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Re: blandr module development
Posted: Mon May 07, 2018 9:23 pm
by jonathon
hmm, not finding it ...
send again?
Re: blandr module development
Posted: Mon May 07, 2018 10:12 pm
by deepankardatta
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
Re: blandr module development
Posted: Mon May 07, 2018 11:46 pm
by jonathon
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
)
jonathon
Re: blandr module development
Posted: Tue May 08, 2018 6:49 am
by deepankardatta
Have tried again
Re: blandr module development
Posted: Tue May 08, 2018 6:54 am
by deepankardatta
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?
Re: blandr module development
Posted: Tue May 08, 2018 6:56 am
by jonathon
you can ignore that. it seems to get through without the CRANs getting upset.
jonathon
Re: blandr module development
Posted: Tue May 08, 2018 7:05 am
by jonathon
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
Re: blandr module development
Posted: Tue Mar 12, 2019 6:30 am
by mfrasch
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
Re: blandr module development
Posted: Tue Mar 12, 2019 10:01 pm
by MAgojam
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 (197.51 KiB) Viewed 10412 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.
Re: blandr module development
Posted: Tue Mar 19, 2019 2:18 pm
by deepankardatta
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.