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ms/ms.qmd

@@ -459,17 +459,17 @@ Increased competition in science has raised the bar with respect to the amount o
 We estimated how long it takes to publish a research paper in ecology and evolution by recording the time between when an article was first posted on *EcoEvoRxiv*, and its final acceptance in a peer-reviewed journal. In total, `r unpub` papers remained unpublished (`r (unpub / nrow(data2))*100`%, n = `r nrow(data2)`) at the time when these data were collected. Not all of these papers, however, are anticipated to be published in a peer-reviewed journal (e.g., reports). Nonetheless, the median time to publication for preprints was `r sum_preprints$median` days (8 months) (mean = `r sum_preprints$mean`; SD = `r sum_preprints$sd` days) with the maximum time to publication being `r sum_preprints$max` days or `r sum_preprints$max/365` years ([@fig-pubsummary]A). Our results largely confirm the extended timeframes that most authors experience between writing their research papers and their publication.
 
 ### *Cautious 'open'-mindedness of research in preprints*
-In addition to speeding up dissemination, preprints and postprints can also be a useful way to ensure that research remains open and accessible to the research community irrespective of the accessibility of the final peer-reviewed paper [@bourne2017ten; @vale2015accelerating]. We evaluated whether articles hosted at *EcoEvoRxiv*, and that were also published in a journal, were published open access. The open access status of each published article was obtained using the R package *roadoi* (v.`r utils::packageVersion("roadoi")`) to connect to the Unpaywall platform [@jahn2024]. Most of the published articles were open access [`r sum_is_oa$valid_percent[2]*100`% (*n* = `r sum_is_oa$n[2]` out of `r sum(sum_is_oa$n[1:2])` where the status was known); [@fig-pubsummary]A]; however, `r sum_is_oa$valid_percent[1]*100`% (*n* = `r sum_is_oa$n[1]`) were published behind paywalls. For articles published in open access journals, the type of open-access also varied widely (e.g., Gold, Hybrid, Green OA etc., [@fig-pubsummary]B). 
+In addition to speeding up dissemination, preprints and postprints can also be a useful way to ensure that research remains open and accessible to the research community irrespective of the accessibility of the final peer-reviewed paper [@bourne2017ten; @vale2015accelerating]. We evaluated whether articles hosted at *EcoEvoRxiv*, and that were also published in a journal, were published open access. The open access status of each published article was obtained using the R package *roadoi* (v.`r utils::packageVersion("roadoi")`) to connect to the Unpaywall platform [@jahn2024]. Most of the published articles were open access [`r sum_is_oa$valid_percent[2]*100`% (*n* = `r sum_is_oa$n[2]` out of `r sum(sum_is_oa$n[1:2])` where the status was known); [@fig-pubsummary]A]; however, `r sum_is_oa$valid_percent[1]*100`% (*n* = `r sum_is_oa$n[1]`) were published behind paywalls. For articles published in open access journals, the type of open access also varied widely (e.g., Gold, Hybrid, Green OA etc., [@fig-pubsummary]B). 
 
-Data and code sharing are also key components of open science [@roche2015public]. In the spirit of 'openness', we expected data and code sharing among preprints to be greater than in many papers published in research journals [@roche2015public; @o2021preferred]. Despite this, we found that `r (preprint_data[1,"n"]/sum(preprint_data[c(1,3),"n"]))*100`%  (*n* = `r preprint_data[1,2]`) of articles relying on data on *EcoEvoRxiv* did not share data, and `r (preprint_code[1,"n"]/sum(preprint_code[c(1,3),"n"]))*100`% (*n* = `r preprint_code[1,2]`) did not share code (counting only data-based articles, i.e excluding reviews, commentaries or theoretical works). 
+Data and code sharing are also key components of open science [@roche2015public]. In the spirit of 'openness', we expected data and code sharing among preprints to be greater than in many papers published in research journals [@roche2015public; @o2021preferred]. Despite this, we found that `r (preprint_data[1,"n"]/sum(preprint_data[c(1,3),"n"]))*100`%  (*n* = `r preprint_data[1,2]`) of articles relying on data on *EcoEvoRxiv* did not share data, and `r (preprint_code[1,"n"]/sum(preprint_code[c(1,3),"n"]))*100`% (*n* = `r preprint_code[1,2]`) did not share code (counting only data-based articles, i.e., excluding reviews, commentaries or theoretical works). 
 
 Authors may be reluctant to share data and code for preprints because of the perceived concern that others may acquire and use their data and code before publication in a journal. Authors of `r pre_article_data[3,"percent"]*100`% (*n* = `r pre_article_data[3,2]`) of articles that did not share data at the preprint stage did ultimately share data when the article was published; whereas authors of `r pre_article_data[2,"percent"]*100`% (*n* = `r pre_article_data[2,2]`) never shared data. However, `r pre_article_data[1,"percent"]*100`% (*n* = `r pre_article_data[1,2]`) shared data at both stages. The same was true for code. Overall, `r pre_article_code[3,"percent"]*100`% (*n* = `r pre_article_code[3,2]`) preprints had no open code at the preprint stage but did at the published article stage and authors of `r pre_article_code[2,"percent"]*100`% (*n* = `r pre_article_code[2,2]`) preprints did not share code at either stage. However, `r pre_article_code[1,"percent"]*100`% (*n* = `r pre_article_code[1,2]`) shared code at both stages. Relatively low code and data-sharing practices in our sample is consistent with analyses of sharing practices for published articles (e.g., [@o2021preferred]), even for journals with strict public data archiving policies [@roche2015public].
 
