|
add_chronology()
|
Add a new chronology into an existing collectionunit. |
|
as.data.frame(<chronology>) as.data.frame(<chronologies>) as.data.frame(<collunit>) as.data.frame(<collunits>) as.data.frame(<contact>) as.data.frame(<contacts>) as.data.frame(<dataset>) as.data.frame(<datasets>) as.data.frame(<authors>) as.data.frame(<publication>) as.data.frame(<publications>) as.data.frame(<site>) as.data.frame(<sites>) as.data.frame(<speleothem>) as.data.frame(<speleothems>) as.data.frame(<taxon>) as.data.frame(<taxa>)
|
as.data.frame |
|
author_classes author-class authors-class
|
An S4 class for the authors of a Neotoma publication. |
|
c(<chronologies>) c(<collunits>) c(<contacts>) c(<contact>) c(<datasets>) c(<publications>) c(<samples>) c(<sites>) c(<missingOrNULL>) c(<speleothems>) c(<taxa>)
|
c - Combine neotoma2 objects |
|
`$<-`(<chronology>) `$<-`(<collunit>) `$<-`(<dataset>) `$<-`(<site>) `$<-`(<speleothem>) `$<-`(<taxon>)
|
cash-set |
|
`$`(<chronology>) `$`(<chronologies>) `$`(<collunit>) `$`(<collunits>) `$`(<contact>) `$`(<contacts>) `$`(<dataset>) `$`(<datasets>) `$`(<publication>) `$`(<samples>) `$`(<sample>) `$`(<site>) `$`(<sites>) `$`(<speleothem>) `$`(<speleothems>) `$`(<taxon>) `$`(<taxa>)
|
cash |
|
check_contacts()
|
Check contact information for a record against Neotoma contributors |
|
chroncontrols(<site>)
|
Recover information about the chron controls for a collectionunit. |
|
chroncontrols(<sites>)
|
Recover information about the chron controls for a collectionunit. |
|
chroncontrols()
|
chroncontrols |
|
chronologies(<collunit>)
|
Extract chronologies from a sites or collunits object. |
|
chronologies()
|
Obtain the chronology from a record or multiple records. |
|
chronologies_classes chronology-class chronologies-class
|
S4 class for chronologies information |
|
cite_data(<sites>)
|
Obtain data citations from multiple records. |
|
cite_data()
|
Generate a data citation from a Neotoma2 object. |
|
clean()
|
clean Neotoma objects to remove duplicates and empty objects. |
|
collunits(<sites>)
|
Extract collunits from a sites object. |
|
collunits()
|
Extract collection units from a sites object |
|
collunits_classes collunit-class collunits-class
|
S4 class for collection units information. |
|
contacts_classes contact-class contacts-class
|
An S4 class for multi-contact information from the Neotoma Paleoecology Database. |
|
coordinates(<sites>)
|
Return the latitude and longitude of sites |
|
coordinates()
|
Obtain coordinates from a sites object. |
|
datasets(<collunits>)
|
Extract datasets from a sites or collunits object. |
|
datasets()
|
Extract datasets from a sites object. |
|
dataset-class datasets-class
|
S4 class for datasets information |
|
doi(<sites>)
|
Obtain dataset DOIs from records. |
|
doi()
|
Obtain the DOI for publications or datasets. |
|
filter()
|
Apply a filter for Neotoma sites objects. |
|
get_contacts()
|
Get contact information for Neotoma contributors |
|
get_datasets()
|
get_datasets |
|
get_documentation()
|
get_documentation |
|
get_downloads()
|
get_downloads |
|
get_manual()
|
get_manual |
|
get_publications()
|
Get publication information for Neotoma records |
|
get_sites()
|
get_sites |
|
get_speleothems()
|
get_speleothems |
|
get_stats()
|
get_stats |
|
get_table()
|
Get table record from Neotoma |
|
get_taxa()
|
get_taxa |
|
get_taxon()
|
get_taxon |
|
getids()
|
Get object IDs |
|
length(<chronologies>) length(<collunits>) length(<contacts>) length(<datasets>) length(<publications>) length(<samples>) length(<sites>) length(<speleothems>) length(<taxa>)
