To do list (1 June 2020)

[itchyshin]

@Mike-Garratt

• [x] work on the MS a bit more
• [x] send @mlagisz a sketch of the idea diagrams

@mlagisz

• [x] work on conceptual diagrams (based on Mike's sketch)
• [x] read the MS again once @itchyshin works on it
• [x] finish off the method section - search-related things

@itchyshin

• [x] carefully read the MS
• [x] create - figs 1-4 (also figure legends)
• [x] add statistics to the text
• [x] write Stats methods etc
• [x] the first draft for Suppl
• [x] finalise Suppl Materials

All

• [x] PRISMA-EcoEvo checklist (to submit to Nat Comm)

[Mike-Garratt]

Hi @mlagisz

Maybe this sketch is not understandable to you - let me know! What we are trying to do is sketch what should happen to sex differences in survival when males are castration, if male gonads are the cause of sex-differences in ageing. If they are, then when males are castrated we should expect that the sex difference will be reduced, because effects of castration will be stronger where females live longer than males, and less or negative when its the other way around. Alternatively, castration may extend male lifespan irrespective of sex-difference, and male gonads are not the cause of sex-specific ageing.

[Mike-Garratt]

There is lots of text on this diagram but it is mainly to try and explain to you what I am trying to convey. Let me know if this doesnt make any sense. Thanks for your help!

[Mike-Garratt]

Sex difference schematic.pdf

[Mike-Garratt]

In this diagram each dot would present a sex difference observed in an individual population. There is a lot of variation, but on average females live longer than males (e.g. male lifespan/female lifespan is negative)

[itchyshin]

@Mike-Garratt - thanks - @mlagisz thinks it is pretty good - she is on it!

[itchyshin]

@Mike-Garratt - @mlagisz had a go at the conceptual fig - could you check

Fig 3

You can download and see from this link castration_effect_v0.pptx

Fig 4

I am nearly finished with tidying up code and turning into a webpage - will start updating and adding to the MS soon

[Mike-Garratt]

Hi @itchyshin and @mlagisz , schematic looks great! We might be able to extenuate the difference a little more by making the sex difference reduction greater in the first panel, but I can do that.

[Mike-Garratt]

@itchyshin , just looking at your figure 4A and I am a little confused about the presentation of the data and male/female and the female/male. I think we talked about presenting all four comparisons as male/female. E.g. male normal/female normal, male sterilized/female normal, male normal/female sterilized.

The top figure in A is labelled as female normal/male normal. This is slightly negative indicating a slight male survival bias benefit. Is that correct? It is the opposite of what have for the male comparison control group

[Mike-Garratt]

[Mike-Garratt]

Maybe its right, its just the mean dot has been pushed across to the other side with the new datapoints

[Mike-Garratt]

Sorry to be a pain, just checking I understand!

[itchyshin]

@Mike-Garratt - sorry I will be away this week for a workshop (townsville). But when I come back, I will resume it again - it will be good to catch up again once I have done my part - I am hoping to catch up with you on the week of 4 July

[Mike-Garratt]

Hi @itchyshin , hope you had a good time at the workshop! I am going to the US and UK leaving on the 9th of July, and will be on leave pretty much until the start of September. I have a conference at the end of July for a week.

Just wondering if we could aim to get the paper out to coauthors at the end of next week? Maybe that is too ambitious and I don't want to hassle you, but we could send out what we have and then work on finalizing the other bits while they are looking at it. If all goes well we could try and submit over the week I am at the conference (end of July), when I will be away from my family.

Let me know what you think and we could maybe have a quick chat if you thought it feasible.

Hope all is well,

Mike

[itchyshin]

@Mike-Garratt - so sorry for the delay - workshop, teaching, marking, 4 new PhD students started etc etc. I am really meaning to work on it but....... Anyway, let me try to see what I can do by 4th (I have a guest on 9 th and 10th). Let's try to meet on 4 th regardless of my progress - what time are you available on 4th?

[itchyshin]

@Mike-Garratt - I set aside some time today to do this so if I have questions, I may be a good idea to have a meeting later tomorrow (my time) - how your late afternoon looking?

