Giters

elizagrames / litsearchr

litsearchr is an R package to partially automate search term selection for systematic reviews using keyword co-occurrence networks. In addition to identifying search terms, it can write Boolean searches and translate them into over 50 languages.

Home Page:https://elizagrames.github.io/litsearchr

Geek Repo:Geek Repo

Github PK Tool:Github PK Tool

usable_databases() doesn't work

lisaminas opened this issue · comments

commented

Hi,
I just started using litsearchr and can not run the first script provided on the example page (https://elizagrames.github.io/litsearchr/introduction_vignette_v010.html): litsearchr::usable_databases(). It seems Rstudio doesn't recognize "usable_databases".
Any suggestions?

Thanks.

commented

Ah, you'll want to actually follow the vignette for v030 since the package has been updated and that function is now obsolete. I keep the v010 vignette up solely because it is connected to the manuscript associated with the package, sorry for the confusion.

commented

Thanks for the update. I have imported my reference list from Web of Science in .txt format and when I run " naiveimport <- litsearchr::import_results(directory = search_directory, verbose = TRUE)" I get a message that the file was not found. I also converted the .txt file to .bib and .ris and it doesn't seem litsearchr can read these files neither (Error in synthesisr::read_refs(filename = filename, return_df = TRUE, :
file not found). Do you have any suggestions? As you suggested above I am following v030 vignette example. Thanks.

commented

This sounds like a problem of the path to the directory where your files are located; it is not the error you would get if they were not readable, but rather that they can't be found. I would suggest double checking that the path to the directory where you have saved your reference list is correct relative to the directory you are working in.

commented

ok that could make sense. This is how I defined my directory etc. (the .txt, .bib, .ris are all in the same "literature" folder):
setwd("C:/_LOCALdata/Geospatial_2020/site/literature")
geospatial_search ="C:/_LOCALdata/Geospatial_2020/site/literature/"
list.files(geospatial_search)
search_directory <- system.file(geospatial_search, package = "synthesisr")
naiveimport <- litsearchr::import_results(directory = search_directory, file = NULL, verbose = TRUE)

What am I missing above?

Thanks

commented

You actually want to set the search_directory directly to the folder with your search results in it (see code below). The "system.file()" line in the vignette is pointing to a directory of results that I know exists on your computer if the package was installed successfully since it is the demo, but I did not explain that part clearly, sorry.

search_directory <- "C:/_LOCALdata/Geospatial_2020/site/literature/"

commented

Thanks. It worked.
I was able to make it up to "taggedkeyword". I am not able to extract keywords using your suggested script. Is it because the keywords don't exist in my database? I got my literature database from WOS in .txt file and when I open it there is no keyword field there. I imported the .txt back to zotero and converted the file to .ris and that is the file I am using. Thanks.

commented

Yeah, if there are no keywords in your file it won't be able to extract anything; the tagged option is pretty fussy and honestly not that helpful anyways. I would suggest just skipping that bit of code and selecting terms from the raked keywords.