|
length |
|
missingOrNULL-class
|
c Method - Combine objects, including NULL |
|
names(<collunit>) names(<contact>) names(<dataset>) names(<publication>) names(<publications>) names(<site>) names(<sites>) names(<speleothem>) names(<taxon>)
|
Get a neotoma2 object's slot names |
|
pingNeotoma()
|
pingNeotoma |
|
plot(<sites>) plot(<site>)
|
Plot site coordinates using a basic plot. |
|
plotLeaflet(<sites>)
|
plotLeaflet |
|
plotLeaflet()
|
plotLeaflet |
|
publications_classes publication-class publications-class
|
An S4 class for Neotoma publications. |
|
repositories_classes repository-class repositories-class
|
S4 class for repository information |
|
samples(<sites>)
|
samples |
|
samples()
|
Obtain samples from a record or multiple records. |
|
samples_classes sample-class samples-class
|
S4 class for samples information |
|
set_chronology()
|
set chronology information for a new record. |
|
set_collunit()
|
set Site Information for Fossil Sites |
|
set_contact()
|
Set contact information for a new record. |
|
set_dataset()
|
set Site Information for Fossil Sites |
|
set_default(<chronologies>)
|
Change the default age model for a record. |
|
set_default()
|
Set the default chronology within a collectionunit. |
|
set_publication()
|
Create a new publication (or publication set) |
|
set_sample()
|
set Sample Information |
|
set_server()
|
Set Neotoma API Source or Server |
|
set_site()
|
set Site Information for Fossil Sites |
|
set_speleothem()
|
Set Speleothem |
|
show(<collunits>) show(<collunit>) show(<contacts>) show(<contact>) show(<dataset>) show(<datasets>) show(<publications>) show(<publication>) show(<site>) show(<sites>) show(<speleothem>) show(<speleothems>) show(<taxon>) show(<taxa>)
|
Display a sites object or nested slots. |
|
sites_classes site-class sites-class
|
An S4 class for sites information |
|
specimens_classes specimen-class specimens-class
|
S4 class for specimens information |
|
speleothemdetails(<sites>)
|
speleothemdetails |
|
speleothemdetails()
|
Obtain speleothems and samples from a record or multiple records. |
|
speleothems(<sites>)
|
speleothems |
|
speleothems()
|
Obtain speleothems from a record or multiple records. |
|
speleothems_classes speleothem-class speleothems-class
|
S4 class for speleothem information |
|
`[[`(<chronologies>,<numeric>) `[[`(<collunits>,<numeric>) `[[`(<contacts>,<numeric>) `[[`(<datasets>,<numeric>) `[[`(<publications>,<numeric>) `[[`(<samples>,<numeric>) `[[`(<sites>,<numeric>) `[[`(<speleothems>,<numeric>) `[[`(<taxa>,<numeric>)
|
sub-sub |
|
`[[<-`(<collunits>) `[[<-`(<datasets>) `[[<-`(<publications>) `[[<-`(<samples>) `[[<-`(<sites>) `[[<-`(<speleothems>) `[[<-`(<taxa>)
|
sub-subset |
|
`[`(<collunits>,<numeric>) `[`(<datasets>,<numeric>) `[`(<sites>,<numeric>) `[`(<site>,<numeric>) `[`(<site>,<character>) `[`(<speleothems>,<numeric>) `[`(<taxa>,<numeric>)
|
sub |
|
`[<-`(<collunit>,<character>) `[<-`(<collunit>,<numeric>) `[<-`(<dataset>,<character>) `[<-`(<dataset>,<numeric>) `[<-`(<sample>,<character>) `[<-`(<site>,<character>) `[<-`(<site>,<numeric>) `[<-`(<speleothem>,<character>) `[<-`(<speleothem>,<numeric>) `[<-`(<taxon>,<character>) `[<-`(<taxon>,<numeric>)
|
subset |
|
summary(<sites>)
|
Summary of objects within a sites object. |
|
taxa(<sites>)
|
Extract taxonomic data from a set of sites. |
|
taxa()
|
taxa |
|
taxa_classes taxon-class taxa-class
|
S4 class for taxa information |
|
toWide()
|
toWide |