'EOL', 'Traitbank' data
     from 'EOL', Coral traits data from http://coraltraits.org, 'nativity' status
     ('Flora Europaea' or 'ITIS'), and 'Birdlife' International.
-Version: 0.0.9.9100
+Version: 0.1.0
 Authors@R: c(
     person("Scott", "Chamberlain", role = c("aut", "cre"), email = "myrmecocystus@gmail.com"),
     person("Zachary", "Foster", role = "aut", email = "zacharyfoster1989@gmail.com"),

diff --git a/inst/vign/traits_intro.Rmd b/inst/vign/traits_intro.Rmd
@@ -44,18 +44,6 @@ salix %>%
 
 ```
 
-Single trait
-
-```{r}
-betydb_trait(id = 10)
-```
-
-All Miscanthus data collected by Becky Arundale 
-
-```{r}
-betydb_search(query = "Miscanthus Arundale")
-```
-
 ## NCBI sequence data
 
 Get sequences by id

diff --git a/inst/vign/traits_intro.md b/inst/vign/traits_intro.md
@@ -69,75 +69,6 @@ salix %>%
 #> 4                 Salix viminalis Vcmax 43.04 19.99 61.29 8
 ```
 
-Single trait
-
-
-```r
-betydb_trait(id = 10)
-#> $created_at
-#> NULL
-#> 
-#> $description
-#> [1] "Leaf Percent Nitrogen"
-#> 
-#> $id
-#> [1] 10
-#> 
-#> $label
-#> NULL
-#> 
-#> $max
-#> [1] "10"
-#> 
-#> $min
-#> [1] "0.02"
-#> 
-#> $name
-#> [1] "leafN"
-#> 
-#> $notes
-#> [1] ""
-#> 
-#> $standard_name
-#> NULL
-#> 
-#> $standard_units
-#> NULL
-#> 
-#> $units
-#> [1] "percent"
-#> 
-#> $updated_at
-#> [1] "2011-06-06T09:40:42-05:00"
-```
-
-All Miscanthus data collected by Becky Arundale 
-
-
-```r
-betydb_search(query = "Miscanthus Arundale")
-#> Source: local data frame [214 x 30]
-#> 
-#>    access_level   author citation_id citation_year       city
-#> 1             4 Arundale         692          2012 Brownstown
-#> 2             4 Arundale         692          2012 Brownstown
-#> 3             4 Arundale         692          2012 Brownstown
-#> 4             4 Arundale         692          2012 Brownstown
-#> 5             4 Arundale         692          2012 Brownstown
-#> 6             4 Arundale         692          2012 Brownstown
-#> 7             4 Arundale         692          2012 Brownstown
-#> 8             4 Arundale         692          2012 Brownstown
-#> 9             4 Arundale         692          2012  Brookings
-#> 10            4 Arundale         692          2012  Brookings
-#> ..          ...      ...         ...           ...        ...
-#> Variables not shown: commonname (chr), cultivar_id (int), date (chr),
-#>   dateloc (chr), genus (chr), id (int), lat (dbl), lon (dbl), mean (chr),
-#>   month (dbl), n (int), notes (chr), result_type (chr), scientificname
-#>   (chr), site_id (int), sitename (chr), species_id (int), stat (chr),
-#>   statname (chr), trait (chr), trait_description (chr), treatment (chr),
-#>   treatment_id (int), units (chr), year (dbl)
-```
-
 ## NCBI sequence data
 
