RStudio character limit

I have been using my makebinary function without any issues, but now that I am working with a much larger tree, I am running into a problem with the number of characters in my newick tree.

My newick tree is 4434 characters long. Add to that the makebinary function call, and the whole command ends up being 4448 characters long. I found out that RStudio truncates commands to be 4096 characters. Fortunately, running it in the normal R console works without issues, but even that seems to have a 4096 character limit:

Note how there is now a new line (headed by the +) at the beginning of the second to last line.

RStudio

I was first introduced to RStudio when I took STA141 with Duncan Temple Lang.  At the time, I was using a PC, and it made things much simpler.  A few of the features that I love about it:

1) Color scheme for scripts.  I can see at a glance what's a comment, and the parentheses pop out at you.  This was something I envied about Macs when I used to use my PC exclusively.  I do wish you could personalize it a little more, but the schemes they have are great.  I personally like Cobalt.

2) Balancing parentheses and quotations.  Yes, this can get obnoxious if you are tweaking existing code rather than starting from scratch, since if you try to type an end quote, it will be interpreted as another beginning quote.  But I find being able to see what's matching your current end parenthesis incredibly helpful.  Besides, if you don't like it, you can easily turn it off in the preferences.

3) Everything in one window.  This wasn't a step up from my PC version since the normal R console keeps everything in one window, but it's so nice to have everything (script, console, history, help pages, graphics) in one window.