 # Paving our future to open, transparent and community-driven science
 
 Our analysis has allowed us to better understand preprinting/postprinting practices in *EcoEvoRxiv*. Overall, *EcoEvoRxiv* articles are diverse but with primary research articles on vertebrates comprising most of the articles posted. North America, Europe and Australia use *EcoEvoRxiv* the most with very few non-English language articles to date. Submitting authors who were earlier in their career and more often with ‘male-associated names’ tended to use  *EcoEvoRxiv* the most. Articles posted to *EcoEvoRxiv* tend to take up to 8 months to become published with many articles not being open access. Code and data sharing was also relatively uncommon at the preprint stage. At the same time, we attempted to collect data on community discussion around preprints no such data was found on preprint landing pages, likely reflecting inadequate functionality and cross-linking with sources where such discussion is occurring. Based on the insights from our analysis, we provide recommendations to authors and the scientific community on ways they can further promote open and transparent research through preprints: 
 
-- First, share your data and code at the preprint stage. Sharing data and code early can help improve the quality of research, establish precedence, and improve the transparency and computational reproducibility of scientific findings [@sarabipour2019value]. Reassuringly, sharing data and code is rarely associated with the 'scooping' of research findings [@soeharjono2021reported]. If authors are worried about data being used unintentionally, clear information surrounding its reuse can be included in a license (see https://choosealicense.com). Data can also be achived with an embargo on its reuse [@roche2014troubleshooting]. 
+- First, share your data and code at the preprint stage. Sharing data and code early can help improve the quality of research, establish precedence, and improve the transparency and computational reproducibility of scientific findings [@sarabipour2019value]. Reassuringly, sharing data and code is rarely associated with the 'scooping' of research findings [@soeharjono2021reported]. If authors are worried about data being used unintentionally, clear information surrounding its reuse can be included in a license (see https://choosealicense.com). Data can also be archived with an embargo on its reuse [@roche2014troubleshooting]. 
 - Second, take advantage of peer-reviewing services such as Peer Community In (PCI). The time between posting a preprint and publication is still quite long (~8 months). One possible explanation is that preprints are not being sent to suitable journals or are struggling to get into review, slowing down constructive feedback that can improve the quality of a paper. Using PCI circumvents editorial decisions without review, yet only `r pci[2,3]*100`% (*n* = `r pci[2,2]`) used PCI. Using such services will ensure that authors receive faster feedback on a paper. Ninety-three journals currently accept PCI reviews and recommendations when considering a paper for publication (https://peercommunityin.org/pci-friendly-journals/).
 - Third, seek out and contribute to constructive feedback on preprints [@bourne2017ten]. While it is clear that preprints help establish precedence and allow findings to be openly accessible, it still seems rare that constructive discussions form around preprints in an open forum (e.g. bioRxiv [@anderson2020biorxiv]). Unfortunately, the *EcoEvoRxiv* website does not provide opportunities for discussion given the limitations of the web server at this point in time. As such, we could not accurately assess how much discourse around a given preprint occurs. Clearly, as a community, we need to provide better platforms that document discussions around preprint findings. Such discussions help authors improve their work and communicate their findings more effectively (when done constructively, of course). One way to facilitate such discussions may be to use open preprint peer-review services such as *Peer Community In* (PCI) or *PubPeer* (see also [@avissar2024recommendations]) to provide feedback on preprints. 
 - Finally, keep your preprints updated. While most preprints get seamlessly connected and merged with their published version, some remain 'disconnected' as separate articles. Incorrect cross-linking by indexing platforms (e.g., Google Scholar) can create confusion and lead to frustration among authors. Thankfully, the reasons for unmatched preprints and publications are well-understood and easily rectified. They often result from a mismatch between preprint and published metadata (e.g., titles and author details). For example, nearly one-third  of articles changed their title from preprint submission to publication [`r titles[2,3]*100`% (*n* = `r titles[2,2]`)]. We found that mismatched metadata almost always contributed to preprints and published articles not being matched automatically in Google Scholar. We recommend that authors update their preprints with the publication DOI when accepted to journals, especially if their title has changed. This is very easy for authors to do on *EcoEvoRxiv* and ensures that the preprint is correctly linked to the published article and citations are appropriately merged. Adding DOIs will also create a link between the final preprint and the published paper so that, no matter the open access status of the publication, the research findings will remain openly accessible, saving costs for authors (i.e., by not having to pay open access fees) and improving the visibility and use of research.