 Get sequences by id

diff --git a/inst/vign/vigncache/unnamed-chunk-11_ada3b3f1a1450ae23592459c4a636d20.RData b/inst/vign/vigncache/unnamed-chunk-11_ada3b3f1a1450ae23592459c4a636d20.RData
diff --git a/...k-13_f94dd409dbb535332c9bd7e907eaf615.rdb → ...k-11_ada3b3f1a1450ae23592459c4a636d20.rdb b/...k-13_f94dd409dbb535332c9bd7e907eaf615.rdb → ...k-11_ada3b3f1a1450ae23592459c4a636d20.rdb
diff --git a/...k-13_f94dd409dbb535332c9bd7e907eaf615.rdx → ...k-11_ada3b3f1a1450ae23592459c4a636d20.rdx b/...k-13_f94dd409dbb535332c9bd7e907eaf615.rdx → ...k-11_ada3b3f1a1450ae23592459c4a636d20.rdx
diff --git a/inst/vign/vigncache/unnamed-chunk-12_0a7edf5ef79e4cc5e247537086a2190e.RData b/inst/vign/vigncache/unnamed-chunk-12_0a7edf5ef79e4cc5e247537086a2190e.RData
diff --git a/...k-12_968271bab968195c0003dfc9169f5bd8.rdb → ...k-12_0a7edf5ef79e4cc5e247537086a2190e.rdb b/...k-12_968271bab968195c0003dfc9169f5bd8.rdb → ...k-12_0a7edf5ef79e4cc5e247537086a2190e.rdb
diff --git a/...k-12_968271bab968195c0003dfc9169f5bd8.rdx → ...k-12_0a7edf5ef79e4cc5e247537086a2190e.rdx b/...k-12_968271bab968195c0003dfc9169f5bd8.rdx → ...k-12_0a7edf5ef79e4cc5e247537086a2190e.rdx
diff --git a/inst/vign/vigncache/unnamed-chunk-12_968271bab968195c0003dfc9169f5bd8.RData b/inst/vign/vigncache/unnamed-chunk-12_968271bab968195c0003dfc9169f5bd8.RData
diff --git a/inst/vign/vigncache/unnamed-chunk-13_e844fdcdaf9e6147281f53ef614b3a01.RData b/inst/vign/vigncache/unnamed-chunk-13_e844fdcdaf9e6147281f53ef614b3a01.RData
diff --git a/...k-14_e29e44c9a00fd6c1c34e07955d9a8327.rdb → ...k-13_e844fdcdaf9e6147281f53ef614b3a01.rdb b/...k-14_e29e44c9a00fd6c1c34e07955d9a8327.rdb → ...k-13_e844fdcdaf9e6147281f53ef614b3a01.rdb
diff --git a/...k-14_e29e44c9a00fd6c1c34e07955d9a8327.rdx → ...k-13_e844fdcdaf9e6147281f53ef614b3a01.rdx b/...k-14_e29e44c9a00fd6c1c34e07955d9a8327.rdx → ...k-13_e844fdcdaf9e6147281f53ef614b3a01.rdx
diff --git a/inst/vign/vigncache/unnamed-chunk-13_f94dd409dbb535332c9bd7e907eaf615.RData b/inst/vign/vigncache/unnamed-chunk-13_f94dd409dbb535332c9bd7e907eaf615.RData
diff --git a/inst/vign/vigncache/unnamed-chunk-14_7ee6ff436644d5077dd2e028563e2f39.RData b/inst/vign/vigncache/unnamed-chunk-14_7ee6ff436644d5077dd2e028563e2f39.RData
diff --git a/inst/vign/vigncache/unnamed-chunk-14_7ee6ff436644d5077dd2e028563e2f39.rdb b/inst/vign/vigncache/unnamed-chunk-14_7ee6ff436644d5077dd2e028563e2f39.rdb
diff --git a/inst/vign/vigncache/unnamed-chunk-14_7ee6ff436644d5077dd2e028563e2f39.rdx b/inst/vign/vigncache/unnamed-chunk-14_7ee6ff436644d5077dd2e028563e2f39.rdx
diff --git a/inst/vign/vigncache/unnamed-chunk-14_e29e44c9a00fd6c1c34e07955d9a8327.RData b/inst/vign/vigncache/unnamed-chunk-14_e29e44c9a00fd6c1c34e07955d9a8327.RData
diff --git a/vignettes/traits_intro.Rmd b/vignettes/traits_intro.Rmd
@@ -69,75 +69,6 @@ salix %>%
 #> 4                 Salix viminalis Vcmax 43.04 19.99 61.29 8
 ```
 
-Single trait
-
-
-```r
-betydb_trait(id = 10)
-#> $created_at
-#> NULL
-#> 
-#> $description
-#> [1] "Leaf Percent Nitrogen"
-#> 
-#> $id
-#> [1] 10
-#> 
-#> $label
-#> NULL
-#> 
-#> $max
-#> [1] "10"
-#> 
-#> $min
-#> [1] "0.02"
-#> 
-#> $name
-#> [1] "leafN"
-#> 
-#> $notes
-#> [1] ""
-#> 
-#> $standard_name
-#> NULL
-#> 
-#> $standard_units
-#> NULL
-#> 
-#> $units
-#> [1] "percent"
-#> 
-#> $updated_at
-#> [1] "2011-06-06T09:40:42-05:00"
-```
-
-All Miscanthus data collected by Becky Arundale 
-
-
-```r
-betydb_search(query = "Miscanthus Arundale")
-#> Source: local data frame [214 x 30]
-#> 
-#>    access_level   author citation_id citation_year       city
-#> 1             4 Arundale         692          2012 Brownstown
-#> 2             4 Arundale         692          2012 Brownstown
-#> 3             4 Arundale         692          2012 Brownstown
-#> 4             4 Arundale         692          2012 Brownstown
-#> 5             4 Arundale         692          2012 Brownstown
-#> 6             4 Arundale         692          2012 Brownstown
-#> 7             4 Arundale         692          2012 Brownstown
-#> 8             4 Arundale         692          2012 Brownstown
-#> 9             4 Arundale         692          2012  Brookings
-#> 10            4 Arundale         692          2012  Brookings
-#> ..          ...      ...         ...           ...        ...
-#> Variables not shown: commonname (chr), cultivar_id (int), date (chr),
-#>   dateloc (chr), genus (chr), id (int), lat (dbl), lon (dbl), mean (chr),
-#>   month (dbl), n (int), notes (chr), result_type (chr), scientificname
-#>   (chr), site_id (int), sitename (chr), species_id (int), stat (chr),
-#>   statname (chr), trait (chr), trait_description (chr), treatment (chr),
-#>   treatment_id (int), units (chr), year (dbl)
-```
-
 ## NCBI sequence data
 
 Get sequences by id