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).
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 numbersAfter 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.