Skip to content

Commit

Permalink
updated news, rebuilt vignettes with knitr::knitr, hopefully fixes vi…
Browse files Browse the repository at this point in the history 
…gnette checking
  • Loading branch information
@sckott
sckott committed Apr 16, 2014
1 parent 5d086b3 commit 6025e24
Show file tree
Hide file tree
Showing 15 changed files with 108 additions and 107 deletions.
3 changes: 2 additions & 1 deletion NEWS
View file
Expand Up @@ -6,6 +6,7 @@ BUG FIXES
* A number of variables changed names to better follow the Darwin Core standard. `latitude` is now `decimalLatitude`. `longitude` is now `decimalLongitude`. `clazz` is now `class`. Code in this package changed to accomodate these changes. `date` is now `eventDate`. `georeferenced` is now `hasCoordinate`. Beware of these changes in your own code using `rgbif` - find and replace for these should be easy.
* Changed `altitude` parameter in `occ_search()` to `elevation` - should have been `elevation` the whole time.
* `occ_count()` function with parameter changes: `nubKey` parameter in changed to `taxonKey`. New parameter `protocol`. Parameter `catalogNumber` gone. Parameter `hostCountry` gone. These parameters are still in the function definition, but if called they throw a useful warning telling you the correct parameter names. (#76)
* Fixed bug in `name_lookup()` function that was labeling facet outputs incorrectly. (#77)

IMPROVEMENTS

Expand All @@ -14,7 +15,7 @@ IMPROVEMENTS
* Now using assertthat package in various places to give better error messages when the wrong input is passed to a function.
* Four parameters have name changes in the `occ_search()` function. These parameters are still in the function definition, but if called they throw a useful warning telling you the correct parameter names. (#75)
* Updated docs in `name_usage`, `name_backbone`, `name_lookup`, and `name_suggest` functions.
*
* `sourceId` parameter in `name_usage()` function doesn't work so error message is thrown when used.

NEW FEATURES

Expand Down
Binary file modified inst/vign/figure/occurrencelist_many.png
View file
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
2 changes: 1 addition & 1 deletion inst/vign/rgbif_vignette.Rmd
View file
@@ -1,5 +1,5 @@
<!--
%\VignetteEngine{knitr}
%\VignetteEngine{knitr::knitr}
%\VignetteIndexEntry{Tutorial for the new GBIF API}
-->

Expand Down
2 changes: 1 addition & 1 deletion inst/vign/rgbif_vignette.md
View file
@@ -1,5 +1,5 @@
<!--
%\VignetteEngine{knitr}
%\VignetteEngine{knitr::knitr}
%\VignetteIndexEntry{Tutorial for the new GBIF API}
-->

Expand Down
2 changes: 1 addition & 1 deletion inst/vign/rgbif_vignette_oldapi.Rmd
View file
@@ -1,5 +1,5 @@
<!--
%\VignetteEngine{knitr}
%\VignetteEngine{knitr::knitr}
%\VignetteIndexEntry{Tutorial for using the old GBIF API}
-->

Expand Down
50 changes: 25 additions & 25 deletions inst/vign/rgbif_vignette_oldapi.md
View file
@@ -1,5 +1,5 @@
<!--
%\VignetteEngine{knitr}
%\VignetteEngine{knitr::knitr}
%\VignetteIndexEntry{Tutorial for using the old GBIF API}
-->