[itchyshin]

Also, @Mike-Garratt - I have finished all the coding (still need to put more text) but this means you could potentially help me filling in some stats values while I write Method - is that possible

Here is all the code and outputs

https://www.dropbox.com/s/tl20xorjnlu1665/Suppl_Mat2.html?dl=0

[itchyshin]

@mlagisz - I am looking at the method - there are some work to be done there for you which I will show - I have just shared the dropbox folder - we have the latest MS in there - will talk later

[Mike-Garratt]

Hi @itchyshin , yes absolutely, I can add the stats, just let me know what the key values are to add to the test (or I can follow what you have done in a recent paper). Tomorrow should be good, there is a small chance that I might take off for the weekend early but it probably won't happen. We can set a time. I'll also be around all day today

[itchyshin]

@Mike-Garratt - do you think you can catch up 30 min at your 5 pm (my 3 pm)? Or is it too late? I will try to work towards that

[Mike-Garratt]

@itchyshin, how about 2.45pm your time? I might be meeting some people at the pub after work. Alternatively I could also talk later, like 5pm your time if that's better?

[itchyshin]

@Mike-Garratt - yes, 5 pm my time is better - I may be slightly late for this. Anyway, I am sending you a zoom link soon

[itchyshin]

@Mike-Garratt and @itchyshin had a meeting and a short list of things to do by Monday

@Mike-Garratt

• [ ] Referencing Figs and panels in the text
• [ ] Wrting about the results form all the combination data
• [ ] Fig legends

@itchyshin

• [x] Fixing labels and effect sizes to Male/Female
• [x] Add dotted lines to Fig 4
• [x] Get stats for male slope (Sex x Maturaity)

[Mike-Garratt]

Morning @itchyshin , just saw you pop onto the manuscript. I've just closed it so you can work on it if you want to

[itchyshin]

@Mike-Garratt - I just log onto the computer - not the MS so keep working please - I will tell you when I am on the MS - today I probably want to be able to do much till the afternoon

[Mike-Garratt]

Hi @itchyshin Ive done most of those bits now, should probably stop and do some of the other annoying work I need to do. Will try and have another look and finalize over the weekend

[Mike-Garratt]

@itchyshin, for figures 4 and 5 it may be worth checking the X-axis legends to check that absolute log response ratio and log response ratio are correct in each case. I wasnt sure about some of them

[itchyshin]

@Mike-Garratt

Thanks for letting me know - absolute values and not just abs(value) - once they have distribution this conversion does not work. We use this formula

So some of the perceived differences may be coming from that - usually folded (absolute values will be larger and this degree is based on how large sampling variances are). Does it make sense? - so many values would seem to have shifted.

But I will double-check the formula and the code.

[itchyshin]

This is from our paper showing how you take absolute values for a distribution will shift the mean value of that distribution

[Mike-Garratt]

Hey @itchyshin , is this something that you have just realized that we should be concerned about, or is it in relation to one of my comments? God statistical artifacts are a nightmare

[itchyshin]

@Mike-Garratt - we have been doing this correct - we have assumed and used folded normal distribution to model magnitude effects and this should be all correct -- many people get this wrong - but we are doing it correctly as statisticians would suggest to do

[Mike-Garratt]

OK thanks, you got me worried for a sec!

[itchyshin]

Fig 4

Fig 5

[itchyshin]

@Mike-Garratt

I have done as much as I can do - @mlagisz is still working on it. But I think we are pretty close. If you have any questions etc, please just ask. We probably do not need to meet on Monday - I pass this on to you to finish off.

Once we are ready to submit, I will create a webpage and add a weblink to the MS as we cannot usually submit a HTML file.

[Mike-Garratt]

@itchyshin Awesome, thanks so much Shinichi for your hard work this week. I'll go through and try to get this ready to send to other authors - this will include removing the track changes but I will make a new version. I'll let you know if I have any questions.

[itchyshin]

@Mike-Garratt - great - I chatted with @mlagisz - what she can do - she can finish what she needs to do tomorrow. Yes, it would be now good to remove track changes etc

[mlagisz]

@Mike-Garratt, @itchyshin - I updated PRISMA and alluvial plots. Added these to the MS text and updated relevant fragments if the Methods and results sections. Also created three supplementary tables in a separate Word document.

[Mike-Garratt]

@itchyshin @mlagisz Thanks so much for all your work on this. Making all those supplementary tables is going above and beyond and I really appreciate it!

I have now made a new version in the "third draft" folder of the Dropbox. I have accepted all track changes, addressed the final comments, added author lists etc. I have put Losia as Co senior author. I also had to add another coauthor who helped me sort out all the studies on human women.

I still need to make a table/list with all the papers included in the meta-analysis. In the meantime are you happy for me to send it out to the other authors? Assuming I can just share the supplementary material html too? Thanks again for the massive amount of work you have put into this. Mike

[itchyshin]

Thanks! - @Mike-Garratt

Yes go ahead! - I will let you know once the webpage is up and send you a link to it

[Mike-Garratt]

Hi @itchyshin and @mlagisz , we have got comments back from a couple of coauthors regarding the meta-analysis and the main comment seems to be that Fig 4 is quite hard to follow. I am thinking about how to revise this and I am wondering if we only need to show A and B as main figures, and we can move the other panels to supplementary. I also think we could add some simple annotation to make it easier to follow.

