# Manual reference retrieval

If you are here, this is because you want to manually retrieve a list of references, outside of the automated task that you might have set up after reading LitFetchR (Tutorial).

## Setup

From your individual review R directory, load `LitFetchR`:

    # Load LitFetchR
    library(LitFetchR)

## Manual reference retrieval

Make sure to have saved your search string using `create_save_search()` as the following function needs to access the file search_list.txt, see LitFetchR (Tutorial).

    # 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

After running `manual_fetch()`, new unique history_dedup_ and citationCSV_ files are created and history_id is updated. See bottom of the page LitFetchR (Tutorial) for more information about those files.