Retrieves references corresponding to the saved search string(s) on up to three platforms (e.g. Web of Science, Scopus and PubMed).
Usage
manual_fetch(
wos = FALSE,
scp = FALSE,
pmd = FALSE,
directory,
dedup = FALSE,
open_file = FALSE,
dry_run = FALSE
)Arguments
- wos
Runs the search on Web of Science (TRUE or FALSE).
- scp
Runs the search on Scopus (TRUE or FALSE).
- pmd
Runs the search on PubMed (TRUE or FALSE).
- directory
Choose the directory in which the search string is saved (Project's directory). That is also where the references metadata will be saved.
- dedup
Deduplicates the retrieved references (TRUE or FALSE).
- open_file
Automatically opens the CSV file after reference retrieval.
- dry_run
Simulation run option.
Value
NULL (invisibly). Called for its side effects: Create a CSV file with the references metadata, a history file of the references retrieved and a history file of the deduplication (if the option is selected).
Examples
# This is a "dry run" example.
# No references will actually be scheduled, it only shows how the function should react.
manual_fetch(wos = TRUE,
scp = TRUE,
pmd = TRUE,
directory,
dedup = TRUE,
open_file = FALSE,
dry_run = TRUE
)
#> This is the message from the dry run showing what you should be
#> seeing when the function will be used:
#> [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 CONSOLE]
#> [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 CONSOLE]
#> [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 CONSOLE]
#> [THE REMOVED LINES CORRESPOND TO MOST OF THE REFERENCE RETRIEVAL COUNTING]
#> [1] "NA 105 / 106"
#> [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