easyPubMed (version 2.13)

articles_to_list: Cast PubMed Data into a List of Articles

Description

Convert an XML object of PubMed records into a list of strings (character vector of length 1) corresponding to individual PubMed articles. PubMed records are identified by a "/PubmedArticle" XML tag. This automatically casts all the content of each PubMed record to a character-class object without removing XML tags.

Usage

articles_to_list(pubmed_data, encoding = "UTF8", simplify = TRUE)

Arguments

pubmed_data

String corresponding to the name of an XML file (typically, the result of a batch_pubmed_download() call). Alternatively, a string including PubMed records with XML tags, such as the object returned by a fetch_pubmed_data() call.

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. "UTF-8" is recommended.

simplify

Logical; should the result be simplified to a character vector. If FALSE, results are returned as a list.

Value

List or character vector including all the records from the original XML object in text format. Elements in the list are not named and are only accessible via their numeric index.

Details

The input is an XML object or a string including PubMed records (with XML tags). These are the output of easyPubMed functions: fetch_pubmed_data() or batch_pubmed_download(). The function returns a list or a character vector where each element is a different PubMed record.

References

https://www.data-pulse.com/dev_site/easypubmed/

Examples

# NOT RUN {
try({
  ## Retrieve PubMed data and return a list ot articles
  my_query <- "Damiano Fantini[AU]"
  my_query <- get_pubmed_ids(pubmed_query_string = my_query)
  my_data <- fetch_pubmed_data(my_query, encoding = "ASCII")
  listed_articles <- articles_to_list(my_data)
  custom_grep(listed_articles[[2]], "ArticleTitle", "char")
}, silent = TRUE)

# }
# NOT RUN {
## Download PubMed data and return a list ot articles
dami_query <- "Damiano Fantini[AU] AND 2018[PDAT]"
outfile <- batch_pubmed_download(dami_query, dest_file_prefix = "easyPM_ex001_")
listed_articles <- articles_to_list(pubmed_data = outfile)
custom_grep(listed_articles[[2]], "ArticleTitle", "char")
# }
# NOT RUN {
# }