Nothing
## ----setup, include=FALSE-----------------------------------------------------
library(ape)
library(occCite)
knitr::opts_chunk$set(echo = TRUE, error = TRUE)
knitr::opts_knit$set(root.dir = system.file('extdata/', package='occCite'))
## ----simple_search, eval=F----------------------------------------------------
# # Simple search
# myOldOccCiteObject <- occQuery(x = "Protea cynaroides",
# datasources = c("gbif", "bien"),
# GBIFLogin = GBIFLogin,
# GBIFDownloadDirectory =
# system.file('extdata/', package='occCite'),
# checkPreviousGBIFDownload = T)
## ----simple_search sssssecret cooking show, eval=T, echo = F------------------
# Simple search
data(myOccCiteObject)
myOldOccCiteObject <- myOccCiteObject
## ----simple_search_loaded_GBIF_results----------------------------------------
#GBIF search results
head(myOldOccCiteObject@occResults$`Protea cynaroides`$GBIF$OccurrenceTable);
#The full summary
summary(myOldOccCiteObject)
## ----getting_citations_from_already-downloaded_GBIF_data----------------------
#Get citations
myOldOccCitations <- occCitation(myOldOccCiteObject)
print(myOldOccCitations)
## ----multispecies_search_with_phylogeny, eval=T, echo=T-----------------------
library(ape)
#Get tree
treeFile <- system.file("extdata/Fish_12Tax_time_calibrated.tre", package='occCite')
phylogeny <- ape::read.nexus(treeFile)
tree <- ape::extract.clade(phylogeny, 22)
#Query databases for names
myPhyOccCiteObject <- studyTaxonList(x = tree,
datasources = "GBIF Backbone Taxonomy")
#Query GBIF for occurrence data
myPhyOccCiteObject <- occQuery(x = myPhyOccCiteObject,
datasources = "gbif",
GBIFDownloadDirectory = system.file('extdata/', package='occCite'),
loadLocalGBIFDownload = T,
checkPreviousGBIFDownload = F)
# What does a multispecies query look like?
summary(myPhyOccCiteObject)
## ----plotting all species, eval=T, message=FALSE, warning=FALSE, paged.print=FALSE, results='hide', fig.hold='hold', out.width="100%"----
plot(myPhyOccCiteObject)
## ----plotting phylogenetic search by species, eval=T, message=FALSE, warning=FALSE, paged.print=FALSE, results='hide', fig.hold='hold', out.width="100%"----
plot(myPhyOccCiteObject, bySpecies = T, plotTypes = c("yearHistogram", "source"))
## ----getting_citations_for_a_multispecies_search, echo=T----------------------
#Get citations
myPhyOccCitations <- occCitation(myPhyOccCiteObject)
#Print citations as text with accession dates.
print(myPhyOccCitations, bySpecies = T)
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