R/saveDF.R

In sbalci/Pathology-Articles-from-Turkey: Pathology Articles from Turkey

# articles ----

# fetched_articles

names_df_articles <-
  slotNames(fetched_articles)

df_articles <-
  setNames(data.frame(matrix(
    ncol = length(names_df_articles),
    nrow = length(
      slot(
        fetched_articles,
        names_df_articles[2]
      )
    )
  )),
  nm = names_df_articles
  )


df_articles[, "PMID"]              <- fetched_articles@PMID
df_articles[, "YearArticleDate"]   <- fetched_articles@YearArticleDate
df_articles[, "MonthArticleDate"]  <- fetched_articles@MonthArticleDate
df_articles[, "ISSN"]              <- fetched_articles@ISSN
df_articles[, "Title"]             <- fetched_articles@Title
df_articles[, "ArticleTitle"]      <- fetched_articles@ArticleTitle
df_articles[, "ELocationID"]       <- fetched_articles@ELocationID
df_articles[, "AbstractText"]      <- fetched_articles@AbstractText
df_articles[, "Language"]          <- fetched_articles@Language
df_articles[, "MedlineTA"]         <- fetched_articles@MedlineTA
df_articles[, "NlmUniqueID"]       <- fetched_articles@NlmUniqueID
df_articles[, "ISSNLinking"]       <- fetched_articles@ISSNLinking
df_articles[, "PublicationStatus"] <- fetched_articles@PublicationStatus
df_articles[, "ArticleId"]         <- fetched_articles@ArticleId
df_articles[, "DOI"]               <- fetched_articles@DOI
df_articles[, "Volume"]            <- fetched_articles@Volume
df_articles[, "Issue"]             <- fetched_articles@Issue
df_articles[, "ISOAbbreviation"]   <- fetched_articles@ISOAbbreviation

df_articles <- df_articles[, c(
  "PMID",
  "YearArticleDate",
  "MonthArticleDate",
  "ISSN",
  "Title",
  "ArticleTitle",
  "ELocationID",
  "AbstractText",
  "Language",
  "MedlineTA",
  "NlmUniqueID",
  "ISSNLinking",
  "PublicationStatus",
  "ArticleId",
  "DOI",
  "Volume",
  "Issue",
  "ISOAbbreviation"
)]

df_articles[["PMID"]] <- as.character(df_articles[["PMID"]])

readr::write_csv(x = df_articles,
                 file = "data/articles.txt",
                 # col_names = TRUE,
                 append = TRUE)

df_articles <- readr::read_csv(file = "data/articles.txt", col_names = TRUE)

df_articles <- unique(x = df_articles,
                      fromLast = TRUE
                      )

df_articles <- dplyr::distinct(df_articles,
                                PMID,
                                .keep_all = TRUE
                                )


df_articles[["PMID"]] <- as.character(df_articles[["PMID"]])

exclude_PMIDs <- read.csv(file = "data/exclude_PMIDs.txt",
                                  header = FALSE,
                                  col.names = "PMID",
                                  colClasses = "character"
)

df_articles <- dplyr::anti_join(df_articles, exclude_PMIDs,
                               by = "PMID")

readr::write_csv(x = df_articles,
                 file = "data/articles.txt",
                 col_names = TRUE
)





