Scales package - do we use it? about spectratrait HOT 7 CLOSED

Ok, I see how I missed it. "alpha" is also part of ggplot2. I was looking in the wrong part of the output.

from spectratrait.

I couldn't find where we use it. It appears to be loaded twice, in apply_sserbin and the simple example, but I don't see it being used. At least according to the package NCmisc

from spectratrait.

Maybe I should look at all the packages we use and see if there is any others we call for but don't use?

from spectratrait.

Thanks! @neo0351 lets wait for a full house cleaning until I have the base package version PR done

from spectratrait.

@neo0351 OK so I know where we use "scales"

We use it to generate the "alpha" transparency in some of the plotting, like in the plotrix::plotCI

alpha(colour, alpha = NA)

from spectratrait.

We should check our code for issues like this and make sure we are using package::function where there are conflicts like this alpha thing.

from spectratrait.

Agreed, the fix for this is to make sure the examples have scales::alpha()

from spectratrait.