added aldex.plot function#24
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tldr:
altered functions or files:
cohensd() - now reports expected values for cohensd, estimate, pooled SD, overlap
ALDEx3-Quickstart - incorporates a plotting section
Namespace to support this
Added:
aldex.plot() function
Explanation:
I have added a simple plotting function for ALDEx3. It now captures the full functionality of ALDEx2 plotting and the old aldex.effect() function.
It can generate volcano, effect, MA (Bland-Altmann) and waterfall plots from the output of aldex(). Many graphical parameters can be altered for the plots
I have tested it on several different pairwise comparisons, and plan to expand to include the ability to plot contrasts from more complex linear models when I have the time
The function uses the aldex.summary() and an updated cohensd() function internally to obtain some information, and pulls other data from the raw output.
I also included a section in the vignette on how to use the plots and their parameters.
All documentation is via roxygen2
This version builds cleanly via devtools::check(vignettes=F).
The vignettes do not build, but they do compile cleanly with rmarkdown::render('ALDEx3_quickstart.Rmd').
rhub fails at the vignette building stage, but is clean otherwise
If you don't like the changes, I can write a different version of cohensd to keep your version intact