From fc2142a4c7dbb7c38f48263a004cf2e2bb6b51f2 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?R=C3=A9mi=20Th=C3=A9riault?=
 <13123390+rempsyc@users.noreply.github.com>
Date: Tue, 12 Mar 2024 22:31:32 +0100
Subject: [PATCH] add suffix to save_process_pubmed_batch

---
 R/clean_journals_continents.R    |   4 ++--
 R/save_process_pubmed_batch.R    |   6 ++++--
 data/journal_field.rda           | Bin 1376 -> 1380 bytes
 man/save_process_pubmed_batch.Rd |   3 +++
 4 files changed, 9 insertions(+), 4 deletions(-)

diff --git a/R/clean_journals_continents.R b/R/clean_journals_continents.R
index 4b2231a..ffde6b4 100644
--- a/R/clean_journals_continents.R
+++ b/R/clean_journals_continents.R
@@ -32,7 +32,7 @@ continent_order <- function(short = FALSE) {
 #' @noRd
 clean_journal_names <- function(journal) {
   x <- gsub("&amp;", "and", journal, fixed = TRUE)
-  # x <- gsub(" of the United States of America", "", x, fixed = TRUE)
+  x <- gsub(" of the United States of America", "", x, fixed = TRUE)
   x <- gsub(":.*", "", x)
   x <- gsub("[(].*", "", x)
   x <- tools::toTitleCase(x)
@@ -55,7 +55,7 @@ detect_missing_journals <- function(data) {
 #'  instead of a regular dataframe (defaults to TRUE).
 #' @export
 table_journal_count <- function(data, datatable = TRUE) {
-  x <- dplyr::count(data, data$journal, data$field, data$year_range, sort = TRUE) %>%
+  x <- dplyr::count(data, .data$journal, .data$field, .data$year_range, sort = TRUE) %>%
     dplyr::mutate(field = stringr::str_to_title(.data$field)) %>%
     as.data.frame() %>%
     dplyr::rename("year range" = "year_range") %>%
diff --git a/R/save_process_pubmed_batch.R b/R/save_process_pubmed_batch.R
index a7017a6..4c86a2e 100644
--- a/R/save_process_pubmed_batch.R
+++ b/R/save_process_pubmed_batch.R
@@ -8,6 +8,7 @@
 #' @param day_low The year the data should start.
 #' @param day_high The year the data should end.
 #' @param data_folder Where to save the data.
+#' @param suffix What suffix to add to the name file.
 #' @param batch_size The download batch size.
 #' @param api_key The api key for faster processing (optional).
 #' @param verbose Whether to include progress messages.
@@ -41,6 +42,7 @@ save_process_pubmed_batch <- function(pubmed_query_string = "",
                                       day_low = "01",
                                       day_high = 31,
                                       data_folder = "data",
+                                      suffix = "",
                                       batch_size = 5000,
                                       api_key = NULL,
                                       verbose = TRUE) {
@@ -118,7 +120,7 @@ save_process_pubmed_batch <- function(pubmed_query_string = "",
   # Get full name country, continent, and region
   articles.df4 <- add_region(articles.df3)
 
-  saveRDS(articles.df4, paste0(data_folder, "/articles_", year_low, "_", year_high, ".rds"))
+  saveRDS(articles.df4, paste0(data_folder, "/articles_", year_low, "_", year_high, suffix, ".rds"))
 
   if (verbose) {
     start <- year_low
@@ -139,7 +141,7 @@ save_process_pubmed_batch <- function(pubmed_query_string = "",
 
     success_message <- c(
       "Operation successfully completed. Congratulations!", print_time(),
-      "File saved in", paste0(data_folder, "/articles_", start, "_", end, ".rds\n\n")
+      "File saved in", paste0(data_folder, "/articles_", start, "_", end, suffix, ".rds\n\n")
     )
 
     cat(success_message)
diff --git a/data/journal_field.rda b/data/journal_field.rda
index 2f016c0d086c64dbe379effbedfebb3662ad50fe..74a6576c43f685dd934edb81edff1fbec9040ccd 100644
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diff --git a/man/save_process_pubmed_batch.Rd b/man/save_process_pubmed_batch.Rd
index 79158c8..e407712 100644
--- a/man/save_process_pubmed_batch.Rd
+++ b/man/save_process_pubmed_batch.Rd
@@ -14,6 +14,7 @@ save_process_pubmed_batch(
   day_low = "01",
   day_high = 31,
   data_folder = "data",
+  suffix = "",
   batch_size = 5000,
   api_key = NULL,
   verbose = TRUE
@@ -38,6 +39,8 @@ save_process_pubmed_batch(
 
 \item{data_folder}{Where to save the data.}
 
+\item{suffix}{What suffix to add to the name file.}
+
 \item{batch_size}{The download batch size.}
 
 \item{api_key}{The api key for faster processing (optional).}