# # pancreas ----
#
# # fetched_pancreas_articles
#
# names_df_pancreas_articles <-
#   slotNames(fetched_pancreas_articles)
#
# df_pancreas <-
#   setNames(data.frame(matrix(
#     ncol = length(names_df_pancreas_articles),
#     nrow = length(
#       slot(
#         fetched_pancreas_articles,
#         names_df_pancreas_articles[2]
#       )
#     )
#   )),
#   nm = names_df_pancreas_articles
#   )
#
#
# df_pancreas[, "PMID"]              <- fetched_pancreas_articles@PMID
# df_pancreas[, "YearArticleDate"]   <- fetched_pancreas_articles@YearArticleDate
# df_pancreas[, "MonthArticleDate"]  <- fetched_pancreas_articles@MonthArticleDate
# df_pancreas[, "ISSN"]              <- fetched_pancreas_articles@ISSN
# df_pancreas[, "Title"]             <- fetched_pancreas_articles@Title
# df_pancreas[, "ArticleTitle"]      <- fetched_pancreas_articles@ArticleTitle
# df_pancreas[, "ELocationID"]       <- fetched_pancreas_articles@ELocationID
# df_pancreas[, "AbstractText"]      <- fetched_pancreas_articles@AbstractText
# df_pancreas[, "Language"]          <- fetched_pancreas_articles@Language
# df_pancreas[, "MedlineTA"]         <- fetched_pancreas_articles@MedlineTA
# df_pancreas[, "NlmUniqueID"]       <- fetched_pancreas_articles@NlmUniqueID
# df_pancreas[, "ISSNLinking"]       <- fetched_pancreas_articles@ISSNLinking
# df_pancreas[, "PublicationStatus"] <- fetched_pancreas_articles@PublicationStatus
# df_pancreas[, "ArticleId"]         <- fetched_pancreas_articles@ArticleId
# df_pancreas[, "DOI"]               <- fetched_pancreas_articles@DOI
# df_pancreas[, "Volume"]            <- fetched_pancreas_articles@Volume
# df_pancreas[, "Issue"]             <- fetched_pancreas_articles@Issue
# df_pancreas[, "ISOAbbreviation"]   <- fetched_pancreas_articles@ISOAbbreviation
#
# df_pancreas <- df_pancreas[, c(
#   "PMID",
#   "YearArticleDate",
#   "MonthArticleDate",
#   "ISSN",
#   "Title",
#   "ArticleTitle",
#   "ELocationID",
#   "AbstractText",
#   "Language",
#   "MedlineTA",
#   "NlmUniqueID",
#   "ISSNLinking",
#   "PublicationStatus",
#   "ArticleId",
#   "DOI",
#   "Volume",
#   "Issue",
#   "ISOAbbreviation"
# )]
#
# df_pancreas[["PMID"]] <- as.character(df_pancreas[["PMID"]])
#
# readr::write_csv(x = df_pancreas,
#                  file = "data/pancreasarticles.txt",
#                  col_names = TRUE,
#                  append = TRUE)
#
# df_pancreas <- readr::read_csv(file = "data/pancreasarticles.txt", col_names = TRUE)
#
# df_pancreas <- unique(df_pancreas)
#
# df_pancreas[["PMID"]] <- as.character(df_pancreas[["PMID"]])
#
# exclude_pancreas_PMIDs <- read.csv(file = "data/exclude_pancreas_PMIDs.txt",
#                                    header = FALSE,
#                                    col.names = "PMID",
#                                    colClasses = "character"
# )
#
# df_pancreas <- dplyr::anti_join(df_pancreas, exclude_pancreas_PMIDs,
#                                 by = "PMID")
#
# readr::write_csv(x = df_pancreas,
#                  file = "data/pancreasarticles.txt",
#                  