#392 Deprecate mergeRows/mergeCols and agglomerateByRank/Prevalence

[Daenarys8]

Deprecate methods with a warning that they have been replaced with another name

• mergeCols -> mergeSamples
• mergeRows -> mergeFeatures
• agglomerateByRank -> mergeFeaturesByRank
• agglomerateByPrevalence -> mergeFeaturesByPrevalence

see #392

[Daenarys8]

Also update:

• unit tests
• vignette
• NEWS file
• DESCRIPTION file (version number)

ACK.

[Daenarys8]

Also update:

• unit tests
• vignette
• NEWS file
• DESCRIPTION file (version number)

ACK

[antagomir]

resolve the conflicts..?

[Daenarys8]

resolve the conflicts..?

ack

[antagomir]

Can we implement the same name change to:

• miaViz
• miaTime
• miaSim

Including R/ files, vignettes, and unit tests.

Should be a straightfwd fix.

(if relevant; might not be used in all these packages?)

@Daenarys8 would be the most handy if you could do this on the same go?

[antagomir]

@ake123 could you update these names to OMA?

[ake123]

I tried to render the OMA book and having some trouble in updating it. Even updating it with the above changes is throwing errors. After syncing the repo I am having this error

Quitting from lines 294-296 [dmm5] (24_clustering.Rmd)
Error:
! 'name' does not a list of DMN objects.
Backtrace:
 1. miaViz::plotDMNFit(tse_dmm, type = "laplace", name = "DMM")
 2. miaViz::plotDMNFit(tse_dmm, type = "laplace", name = "DMM")
 3. miaViz (local) .local(x, name, type, ...)
 5. mia::getDMN(x, name)
 6. mia (local) .local(x, name, ...)
 7. mia:::.get_dmn(x, name)
Execution halted
Error in Rscript_render(f, render_args, render_meta, add1, add2) : 
  Failed to compile 24_clustering.Rmd

[antagomir]

@BananaCancer ?

[BananaCancer]

Could I see the dmm related code being executed @ake123 ? The OMA book passed the checks and runned well on my end last time I checked.

Maybe the latest version of miaViz isn't being used?

[ake123]

Installed the necessary dependencies to build the book before rendering using "BiocManager::install(remotes::local_package_deps(dependencies=TRUE))"

[antagomir]

Ok - and that's an OMA issue (to be discussed in github/OMA). Indeed the latest miaX pkgs need to be updated to Bioc first.. usually in that order.