added vignettes to vignettes folder from inst/vign

Makefile

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+all: move pandoc rmd2md
+
+vignettes: 
+		cd inst/vign;\
+		Rscript -e 'library(knitr); knit("rgbif_vignette.Rmd"); knit("rgbif_vignette.Rmd")'
+		Rscript -e 'library(knitr); knit("rgbif_vignette_oldapi.Rmd"); knit("rgbif_vignette_oldapi.Rmd")'
+
+move:
+		cp inst/vign/rgbif_vignette.md vignettes;\
+		cp inst/vign/rgbif_vignette_oldapi.md vignettes;\
+		cp -r inst/vign/figure/ vignettes/figure/
+
+pandoc:
+		cd vignettes;\
+		pandoc -H margins.sty rgbif_vignette.md -o rgbif_vignette.html;\
+		pandoc -H margins.sty rgbif_vignette.md -o rgbif_vignette.pdf;\
+		pandoc -H margins.sty rgbif_vignette_oldapi.md -o rgbif_vignette_oldapi.html;\
+		pandoc -H margins.sty rgbif_vignette_oldapi.md -o rgbif_vignette_oldapi.pdf
+
+rmd2md:
+		cd vignettes;\
+		cp rgbif_vignette.md rgbif_vignette.Rmd;\
+		cp rgbif_vignette_oldapi.md rgbif_vignette_oldapi.Rmd
+
+cleanup:
+		cd inst/vign;\
+		rm rgbif_vignette.md rgbif_vignette_oldapi.md
+		rm -r vignettes/figure/

inst/vign/cache/__packages

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+base
+bitops
+ggplot2
+knitr
+maps
+plyr
+RCurl
+rgbif
+rjson
+XML

inst/vign/rgbif_vignette.Rmd

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+<!--
+%\VignetteEngine{knitr}
+%\VignetteIndexEntry{Tutorial for the new GBIF API}
+-->
+
+rgbif vignette - Seach and retrieve data from the Global Biodiverity Information Facilty (GBIF)
+======
+
+## About the package
+
+`rgbif` is an R package to search and retrieve data from the Global Biodiverity Information Facilty (GBIF). `rgbif` wraps R code around the [GBIF API][gbifapi] to allow you to talk to GBIF from R. 
+
+********************
+
+## Install rgbif and dependencies
+
+```{r install, eval=FALSE}
+install.packages("rgbif")
+```
+
+## Load rgbif and dependencies
+
+```{r load, comment=NA, warning=FALSE, message=FALSE}
+library(rgbif); library(XML); library(RCurl); library(plyr); library(ggplot2); library(maps)
+```
+
+********************
+
+## Get number of occurrences for a set of search parameters
+
+### Search by type of record, all observational in this case
+
+```{r occ_count1, comment=NA, warning=FALSE, message=FALSE, cache=TRUE}
+occ_count(basisOfRecord='OBSERVATION')
+```
+
+### Records for **Puma concolor** with lat/long data (georeferened) only
+
+```{r occ_count2, comment=NA, warning=FALSE, message=FALSE, cache=TRUE}
+occ_count(nubKey=2435099, georeferenced=TRUE)
+```
+
+### All georeferenced records in GBIF
+
+```{r occ_count3, comment=NA, warning=FALSE, message=FALSE, cache=TRUE}
+occ_count(georeferenced=TRUE)
+```
+
+### Records from Denmark
+
+```{r occ_count4, comment=NA, warning=FALSE, message=FALSE, cache=TRUE}
+occ_count(country='DENMARK')
+```
+
+### Records from France
+
+```{r occ_count5, comment=NA, warning=FALSE, message=FALSE, cache=TRUE}
+occ_count(hostCountry='FRANCE')
+```
+
+### Number of records in a particular dataset
+
+```{r occ_count6, comment=NA, warning=FALSE, message=FALSE, cache=TRUE}
+occ_count(datasetKey='9e7ea106-0bf8-4087-bb61-dfe4f29e0f17')
+```
+
+### All records from 2012
+
+```{r occ_count7, comment=NA, warning=FALSE, message=FALSE, cache=TRUE}
+occ_count(year=2012)
+```
+
+### Records for a particular dataset, and only for preserved specimens
+
+```{r occ_count8, comment=NA, warning=FALSE, message=FALSE, cache=TRUE}
+occ_count(datasetKey='8626bd3a-f762-11e1-a439-00145eb45e9a', basisOfRecord='PRESERVED_SPECIMEN')
+```
+
+********************
+
+## Get possible values to be used in taxonomic rank arguments in functions
+
+```{r taxrank, comment=NA, warning=FALSE, message=FALSE, cache=TRUE}
+taxrank()
+```
+
+********************
+
+## Search for taxon information
+
+### Search for a genus 
+
+```{r name_lookup1, comment=NA, warning=FALSE, message=FALSE}
+head(name_lookup(query='Cnaemidophorus', rank="genus", return="data"))
+```
+
+### Search for the class mammalia
+
+```{r name_lookup2, comment=NA, warning=FALSE, message=FALSE}
+head(name_lookup(query='mammalia')$data)
+```
+
+### Look up the species Helianthus annuus
+
+```{r name_lookup3, comment=NA, warning=FALSE, message=FALSE}
+head(name_lookup('Helianthus annuus', rank="species")$data)
+```
+
+********************
+
+## Get data for a single occurrence. Note that data is returned as a list, with slots for metadata and data, or as a hierarchy, or just data.
+
+### Just data 
+
+```{r occ_get1, comment=NA, warning=FALSE, message=FALSE, cache=TRUE}
+occ_get(key=773433533, return='data')
+```
+
+### Just taxonomic hierarchy
+
+```{r occ_get2, comment=NA, warning=FALSE, message=FALSE, cache=TRUE}
+occ_get(key=773433533, return='hier')
+```
+
+### All data, or leave return parameter blank
+
+```{r occ_get3, comment=NA, warning=FALSE, message=FALSE, cache=TRUE}
+occ_get(key=773433533, return='all')
+```
+
+### Get many occurrences. `occ_get` is vectorized
+
+```{r occ_get4, comment=NA, warning=FALSE, message=FALSE, cache=TRUE}
+occ_get(key=c(773433533,101010,240713150,855998194,49819470), return='data')
+```
+
+********************
+
+## Maps
+
+### Static map using the ggplot2 package
+
+Make a map of **Puma concolor** occurrences
+
+```{r gbifmap1, comment=NA, warning=FALSE, message=FALSE, cache=TRUE}
+key <- name_backbone(name='Puma concolor', kingdom='plants')$speciesKey
+dat <- occ_search(taxonKey=key, return='data', limit=300, minimal=FALSE)
+gbifmap(input=dat)
+```
+
+[gbifapi]: http://data.gbif.org/tutorial/services