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itchyshin / publication_bias

Publication bias in meta-analyses
https://itchyshin.github.io/publication_bias/
MIT License
3 stars 1 forks source link

Further imporvements #8

Open itchyshin opened 3 years ago

itchyshin commented 3 years ago

Thanks again for @roseodea and @daniel1noble going through the appendix.

@ASanchez-Tojar and @Yefeng0920 - Please go through the latest version of Rmd and you can look at HTML (easier to read). There are some repetitions and redundancy and parts that are difficult to understand. So please improve.

You can also find @TO-DO and @DanNoble - where I want you to address these comments.

@daniel1noble - I leave you to get Klippy working.

Thanks!

Shinichi

itchyshin commented 3 years ago

@ASanchez-Tojar and @Yefeng0920

Some these comments are hidden <!--- xxxx ---> so you will need to see (try the find function) Rmd file not HTML.

Thanks

ASanchez-Tojar commented 3 years ago

Awesome! Thank you all for going through the supplements, they look great! I just went through it quickly to understand exactly what sort of changes we (@Yefeng0920 and I) need to implement, and it looks like it is just a few things, in principle. @itchyshin , do I understand correctly that you also want @Yefeng0920 and myself to go through our writing once more and try to avoid text repetitions and to make the text simpler at times, or did you guys provided some edit suggestions somewhere that I can't find. Regarding the references, do we still need to deal with anything in that respect or all references from all sections are now added? (seems so, but just to confirm).

@Yefeng0920 I need to take care of a few deadlines today and over the weekend, would it be possible for you to give it a go first, and then pass it on to me? I will have more time to breathe from Thursday on. Have a great weekend y'all.

itchyshin commented 3 years ago

@ASanchez-Tojar - yes you are correct - please treat this as something many people read and in a way, this file is more important than the MS.

Also, in the Rmd file - look for @TO-DO or @DanNoble in the file and try to address what they requested.

Thanks!

ASanchez-Tojar commented 3 years ago

Brilliant. Thanks!

daniel1noble commented 3 years ago

Thanks @itchyshin, @ASanchez-Tojarhttps://github.com/ASanchez-Tojar and @Yefeng0920https://github.com/Yefeng0920! I just got back. I’m happy to go through everything again. I just did what I could before I had to leave, but I can go through another round of things.

@itchyshin - skilled shouldn’t be a problem. @ASanchez-Tojarhttps://github.com/ASanchez-Tojar if rendering it, you should be able to get this to work quite easily. I added the relevant code chunk in already. You just need to remote install klippy. If you’re having troubles, no issues on my end.

Thanks, Dan

On 9 Apr 2021, at 8:03 am, Shinichi Nakagawa @.**@.>> wrote:

Thanks again for @roseodeahttps://github.com/roseodea and @daniel1noblehttps://github.com/daniel1noble going through the appendix.

@ASanchez-Tojarhttps://github.com/ASanchez-Tojar and @Yefeng0920https://github.com/Yefeng0920 - Please go through the latest version of Rmd and you can look at HTML (easier to read). There are some repetitions and redundancy and parts that are difficult to understand. So please improve.

You can also find @to-dohttps://github.com/to-do and @dannoblehttps://github.com/dannoble - where I want you to address these comments.

@daniel1noblehttps://github.com/daniel1noble - I leave you to get Klippy working.

Thanks!

Shinichi

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ASanchez-Tojar commented 3 years ago

Hi all. I went through the .Rmd doc updated by @Yefeng0920. I have added a few edits to improve the text and try to deal with all to-do's. See what's left below.

@Yefeng0920 I managed to fix the warning message about fun(), but please, have a double-check to see if it works as expected since it was in your part of the code. In addition, I believe there are captions missing for two of your tables, Table S4.3, Table S4.4; and for some of your figures too. If so, could you please add them?

Some clarifications below:

  1. <!-- @DanComment: Note you can add table legends with Kable. This is useful for keeping all the figure and table legends together as currently they are disjointed at times. --->

For the time being, I ignored this comment because, if I understand correctly, it would mean we have to re-do all tables done in the R package ‘gt’ to do them in ‘kable’ instead? Also, I did not really see what @daniel1noble meant by “disjointed”. As far as I can see, all table captions are right underneath each table with no space in between the table and the caption. What I think it looks a bit off is the figure captions, because by using fig.cap the captions are now placed underneath the figures, but the figure number is shown on top. Please, let me know if I misunderstood something.

  1. # @TO-DO: is 1000 really necessary here? It takes a very long time and the dataframe is enormous (because it's 1000 x all the years)

There was this comment for Yefeng’s dataset, which is very big and therefore the for loop seems to take forever. I wasn’t sure what to do with it. Do you want to use 500 instead or shall we proceed with 1000?

Otherwise, I believe everything else is finished, although I did not try to knitt. Please, let me know if something is unclear, incomplete or if I can help with anything else. Thank you all.

Yefeng0920 commented 3 years ago

Thanks! Just fixed captions. Will check other mentioned points