blandr module development

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by deepankardatta » Sat Feb 17, 2018 8:46 am

Dear all

I am not sure of the general etiquette, but I was looking for a few people to test a module and have some feedback on whether the module works, and on multiple different operating systems.

It's a Jamovi library for a Bland-Altman method comparison tool. The module itself can be found here if anyone is free and keen to test: https://github.com/deepankardatta/blandr/blob/master/blandr.jmo

With Thanks
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by jonathon » Sat Feb 17, 2018 9:44 pm

Yes!

I'll take a look in the next 24 hours or so.

Cheers

Jonathon
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by MAgojam » Sat Feb 17, 2018 10:54 pm

Hi, deepankardatta.

I have downloaded and compiled your source by creating the blandr.jmo module.
Loaded in jamovi 0.8.2.2, tested with win7pro and win10pro, it works (screenshot).

However, there are Messages, not informative for the user, to be deleted.
When you select Bland-Altman statistics, the message will appear in the output area:
'Names' attribute [1] must be the same length as the vector [0]

When you select Bland-Altman statistics, the message will appear in the output area:
attempt to select less than one element in get1index

This happens when the two textboxes for the input of the variables to be compared are still empty.
The msg disappear when the two variables of interest are inserted.

Always available to try updates.

Best regards.
Maurizio
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by deepankardatta » Sun Feb 18, 2018 12:51 am

MAgojam wrote:This happens when the two textboxes for the input of the variables to be compared are still empty.
The msg disappear when the two variables of interest are inserted.


Thanks very much for testing. It's great that you've pointed out the obviousness of this flaw. I've uploaded a new version that uses code from another thread here (https://forum.jamovi.org/viewtopic.php?f=11&t=117) to only run the code if both inputs are supplied. It's a learning process, but I'm getting there. I'll eventually add more analyses to the Jamovi front-end, and see if I can integrate it into the next CRAN release.

With Thanks
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by dropmann » Sun Feb 18, 2018 2:29 am

Hi deepankardatta,

One small improvement that could be done is to the Bland-Altman table. The last two columns seem to be related and the column labels are very long. A way to over come this is by adding a super title over the two columns. This can be done by adding the following properties to both the column definitions in the r.yaml file.

Second Last Column
Code: Select all
superTitle: Agreement Limits
title: Upper


Last Column
Code: Select all
superTitle: Agreement Limits
title: Lower


I work mostly with options UI layout but I think this would be helpful for the tables aesthetic and readability.

Also the table title 'Bland-Altman table' can probably just be 'Bland-Altman'. The fact that it is a table is already evident.

Finally, the group title 'Bland-Altman Plot' i feel can be comfortably reduced to just 'Plot' as it already falls underneath the title 'Bland-Altman analysis'. ('analysis' should also be capitalized inline with other analyses)

I hope this is helpful. A small tidy to what otherwise looks sharp. :)
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by jonathon » Sun Feb 18, 2018 6:07 am

here's a couple of suggestions from me:

https://github.com/deepankardatta/blandr/pull/1
https://github.com/deepankardatta/blandr/pull/2

again, don't feel like you have to merge, just some suggestions, and feel free to make these edits yourself too.

i'd also not store the .jmo file in your repo, because that means your repo will get very big, very quickly. you can also add the build/js and build/R folders to .gitignore

cheers

jonathon
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by MAgojam » Sun Feb 18, 2018 12:09 pm

Hi, jonathon.
Forgive me if I ask you a question that could be OT.

Looking at the here:
jonathon wrote:here's a couple of suggestions from me:
https://github.com/deepankardatta/blandr/pull/1

your comment for @deepankardatta, I saw in the image the presence of Update options (very interesting).

I can not find them in version 0.8.2.2 for windows I use.
Will there be soon or otherwise?

Thanks, as always, for the great work.
Maurizio
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by deepankardatta » Sun Feb 18, 2018 12:17 pm

I've integrated jonathon's changes into the main branch in GitHub. My level of coding knowledge is nowhere near as good as yours!

The module seems workable to a point that I can make iterative improvements to both the main code and the Jamovi module over time.

Thanks to MAgojam, jonathon and dropmann for the contributions and suggestions.
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by MAgojam » Sun Feb 18, 2018 1:33 pm

Hi, deepankardatta.

deepankardatta wrote:I've integrated jonathon's changes into the main branch in GitHub.


I tried your update.
It's ok for Bland-Altman statistics.

For the Bland-Altman analysis the msg appears: argument is of lenght zero
and does not generate the Plot, if the Plot Title field is empty.

Entering a title the msg disappears and generates the plot.
If you subsequently delete the given title, the plot regenerates with the title Bland-Altman Plot.

Greetings,
Maurizio
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by deepankardatta » Sun Feb 18, 2018 7:42 pm

I'll work on it over the next few days. I still haven't quite worked out the syntax I need to get this working. And I'm procrastinating too much doing this...
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