R/scrap_pubmed.R

In hazirliver/PubmedScraper:

#' @title Main function
#'
#' @param PMID_list A character vector of PMIDs of interesting papers.
#' @param filename_base A character contains path to output and filename base
#' @param n_cites_threshold An integer. The minimum number of papers that a given article should refer to.
#' @param n_refers_treshold An integer. The minimum number of papers that a given article should refer to.
#' @param pubmed_api_key Your pubmed API key.
#'
#'
#' @import reticulate
#' @importFrom rentrez set_entrez_key
#'
#' @return List of two data.frame's. First -- about papers that cites given \code{PMID_list}, second -- about papers on which refer given \code{PMID_list}.
#' @export
#'
scrap_pubmed <- function(PMID_list, filename_base,
                         n_cites_threshold = 2, n_refers_treshold = 2,
                         pubmed_api_key,
                         year_left,
                         year_right = substr(Sys.Date(), 1, 4))
{
  PMID_list <- unique(PMID_list)

  set_entrez_key(pubmed_api_key)

  cit_tab <- graph_foo_citation(PMID_list, filename_base, n_cites_threshold)
  cit_tab_medline <- add_medline(cit_tab)



  references_tab <- graph_foo_references(PMID_list, filename_base, n_refers_treshold)
  references_tab_medline <- add_medline(references_tab)


  similar_tab <- graph_foo_similar(PMID_list,
                                   filename_base,
                                   n_similar_threshold = 1,
                                   year_left,
                                   year_right = substr(Sys.Date(), 1, 4))
  similar_tab_mdeline <- add_medline(similar_tab)

  return(list(`Цитируют` = cit_tab_medline,
              `Ссылаются` = references_tab_medline,
              `Похожие` = similar_tab_mdeline))

}