col_names = TRUE
# )
#

# # ampulla ----
#
# # fetched_ampulla_articles
#
#
# names_df_ampulla_articles <-
#   slotNames(fetched_ampulla_articles)
#
# df_ampulla <-
#   setNames(data.frame(matrix(
#     ncol = length(names_df_ampulla_articles),
#     nrow = length(
#       slot(
#         fetched_ampulla_articles,
#         names_df_ampulla_articles[2]
#       )
#     )
#   )),
#   nm = names_df_ampulla_articles
#   )
#
#
# df_ampulla[, "PMID"]              <- fetched_ampulla_articles@PMID
# df_ampulla[, "YearArticleDate"]   <- fetched_ampulla_articles@YearArticleDate
# df_ampulla[, "MonthArticleDate"]  <- fetched_ampulla_articles@MonthArticleDate
# df_ampulla[, "ISSN"]              <- fetched_ampulla_articles@ISSN
# df_ampulla[, "Title"]             <- fetched_ampulla_articles@Title
# df_ampulla[, "ArticleTitle"]      <- fetched_ampulla_articles@ArticleTitle
# df_ampulla[, "ELocationID"]       <- fetched_ampulla_articles@ELocationID
# df_ampulla[, "AbstractText"]      <- fetched_ampulla_articles@AbstractText
# df_ampulla[, "Language"]          <- fetched_ampulla_articles@Language
# df_ampulla[, "MedlineTA"]         <- fetched_ampulla_articles@MedlineTA
# df_ampulla[, "NlmUniqueID"]       <- fetched_ampulla_articles@NlmUniqueID
# df_ampulla[, "ISSNLinking"]       <- fetched_ampulla_articles@ISSNLinking
# df_ampulla[, "PublicationStatus"] <- fetched_ampulla_articles@PublicationStatus
# df_ampulla[, "ArticleId"]         <- fetched_ampulla_articles@ArticleId
# df_ampulla[, "DOI"]               <- fetched_ampulla_articles@DOI
# df_ampulla[, "Volume"]            <- fetched_ampulla_articles@Volume
# df_ampulla[, "Issue"]             <- fetched_ampulla_articles@Issue
# df_ampulla[, "ISOAbbreviation"]   <- fetched_ampulla_articles@ISOAbbreviation
#
# df_ampulla <- df_ampulla[, c(
#   "PMID",
#   "YearArticleDate",
#   "MonthArticleDate",
#   "ISSN",
#   "Title",
#   "ArticleTitle",
#   "ELocationID",
#   "AbstractText",
#   "Language",
#   "MedlineTA",
#   "NlmUniqueID",
#   "ISSNLinking",
#   "PublicationStatus",
#   "ArticleId",
#   "DOI",
#   "Volume",
#   "Issue",
#   "ISOAbbreviation"
# )]
#
# df_ampulla[["PMID"]] <- as.character(df_ampulla[["PMID"]])
#
# readr::write_csv(x = df_ampulla,
#                  file = "data/ampullaarticles.txt",
#                  col_names = TRUE,
#                  append = TRUE)
#
# df_ampulla <- readr::read_csv(file = "data/ampullaarticles.txt", col_names = TRUE)
#
# df_ampulla <- unique(df_ampulla)
#
# df_ampulla[["PMID"]] <- as.character(df_ampulla[["PMID"]])
#
# exclude_ampulla_PMIDs <- read.csv(file = "data/exclude_ampulla_PMIDs.txt",
#                                    header = FALSE,
#                                    col.names = "PMID",
#                                    colClasses = "character"
# )
#
# df_ampulla <- dplyr::anti_join(df_ampulla, exclude_ampulla_PMIDs,
#                                by = "PMID")
#
# readr::write_csv(x = df_ampulla,
#                  file = "data/ampullaarticles.txt",
#                  col_names = TRUE
# )
#

