nealhaddaway / citationchaser

Perform forward and backward citation chasing as part of an evidence synthesis project

Hi there! My name is Neal Haddaway, and I'm a researcher/photographer. My background is in conservation biology, but I've spent the best part of 15 years conducting research into various aspects of environmental science, from invasion biology to social science and a bit of everything in between. Since 2012, I've been working with evidence synthesis - the collation and appraisal of research evidence to support better decision making. I've developed methods for evidence synthesis, with an emphasis on using technology to support more accessible, comprehensive, transparent and rigorous syntheses.

In 2017, I started the Evidence Synthesis Hackathon, a series of events to develop needs-based, Open Source tools for evidence synthesis. In 2020, I established the Evidence Synthesis and Meta-Analysis in R Conference (ESMARConf), which has run annually since 2021. This online, free conference highlights tools for evidence synthesis in R and supports a large, vibrant community of practice across the globe interested in learning about, developing and using R for evidence synthesis.

I'm also a photographer, with a keen interest in documentary photography and photojournalism for communicating some of our toughest social and environmental problems. Check out my latest project, 'Hope? and how to grieve for the planet'.

citationchaser's Issues

Add scite.ai tally contextual citation data to supplement citations

Issue

We'd (scite.ai) like to contribute a PR that uses, optionally, scite.ai tally citation classification data (Supporting, Disputing, Mentioning) to help users and ourselves get better-contextualized citations.

@nealhaddaway Is this something you would be open to?

Our current API docs are (https://documenter.getpostman.com/view/7840038/SzYaVdeo?version=latest#ece530f0-7316-457c-b48f-8205b4e9abb9) though we are working on newer ones.

Support import of BibTex files

Besides RIS, BibTex files are the next most popular file formats.

Various tools like Connected Papers, Litmaps also export results only in BibTex but not RIS. While it's fairly simple to import Bibtex into a reference manager and export in RIS, would be nice if Citationchaser could support this directly.

Add deduplication option for results

Add deduplication option for results

Error when using type = "lens_id"

[Last thing I promise!]

When trying to manually implement the step-wise functionality described in #3, I hit an issue in that the type = "lens_id" option doesn't seem to work:

# Get records citing our {robvis} paper
cit <-
  citationchaser::get_refs(
    article_list = "10.1002/jrsm.1411",
    get_records = "citations",
    type = "doi",
    token = <TOKEN>
  )

# Pass IDs of records identified by the initial run back to get_refs()
# Use type = "lens_id" as this is the only ID provided by the inital output 
cit2 <-
  citationchaser::get_refs(
    article_list = as.list(cit$citations_df$data.lens_id),
    type = "lens_id",
    get_records = "citations",
    token = <TOKEN>
  )

This gives:

Error in citationchaser::get_refs(article_list = as.list(cit$citations_df$data.lens_id),  : 
  Please provide articles in one of the following formats: "doi" (digital object identifier, in this format: "10.1186/s13750-018-0126-2"), "pmid" (PubMed ID), "pmcid" (PubMed Central ID), "magid" (Microsoft Academic ID), "coreid" (CORE identifier), lens_id" (The Lens.org ID), "title" (article title; much lower specificity)

Fix input reset button error

Error warning appears after input reset - fix

Strip off 'https://doi.org/' from uploaded dois

Remove the prefix 'https://doi.org/' from any dois uploaded - using gsub('https://doi.org/', '', dois)

Add argument to define number of steps [feature request]

Hi @nealhaddaway,

As a feature request for this package, I would love to have an argument to define the number of steps away from the initial article(s) provided the function returns. So for example if steps = 1 and get_records = "citations", you get just the records cited by that reference. But if steps = 2, you get the records cited by that initial reference, and then records cited by the records cited by the original reference.

You can do this manually at the moment by taking the output of the initial run of the function and passing it back to get_refs(), but having it baked into the function (with appropriate deduplication) would be amazing!

Error when trying to install citation chaser

Currently getting this error :-/ Using devtools install_github("nealhaddaway/citationchaser"), R 4.0.0

Error: Failed to install 'citationchaser' from GitHub:
System command 'R' failed, exit status: 1, stdout + stderr (last 10 lines):
E> * checking DESCRIPTION meta-information ... ERROR
E> Malformed Authors@R field:
E> :6:53: unexpected ','
E> 5: email = "[email protected]",
E> 6: comment = c(ORCID = "0000-0003-3902-2234")),
E> ^
E>
E> See section 'The DESCRIPTION file' in the 'Writing R Extensions'
E> manual.

Ris upload

Allow ris upload in the shiny app with function for DOI extraction

Change license to GPL?

@nealhaddaway perhaps we should change the license to ensure derivatives have to be open source

Add a one-click button to perform both forward and backward citation chasing on article input page

Add button that performs forward and backward citation chasing simultaneously (may need to use multiple cores) - place on article input page

0 day issue

Error: object 'vlookup' is not exported by 'namespace:expss' when I load package

Lens.org token free trial query

Hi @nealhaddaway

This looks like a great package! One thing to flag from an "openness" point of view is that when I signed-up, Lens.org came back to say that I could have a free trial but would need to pay for institutional access after that. Might be worth flagging this (that you need to pay for persistent access) in the packages README?

Thanks for this request. You will be granted a 14-day free trial to enable you to download the data needed. You will receive shortly an email with instructions on how to generate your token. Please make sure to download your data within the allocated time. For any continued access, your library or your institution would need to take up a paid subscription to help support the public resource of the Lens and take advantage new added-value institutional tools. Please remember to read carefully the Lens data terms of use.

Title matching as an alternative lookup id

Set up search for exact title matches

Issue when importing .ris into mendeley

Hi,

I'm having issues when importing the resulting RIS file from citationchaser into mendeley, as the author order is wrong.

The issue seems to be the AU field in the RIS file.
Current RIS:

TY  - JOUR
AU  - Sánchez-Cordón, Pedro J.; Montoya, Maria; Reis, Ana Luisa; Dixon, Linda K.
TI  - African swine fever: A re-emerging viral disease threatening the global pig industry
...

Mendeley reads it correctly when it's the following format:

TY  - JOUR
A1  - Sánchez-Cordón, Pedro J.
A1  - Montoya, Maria
A1  - Reis, Ana Luisa
A1  - Dixon, Linda K.
TI  - African swine fever: A re-emerging viral disease threatening the global pig industry
...

Would it be possible to download in this format?

Unclear how to combine ?dois=/?pmids=etc as worked example contains only doi

When running a review I often find I have mixed identifiers available for the included studies which I wish to review citations and references for. However, AMAZING though the citaitonchaser is, it would be even more amazing if we could run all included studies even with mixed identifiers, and find the list of all the Unique article IDs for citations for the complete group, instead of needing to download and then combine those for each ID type. Is it possible to add a note to the Readme explaining how to do this?

Add download network button

Need a static and dynamic (html) options

Colour the edges and not the nodes in the network

https://twitter.com/aarontay/status/1361958669655531522?s=20

Update the lens token

When the old token expires we need to add the new one

Expand citation analysis (co-citation)

Build in analysis of second order citation network (citing/cited records for citation chaser results), prioritised by frequency of citations/co-citation