docs: link to replacements of deprecated functions

[szhorvat]

This is a simple find-and-replace job to actually link to replacements of deprecated functions instead of simply mentioning them.

Is there a reason it wasn't done this way? Perhaps it is not standard in the R world?

Do we want [`some_fun()`] (inline code) or simply [some_fun()] (not in code style)? I see both styles used at the moment.

I am hoping this encourages people to upgrade to the non-deprecated alternative more quickly. I still see tutorials published with the old names ...

The search pattern was:

was renamed to (`.+?`)

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[krlmlr]

Would you like to share the code that did the search+replace? We might run into conflicts, I'd also like to tweak a detail.

[szhorvat]

There's no code. I did it with a text editor, and regex find/replace, so that I could review at least a subset of replacements before proceeding.

[krlmlr]

I now see you asked, [some_fun()] is preferred and could be changed everywhere as part of this PR. I'll remember merging this when all other ready PRs are done to keep conflicts contained.

[szhorvat]

[some_fun()] is preferred

I can fix this without too much trouble.

[szhorvat]

@krlmlr, this is done now.

Replacement across all files in /R:

\[`(.+?\(\))`\] $\longrightarrow$ [$1]

I didn't notice anything going wrong.

But I did notice an unusual way to refer to a class (use of parentheses), which is also fixed now.