# # bileduct ----
#
# # fetched_bileduct_articles
#
#
#
# names_df_bileduct_articles <-
#   slotNames(fetched_bileduct_articles)
#
# df_bd <-
#   setNames(data.frame(matrix(
#     ncol = length(names_df_bileduct_articles),
#     nrow = length(
#       slot(
#         fetched_bileduct_articles,
#         names_df_bileduct_articles[2]
#       )
#     )
#   )),
#   nm = names_df_bileduct_articles
#   )
#
#
# df_bd[, "PMID"]              <- fetched_bileduct_articles@PMID
# df_bd[, "YearArticleDate"]   <- fetched_bileduct_articles@YearArticleDate
# df_bd[, "MonthArticleDate"]  <- fetched_bileduct_articles@MonthArticleDate
# df_bd[, "ISSN"]              <- fetched_bileduct_articles@ISSN
# df_bd[, "Title"]             <- fetched_bileduct_articles@Title
# df_bd[, "ArticleTitle"]      <- fetched_bileduct_articles@ArticleTitle
# df_bd[, "ELocationID"]       <- fetched_bileduct_articles@ELocationID
# df_bd[, "AbstractText"]      <- fetched_bileduct_articles@AbstractText
# df_bd[, "Language"]          <- fetched_bileduct_articles@Language
# df_bd[, "MedlineTA"]         <- fetched_bileduct_articles@MedlineTA
# df_bd[, "NlmUniqueID"]       <- fetched_bileduct_articles@NlmUniqueID
# df_bd[, "ISSNLinking"]       <- fetched_bileduct_articles@ISSNLinking
# df_bd[, "PublicationStatus"] <- fetched_bileduct_articles@PublicationStatus
# df_bd[, "ArticleId"]         <- fetched_bileduct_articles@ArticleId
# df_bd[, "DOI"]               <- fetched_bileduct_articles@DOI
# df_bd[, "Volume"]            <- fetched_bileduct_articles@Volume
# df_bd[, "Issue"]             <- fetched_bileduct_articles@Issue
# df_bd[, "ISOAbbreviation"]   <- fetched_bileduct_articles@ISOAbbreviation
#
# df_bd <- df_bd[, c(
#   "PMID",
#   "YearArticleDate",
#   "MonthArticleDate",
#   "ISSN",
#   "Title",
#   "ArticleTitle",
#   "ELocationID",
#   "AbstractText",
#   "Language",
#   "MedlineTA",
#   "NlmUniqueID",
#   "ISSNLinking",
#   "PublicationStatus",
#   "ArticleId",
#   "DOI",
#   "Volume",
#   "Issue",
#   "ISOAbbreviation"
# )]
#
# df_bd[["PMID"]] <- as.character(df_bd[["PMID"]])
#
# readr::write_csv(x = df_bd,
#                  file = "data/bileductarticles.txt",
#                  col_names = TRUE,
#                  append = TRUE)
#
# df_bd <- readr::read_csv(file = "data/bileductarticles.txt", col_names = TRUE)
#
# df_bd <- unique(df_bd)
#
# df_bd[["PMID"]] <- as.character(df_bd[["PMID"]])
#
# exclude_bileduct_PMIDs <- read.csv(file = "data/exclude_bileduct_PMIDs.txt",
#                                    header = FALSE,
#                                    col.names = "PMID",
#                                    colClasses = "character"
# )
#
# df_bd <- dplyr::anti_join(df_bd, exclude_bileduct_PMIDs,
#                           by = "PMID")
#
# readr::write_csv(x = df_bd,
#                  file = "data/bileductarticles.txt",
#                  col_names = TRUE
# )
#
#
#
#
# # gallbladder ----
#
# # fetched_gallbladder_articles
#
# names_df_gallbladder_articles <-
#   slotNames(fetched_gallbladder_articles)
#
# df_gb <-
#   setNames(data.frame(matrix(
#     ncol = length(names_df_gallbladder_articles),
#     nrow = length(
#       slot(
#         fetched_gallbladder_articles,
#         names_df_gallbladder_articles[2]
#       )
#     )
#   )),
#   nm = names_df_gallbladder_articles
#   )
#
#
# df_gb[, "PMID"]              <- fetched_gallbladder_articles@PMID
# df_gb[, "YearArticleDate"]   <- fetched_gallbladder_articles@YearArticleDate
# df_gb[, "MonthArticleDate"]  <- fetched_gallbladder_articles@MonthArticleDate
# df_gb[, "ISSN"]              <- fetched_gallbladder_articles@ISSN
# df_gb[, "Title"]             <- fetched_gallbladder_articles@Title
# df_gb[, "ArticleTitle"]      <- fetched_gallbladder_articles@ArticleTitle
# df_gb[, "ELocationID"]       <- fetched_gallbladder_articles@ELocationID
# df_gb[, "AbstractText"]      <- fetched_gallbladder_articles@AbstractText
# df_gb[, "Language"]          <- fetched_gallbladder_articles@Language
# df_gb[, "MedlineTA"]         <- fetched_gallbladder_articles@MedlineTA
# df_gb[, "NlmUniqueID"]       <- fetched_gallbladder_articles@NlmUniqueID
# df_gb[, "ISSNLinking"]       <- fetched_gallbladder_articles@ISSNLinking
# df_gb[, "PublicationStatus"] <- fetched_gallbladder_articles@PublicationStatus
# df_gb[, "ArticleId"]         <- fetched_gallbladder_articles@ArticleId
# df_gb[, "DOI"]               <- fetched_gallbladder_articles@DOI
# df_gb[, "Volume"]            <- fetched_gallbladder_articles@Volume
# df_gb[, "Issue"]             <- fetched_gallbladder_articles@Issue
# df_gb[, "ISOAbbreviation"]   <- fetched_gallbladder_articles@ISOAbbreviation
#
# df_gb <- df_gb[, c(
#   "PMID",
#   "YearArticleDate",
#   "MonthArticleDate",
#   "ISSN",
#   "Title",
#   "ArticleTitle",
#   "ELocationID",
#   "AbstractText",
#   "Language",
#   "MedlineTA",
#   "NlmUniqueID",
#   "ISSNLinking",
#   "PublicationStatus",
#   "ArticleId",
#   "DOI",
#   "Volume",
#   "Issue",
#   "ISOAbbreviation"
# )]
#
# df_gb[["PMID"]] <- as.character(df_gb[["PMID"]])
#
# readr::write_csv(x = df_gb,
#                  file = "data/gallbladderarticles.txt",
#                  col_names = TRUE,
#                  append = TRUE)
#
# df_gb <- readr::read_csv(file = "data/gallbladderarticles.txt", col_names = TRUE)
#
# df_gb <- unique(df_gb)
#
# df_gb[["PMID"]] <- as.character(df_gb[["PMID"]])
#
# exclude_gallbladder_PMIDs <- read.csv(file = "data/exclude_gallbladder_PMIDs.txt",
#                                    header = FALSE,
#                                    col.names = "PMID",
#                                    colClasses = "character"
#                                    )
#
# df_gb <- dplyr::anti_join(df_gb, exclude_gallbladder_PMIDs,
#                           by = "PMID")
#
# readr::write_csv(x = df_gb,
#                  file = "data/gallbladderarticles.txt",
#                  col_names = TRUE
# )
#