table_articles_byAuth | R Documentation |
Extract Publication Info from PubMed records and cast data into a data.frame where each row corresponds to a different author. It is possible to limit data extraction to first authors or last authors only, or get information about all authors of each PubMed record.
table_articles_byAuth(
pubmed_data,
included_authors = "all",
max_chars = 500,
autofill = TRUE,
dest_file = NULL,
getKeywords = TRUE,
encoding = "UTF8"
)
pubmed_data |
PubMed Data in XML format: typically, an XML file resulting from a batch_pubmed_download() call or an XML object, result of a fetch_pubmed_data() call. |
included_authors |
Character: c("first", "last", "all"). Only includes information from the first, the last or all authors of a PubMed record. |
max_chars |
This argument is ignored. In this version of the function, the whole Abstract Text is returned. |
autofill |
Logical. If TRUE, missing affiliations are imputed according to the available values (from the same article). |
dest_file |
String (character of length 1). Name of the file that will be written for storing the output. If NULL, no file will be saved. |
getKeywords |
This argument is ignored. In this version of the function MeSH terms and codes (i.e., keywords) are parsed by default. |
encoding |
The encoding of an input/output connection can be specified by name (for example, "ASCII", or "UTF-8", in the same way as it would be given to the function base::iconv(). See iconv() help page for how to find out more about encodings that can be used on your platform. Here, we recommend using "UTF-8". |
The 'table_articles_byAuth()' function is now obsolete. You should use the 'epm_parse()' function instead. Please, have a look at the manual or the vignette. The 'table_articles_byAuth()' function will be retired in the second half of 2024.
Data frame including the following fields: 'c("pmid", "doi", "title", "abstract", "year", "month", "day", "jabbrv", "journal", "keywords", "mesh", "lastname", "firstname", "address", "email")'.
Damiano Fantini damiano.fantini@gmail.com
https://www.data-pulse.com/dev_site/easypubmed/
# Note: a time limit can be set in order to kill the operation when/if
# the NCBI/Entrez server becomes unresponsive.
setTimeLimit(elapsed = 4.9)
try({
q0 <- 'Damiano Fantini[AU] AND "2018"[PDAT]'
q1 <- easyPubMed::get_pubmed_ids(pubmed_query_string = q0)
q2 <- fetch_pubmed_data(pubmed_id_list = q1)
df <- table_articles_byAuth(q2, included_authors = 'first')
df[, c('pmid', 'lastname', 'jabbrv', 'year', 'month', 'day')]
}, silent = TRUE)
setTimeLimit(elapsed = Inf)
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