Expand Down Expand Up @@ -99,38 +99,38 @@ gbifdata(dat)

```
taxonName occurrenceID country decimalLatitude
1 Accipiter erythronemius 699417490 Guyana 5.267
2 Accipiter erythronemius 686297260 Guyana 5.267
3 Accipiter erythronemius 621073310 Argentina -27.352
4 Accipiter erythronemius 621073311 Argentina -27.352
5 Accipiter erythronemius 699199204 Argentina -25.861
6 Accipiter erythronemius 699199195 Argentina -25.861
7 Accipiter erythronemius 621073312 Argentina -27.352
8 Accipiter erythronemius 699199198 Argentina -25.911
9 Accipiter erythronemius 213206174 W. Colombia 3.767
10 Accipiter erythronemius 352220558 Argentina -31.133
1 Accipiter erythronemius 352220558 Argentina -31.133
2 Accipiter erythronemius 213206174 W. Colombia 3.767
3 Accipiter erythronemius 699199195 Argentina -25.861
4 Accipiter erythronemius 699199198 Argentina -25.911
5 Accipiter erythronemius 621073311 Argentina -27.352
6 Accipiter erythronemius 621073312 Argentina -27.352
7 Accipiter erythronemius 621073310 Argentina -27.352
8 Accipiter erythronemius 699199204 Argentina -25.861
9 Accipiter erythronemius 699417490 Guyana 5.267
10 Accipiter erythronemius 686297260 Guyana 5.267
decimalLongitude catalogNumber earliestDateCollected
1 -60.73 3998 2001-04-03
2 -60.73 93439 2001-04-03
3 -65.60 42229 <NA>
4 -65.60 42228 <NA>
5 -54.52 38015 <NA>
6 -54.52 39196 <NA>
7 -65.60 42227 <NA>
8 -54.36 38199 <NA>
9 -76.75 Skin-470489 <NA>
10 -59.02 YPM ORN 065671 1961-04-30
1 -59.02 YPM ORN 065671 1961-04-30
2 -76.75 Skin-470489 <NA>
3 -54.52 39196 <NA>
4 -54.36 38199 <NA>
5 -65.60 42228 <NA>
6 -65.60 42227 <NA>
7 -65.60 42229 <NA>
8 -54.52 38015 <NA>
9 -60.73 3998 2001-04-03
10 -60.73 93439 2001-04-03
latestDateCollected
1 2001-04-03
2 2001-04-03
1 1961-04-30
2 <NA>
3 <NA>
4 <NA>
5 <NA>
6 <NA>
7 <NA>
8 <NA>
9 <NA>
10 1961-04-30
9 2001-04-03
10 2001-04-03
```


Expand Down
Binary file modified vignettes/figure/occurrencelist_many.png
View file
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
2 changes: 1 addition & 1 deletion vignettes/rgbif_vignette.Rmd
View file
@@ -1,5 +1,5 @@
<!--
%\VignetteEngine{knitr}
%\VignetteEngine{knitr::knitr}
%\VignetteIndexEntry{Tutorial for the new GBIF API}
-->

Expand Down
2 changes: 1 addition & 1 deletion vignettes/rgbif_vignette.html
View file
Expand Up @@ -29,7 +29,7 @@
</head>
<body>
<!--
%\VignetteEngine{knitr}
%\VignetteEngine{knitr::knitr}
%\VignetteIndexEntry{Tutorial for the new GBIF API}
-->

Expand Down
2 changes: 1 addition & 1 deletion vignettes/rgbif_vignette.md
View file
@@ -1,5 +1,5 @@
<!--
%\VignetteEngine{knitr}
%\VignetteEngine{knitr::knitr}
%\VignetteIndexEntry{Tutorial for the new GBIF API}
-->

Expand Down
Binary file modified vignettes/rgbif_vignette.pdf
View file
Binary file not shown.
50 changes: 25 additions & 25 deletions vignettes/rgbif_vignette_oldapi.Rmd
View file
@@ -1,5 +1,5 @@
<!--
%\VignetteEngine{knitr}
%\VignetteEngine{knitr::knitr}
%\VignetteIndexEntry{Tutorial for using the old GBIF API}
-->