I've tried to play around with making a new main figure in powerpoint, hopefully so that you guys don't have to do more work! However, I was wondering if you can export a higher quality graphic of this figure so I can play around with it without losing image quality? I'll paste what I have tried to make in a moment so you can see what you think, but if there is a way of exporting the figure in a higher quality format I can try to make something neater.

Hope all is going well, Mike

[Mike-Garratt]

Revised fig 4 schematic.pdf

[mlagisz]

@Mike-Garratt https://github.com/Mike-Garratt - Shinichi is a bit unwell today, he will get back to you once he recovers

On Tue, Jul 19, 2022 at 2:13 AM Mike-Garratt @.***> wrote:

Revised fig 4 schematic.pdf https://github.com/itchyshin/castration_meta-analysis/files/9133574/Revised.fig.4.schematic.pdf

— Reply to this email directly, view it on GitHub https://github.com/itchyshin/castration_meta-analysis/issues/18#issuecomment-1187693334, or unsubscribe https://github.com/notifications/unsubscribe-auth/ADDIDL7FJVQ2IFHBNIPCQL3VUV7BLANCNFSM5XTT7MUA . You are receiving this because you were mentioned.Message ID: @.***>

[Mike-Garratt]

Oh no, hope he's doing ok!

No rush, Mike

---

From: Malgorzata Lagisz @.> Sent: Tuesday, July 19, 2022 2:43 PM To: itchyshin/castration_meta-analysis @.> Cc: Mike Garratt @.>; Mention @.> Subject: Re: [itchyshin/castration_meta-analysis] To do list (1 June 2020) (Issue #18)

@Mike-Garratt https://github.com/Mike-Garratt - Shinichi is a bit unwell today, he will get back to you once he recovers

On Tue, Jul 19, 2022 at 2:13 AM Mike-Garratt @.***> wrote:

Revised fig 4 schematic.pdf https://github.com/itchyshin/castration_meta-analysis/files/9133574/Revised.fig.4.schematic.pdf

— Reply to this email directly, view it on GitHub https://github.com/itchyshin/castration_meta-analysis/issues/18#issuecomment-1187693334, or unsubscribe https://github.com/notifications/unsubscribe-auth/ADDIDL7FJVQ2IFHBNIPCQL3VUV7BLANCNFSM5XTT7MUA . You are receiving this because you were mentioned.Message ID: @.***>

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[itchyshin]

@Mike-Garratt - I am much better today but I probably won't have time till tomorrow or Friday. How were comments from others? All positive or some difficult things to address? - apart from Fig 4

[Mike-Garratt]

Hi @itchyshin, yep everything is very positive although all three people who have replied said that figure 4 was confusing. I think if we try and simplify it, add notation and put part in supplementary it should be clearer. I'll also try to revise fig 3 a bit.

No worries about the timing, and if you just try and send a high quality of the original through first I can crop it and make it up a draft in powerpoint. Glad you're feeling better, Mike

[itchyshin]

@Mike-Garratt Here are new fig 4 (along with fig 5 - which is not changed) but I think you may want to do some touch up on this too.

Are they good quality enough? - I saved it as TIFF

Archive.zip

[Mike-Garratt]

Hi @itchyshin and @mlagisz I have revised the manuscript in relation to everyones comments. The main thing was revising figure 4 and being consistent with the terminology used when discussing survival effects, rather than using ageing (this was the main point of Jean-Michel).

I will add here the revised version. I think we are nearly ready to submit. I need to put the references used in the meta-analysis into a table ( think for now I will put this in supplementary), write the cover letter, and put the figures that I have removed from figure 4 into a supplementary figure.

@itchyshin - Is the supplementary html file ready to have the web link added? There is a highlighted section in the manuscript.

Let me know what you think. I am keen to get this submitted as soon as we think it is ready!

Mike

[Mike-Garratt]

Castration meta analysis 4 270722.docx

[itchyshin]

@Mike-Garratt - thanks for this. @mlagisz and I will attend to it over the weekend.

Actually, I found out Nature submission system can take a zip file so we can put our html file into a zip. I will try to make a webpage but this does not happen. We can still send the html.

I will try to finalise it as soon as I can - probably tomorrow

[Mike-Garratt]

Awesome, thanks Shinichi. I have also drafted a rough cover letter if you and/or Losia want to look at it. It might be a bit long and I am not sure whether we want to mention something about the meta-analysis methods.

Hope all is well,

Mike

[Mike-Garratt]

Cover letter.docx