Convert log to ln

[e-perl-NOAA]

Originally posted by @iantaylor-NOAA in #232 (comment)

I've been in the habit of always using log() to mean ln(), but reading more about the two options, it's clear that the interpretation of log() depends on the discipline, context, or country (see https://en.wikipedia.org/wiki/Natural_logarithm#Notational_conventions for instance).

Since SS3 is used by folks with different backgrounds I'm now convinced that using ln() throughout the documentation (and my own future writing) makes sense for clarity. I would still use the spelling "log" in terms like log-likelihood, and I'm not worried about how it's represented in the code, or the output files, but in user manual equations I like the idea of switching from log() to ln().