Expand Down Expand Up @@ -99,38 +99,38 @@ gbifdata(dat)

```
taxonName occurrenceID country decimalLatitude
1 Accipiter erythronemius 699417490 Guyana 5.267
2 Accipiter erythronemius 686297260 Guyana 5.267
3 Accipiter erythronemius 621073310 Argentina -27.352
4 Accipiter erythronemius 621073311 Argentina -27.352
5 Accipiter erythronemius 699199204 Argentina -25.861
6 Accipiter erythronemius 699199195 Argentina -25.861
7 Accipiter erythronemius 621073312 Argentina -27.352
8 Accipiter erythronemius 699199198 Argentina -25.911
9 Accipiter erythronemius 213206174 W. Colombia 3.767
10 Accipiter erythronemius 352220558 Argentina -31.133
1 Accipiter erythronemius 352220558 Argentina -31.133
2 Accipiter erythronemius 213206174 W. Colombia 3.767
3 Accipiter erythronemius 699199195 Argentina -25.861
4 Accipiter erythronemius 699199198 Argentina -25.911
5 Accipiter erythronemius 621073311 Argentina -27.352
6 Accipiter erythronemius 621073312 Argentina -27.352
7 Accipiter erythronemius 621073310 Argentina -27.352
8 Accipiter erythronemius 699199204 Argentina -25.861
9 Accipiter erythronemius 699417490 Guyana 5.267
10 Accipiter erythronemius 686297260 Guyana 5.267
decimalLongitude catalogNumber earliestDateCollected
1 -60.73 3998 2001-04-03
2 -60.73 93439 2001-04-03
3 -65.60 42229 <NA>
4 -65.60 42228 <NA>
5 -54.52 38015 <NA>
6 -54.52 39196 <NA>
7 -65.60 42227 <NA>
8 -54.36 38199 <NA>
9 -76.75 Skin-470489 <NA>
10 -59.02 YPM ORN 065671 1961-04-30
1 -59.02 YPM ORN 065671 1961-04-30
2 -76.75 Skin-470489 <NA>
3 -54.52 39196 <NA>
4 -54.36 38199 <NA>
5 -65.60 42228 <NA>
6 -65.60 42227 <NA>
7 -65.60 42229 <NA>
8 -54.52 38015 <NA>
9 -60.73 3998 2001-04-03
10 -60.73 93439 2001-04-03
latestDateCollected
1 2001-04-03
2 2001-04-03
1 1961-04-30
2 <NA>
3 <NA>
4 <NA>
5 <NA>
6 <NA>
7 <NA>
8 <NA>
9 <NA>
10 1961-04-30
9 2001-04-03
10 2001-04-03
```


Expand Down
50 changes: 25 additions & 25 deletions vignettes/rgbif_vignette_oldapi.html
View file
Expand Up @@ -29,7 +29,7 @@
</head>
<body>
<!--
%\VignetteEngine{knitr}
%\VignetteEngine{knitr::knitr}
%\VignetteIndexEntry{Tutorial for using the old GBIF API}
-->

Expand Down Expand Up @@ -78,38 +78,38 @@ <h2 id="occurrencelist-searches-for-taxon-concept-records-matching-a-range-of-fi
<span class="dt">maxresults =</span> <span class="dv">10</span>)
<span class="kw">gbifdata</span>(dat)</code></pre>
<pre><code> taxonName occurrenceID country decimalLatitude
1 Accipiter erythronemius 699417490 Guyana 5.267
2 Accipiter erythronemius 686297260 Guyana 5.267
3 Accipiter erythronemius 621073310 Argentina -27.352
4 Accipiter erythronemius 621073311 Argentina -27.352
5 Accipiter erythronemius 699199204 Argentina -25.861
6 Accipiter erythronemius 699199195 Argentina -25.861
7 Accipiter erythronemius 621073312 Argentina -27.352
8 Accipiter erythronemius 699199198 Argentina -25.911
9 Accipiter erythronemius 213206174 W. Colombia 3.767
10 Accipiter erythronemius 352220558 Argentina -31.133
1 Accipiter erythronemius 352220558 Argentina -31.133
2 Accipiter erythronemius 213206174 W. Colombia 3.767
3 Accipiter erythronemius 699199195 Argentina -25.861
4 Accipiter erythronemius 699199198 Argentina -25.911
5 Accipiter erythronemius 621073311 Argentina -27.352
6 Accipiter erythronemius 621073312 Argentina -27.352
7 Accipiter erythronemius 621073310 Argentina -27.352
8 Accipiter erythronemius 699199204 Argentina -25.861
9 Accipiter erythronemius 699417490 Guyana 5.267
10 Accipiter erythronemius 686297260 Guyana 5.267
decimalLongitude catalogNumber earliestDateCollected
1 -60.73 3998 2001-04-03
2 -60.73 93439 2001-04-03
3 -65.60 42229 &lt;NA&gt;
4 -65.60 42228 &lt;NA&gt;
5 -54.52 38015 &lt;NA&gt;
6 -54.52 39196 &lt;NA&gt;
7 -65.60 42227 &lt;NA&gt;
8 -54.36 38199 &lt;NA&gt;
9 -76.75 Skin-470489 &lt;NA&gt;
10 -59.02 YPM ORN 065671 1961-04-30
1 -59.02 YPM ORN 065671 1961-04-30
2 -76.75 Skin-470489 &lt;NA&gt;
3 -54.52 39196 &lt;NA&gt;
4 -54.36 38199 &lt;NA&gt;
5 -65.60 42228 &lt;NA&gt;
6 -65.60 42227 &lt;NA&gt;
7 -65.60 42229 &lt;NA&gt;
8 -54.52 38015 &lt;NA&gt;
9 -60.73 3998 2001-04-03
10 -60.73 93439 2001-04-03
latestDateCollected
1 2001-04-03
2 2001-04-03
1 1961-04-30
2 &lt;NA&gt;
3 &lt;NA&gt;
4 &lt;NA&gt;
5 &lt;NA&gt;
6 &lt;NA&gt;
7 &lt;NA&gt;
8 &lt;NA&gt;
9 &lt;NA&gt;
10 1961-04-30</code></pre>
9 2001-04-03
10 2001-04-03</code></pre>
<p>Search for many species and make a map</p>
<pre class="sourceCode r"><code class="sourceCode r">splist &lt;-<span class="st"> </span><span class="kw">c</span>(<span class="st">&quot;Accipiter erythronemius&quot;</span>, <span class="st">&quot;Junco hyemalis&quot;</span>, <span class="st">&quot;Aix sponsa&quot;</span>)
out &lt;-<span class="st"> </span><span class="kw">occurrencelist_many</span>(splist, <span class="dt">coordinatestatus =</span> <span class="ot">TRUE</span>, <span class="dt">maxresults =</span> <span class="dv">20</span>)
Expand Down
50 changes: 25 additions & 25 deletions vignettes/rgbif_vignette_oldapi.md
View file
@@ -1,5 +1,5 @@
<!--
%\VignetteEngine{knitr}
%\VignetteEngine{knitr::knitr}
%\VignetteIndexEntry{Tutorial for using the old GBIF API}
-->

