## ----include = FALSE----------------------------------------------------------
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

## ----eval = FALSE-------------------------------------------------------------
# # Load LitFetchR
# library(LitFetchR)

## ----eval=FALSE---------------------------------------------------------------
# # Load LitFetchR
# library(LitFetchR)
# 
# # Retrieve the list of references corresponding to your saved search string(s)
# #We recommend choosing the R project directory as the directory in the function. It has to be the directory where "search_list.txt" and "history_search.xlsx" have been saved.
# 
# # Example of what you should see:
# # > manual_fetch(wos = TRUE,
# #                scp = TRUE,
# #                pmd = TRUE,
# #                directory = "C:/path-to-project-directory",
# #                dedup = TRUE,
# #                open_file = FALSE)
# # [1] 126
# # Finished batch number 1
# # Finished batch number 2
# # [1] "10.1016/j.aaf.2023.11.002 1 / 126"
# # [1] "10.3390/fishes10090439 2 / 126"
# # [FOR THE PURPOSE OF THIS EXAMPLE WE ARE NOT SHOWING EACH LINE OF THE COMMAND]
# # [THE REMOVED LINES CORRESPOND TO MOST OF THE REFERENCE RETRIEVAL COUNTING]
# # [1] "NA 125 / 126"
# # [1] "NA 126 / 126"
# # [1] 22
# # Finished batch number 1
# # File already exists
# # [1] "10.1007/s12602-023-10207-x 1 / 22"
# # [1] "10.1016/j.fsi.2025.110189 2 / 22"
# # [FOR THE PURPOSE OF THIS EXAMPLE WE ARE NOT SHOWING EACH LINE OF THE COMMAND]
# # [THE REMOVED LINES CORRESPOND TO MOST OF THE REFERENCE RETRIEVAL COUNTING]
# # [1] "10.1111/j.1472-765X.2010.02894.x 21 / 22"
# # [1] "NA 22 / 22"
# # [1] 106
# # Finished batch 1 for fish AND "vibrio harveyi" AND diagnostic
# # File already exists
# # [1] "10.1016/j.fsi.2025.110503 1 / 106"
# # [1] "10.1016/j.fsi.2025.110501 2 / 106"
# # [FOR THE PURPOSE OF THIS EXAMPLE WE ARE NOT SHOWING EACH LINE OF THE COMMAND][1] "NA 105 / 106"
# # [THE REMOVED LINES CORRESPOND TO MOST OF THE REFERENCE RETRIEVAL COUNTING]
# # [1] "NA 106 / 106"
# # Warning: The following columns are missing: pages, number, record_id, isbn
# # formatting data...
# # identifying potential duplicates...
# # identified duplicates!
# # flagging potential pairs for manual dedup...
# # Joining with `by = join_by(duplicate_id.x, duplicate_id.y)`
# # 254 citations loaded...
# # 14 duplicate citations removed...
# # 240 unique citations remaining!
# # Deduplication script has been executed, concatenated deduplicated references had been exported.
# # Warning message:
# # In add_missing_cols(raw_citations) :
# #   Search contains missing values for the record_id column. A record_id will be created using row numbers