get_publications: Get publication information for Neotoma records

In neotoma2: Working with the Neotoma Paleoecology Database

Get publication information for Neotoma records

Description

Uses the Neotoma API to search and access information about publications associated with data in the Neotoma Paleoecology Database

Usage

get_publications(x = NA, ...)

## Default S3 method:
get_publications(...)

## S3 method for class 'numeric'
get_publications(x, ...)

## S3 method for class 'publication'
get_publications(x, ...)

## S3 method for class 'publications'
get_publications(x, ...)

## S3 method for class 'sites'
get_publications(x, ...)

Arguments

x

integer A contact ID

...

publicationid The unique numeric identifier associated with a publication in Neotoma. datasetid A unique identifier for a Neotoma dataset that is associated with a publication. familyname The full or partial last name for an individual author. pubtype The publication type, from get_tables("publicationtypes"). year The year the publication was released. search A plain text search string used to search the citation.

Value

publications object

Examples

# How old are the papers in Neotoma that include the term "mammut"?
tryCatch({
  mammoth_papers <- get_publications(search="mammut") %>%
    as.data.frame()
  hist(as.numeric(mammoth_papers$year))
}, error = function(e) {
 message("Neotoma server not responding. Try again later.")
})
# We want the paper identified in Neotoma as 666:
tryCatch({
get_publications(666)
}, error = function(e) {
message("Neotoma server not responding. Try again later.")
})
# Take a publication object and purposely degrade the metadata:
tryCatch({
  bad_pub <- get_publications(666)
  # Note this only changes the reported year, not the citation string.
  bad_pub[[1]]@year <- "1923"
  bad_pub[[1]]@publicationid <- NA_integer_
  updated_pubs <- get_publications(bad_pub[[1]])
  attr(updated_pubs, "matches")
  # we see the proper citation in the record:
  updated_pubs <- attr(updated_pubs, "matches")[[3]]
}, error = function(e) {
 message("Neotoma server not responding. Try again later.")
})

neotoma2 documentation built on Dec. 6, 2025, 5:07 p.m.