Expand Down Expand Up @@ -99,38 +99,38 @@ gbifdata(dat)

```
taxonName occurrenceID country decimalLatitude
1 Accipiter erythronemius 699417490 Guyana 5.267
2 Accipiter erythronemius 686297260 Guyana 5.267
3 Accipiter erythronemius 621073310 Argentina -27.352
4 Accipiter erythronemius 621073311 Argentina -27.352
5 Accipiter erythronemius 699199204 Argentina -25.861
6 Accipiter erythronemius 699199195 Argentina -25.861
7 Accipiter erythronemius 621073312 Argentina -27.352
8 Accipiter erythronemius 699199198 Argentina -25.911
9 Accipiter erythronemius 213206174 W. Colombia 3.767
10 Accipiter erythronemius 352220558 Argentina -31.133
1 Accipiter erythronemius 352220558 Argentina -31.133
2 Accipiter erythronemius 213206174 W. Colombia 3.767
3 Accipiter erythronemius 699199195 Argentina -25.861
4 Accipiter erythronemius 699199198 Argentina -25.911
5 Accipiter erythronemius 621073311 Argentina -27.352
6 Accipiter erythronemius 621073312 Argentina -27.352
7 Accipiter erythronemius 621073310 Argentina -27.352
8 Accipiter erythronemius 699199204 Argentina -25.861
9 Accipiter erythronemius 699417490 Guyana 5.267
10 Accipiter erythronemius 686297260 Guyana 5.267
decimalLongitude catalogNumber earliestDateCollected
1 -60.73 3998 2001-04-03
2 -60.73 93439 2001-04-03
3 -65.60 42229 <NA>
4 -65.60 42228 <NA>
5 -54.52 38015 <NA>
6 -54.52 39196 <NA>
7 -65.60 42227 <NA>
8 -54.36 38199 <NA>
9 -76.75 Skin-470489 <NA>
10 -59.02 YPM ORN 065671 1961-04-30
1 -59.02 YPM ORN 065671 1961-04-30
2 -76.75 Skin-470489 <NA>
3 -54.52 39196 <NA>
4 -54.36 38199 <NA>
5 -65.60 42228 <NA>
6 -65.60 42227 <NA>
7 -65.60 42229 <NA>
8 -54.52 38015 <NA>
9 -60.73 3998 2001-04-03
10 -60.73 93439 2001-04-03
latestDateCollected
1 2001-04-03
2 2001-04-03
1 1961-04-30
2 <NA>
3 <NA>
4 <NA>
5 <NA>
6 <NA>
7 <NA>
8 <NA>
9 <NA>
10 1961-04-30
9 2001-04-03
10 2001-04-03
```


Expand Down
Binary file modified vignettes/rgbif_vignette_oldapi.pdf
View file
Binary file not shown.

0 comments on commit 6025e24

Please sign in to comment.