blandr module development

Everything related to the development of modules in jamovi

by jonathon » Mon May 07, 2018 9:23 pm

hmm, not finding it ...

send again?
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by deepankardatta » Mon May 07, 2018 10:12 pm

Sent again. If you're not getting it will try from another address.

Everything should be finalised to the CRAN version 0.5.0 codebase - https://CRAN.R-project.org/package=blandr
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by jonathon » Mon May 07, 2018 11:46 pm

yeah, i'm really not getting it.

and i never don't get emails (although some have suggested there's some 'selection bias' in this assessment :P)

jonathon
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by deepankardatta » Tue May 08, 2018 6:49 am

Have tried again
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by deepankardatta » Tue May 08, 2018 6:54 am

As an aside a bit of advice on CRAN submission would be great with regards to the Jamovi imports. So I've got m y package accepted into CRAN. However there are some errors with the webcheck: https://cran.r-project.org/web/checks/c ... landr.html

The area that I wanted to get a bit of advice from was this:
"Result: NOTE
Namespaces in Imports field not imported from:
‘R6’ ‘jmvcore’ ‘knitr’
All declared Imports should be used. "

How did you get around this issue previously, or did you put these in the suggest field?
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by jonathon » Tue May 08, 2018 6:56 am

you can ignore that. it seems to get through without the CRANs getting upset.

jonathon
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by jonathon » Tue May 08, 2018 7:05 am

a bit more background, we deliberately don't put imports in the NAMESPACE.

if you do, the package loads *all* the dependencies when it's first used, leading to a long delay when first used, and lots of RAM usage. this won't be a big issue for blandr because it only has few dependencies, so you can put some entries for these packages in the NAMESPACE if you like.

but for jmv, we have *dozens* of dependencies, and this is a total killer.

if you leave them out of the NAMESPACE and refer to them with the packageName::foo(), then they are only loaded on demand. this is way better.

jonathon
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by mfrasch » Tue Mar 12, 2019 6:30 am

Thank you for creating an elegant package for Bland-Altman testing! I used it within JAMOVI and have a question about the plot's Y axis "Difference" the GUI / R package generate. Is it following the default setting for "difference" that's being plotted? Is it possible to adjust it for the alternative argument that the R package blandr.draw provides via "y.plot.mode" (proportional difference).

The broader question is: Can the optional switches in blandr.draw be used from within JAMOVI?

Thank you!

Martin
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by MAgojam » Tue Mar 12, 2019 10:01 pm

Hi, @mfrasch.
The blandr module for jamovi, uses the function jamoviBAanalysis, which at the moment, lacks some options, present instead in blandr.draw.
The option (y.plot.mode = 'proportion') is one of the missing ones and by default is (y.plot.mode = 'difference').
If you have installed the Rj module you can try this simple code with its editor
Code: Select all
library(blandr)
library(ggplot2)
jamoviBAanalysis(data,
                 method1     = 'MiniWrightFirst',
                 method2     = 'MiniWrightSecond',
                 overlapping = FALSE)

blandr.draw(data,
            method1     = data$MiniWrightFirst,
            method2     = data$MiniWrightSecond,
            overlapping = FALSE,
            y.plot.mode = 'proportion')

and get an answer to your question, as you can see in the attached screenshot.

ScreenShot_bland.altman.PEFR.1986.png
ScreenShot_bland.altman.PEFR.1986.png (197.51 KiB) Viewed 1338 times

I think and I hope that @depankardatta, as soon as he has some time, will come back to work on this excellent and very interesting module.

Cheers
Maurizio

-------
Note:
Forgive me, my English is poor, but reading what I write can have the advantage of helping to solve possible problems of constipation. :stuck_out_tongue_winking_eye:
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by deepankardatta » Tue Mar 19, 2019 2:18 pm

Hi to both @mfrasch and @MAgojam

I'd be a bit cautious with using the proportion mode at the moment. It is slightly broken. However I am planning to update it within the next version of blandr, which hopefully I can wrap up finishing in the next week or so. After this has been done I'll update the jamovi module.

In essence the Jamovi module was just made to be a simple interface to the blandr library. I've just not got round to working on it for some time. I will let you know once things are updated.
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