fix issue #56

[dhicks]

Implements fix to issue #56 proposed by @Maren-Eckhoff

[cpsievert]

Thanks, and sorry for the long wait...@kshirley merging #80 doesn't necessarily fix #56, so lets check for 0 as well?

[cpsievert]

perhaps a more robust solution would be:

jensenShannon <- function(x, y) {
    m <- 0.5*(x + y)
    val <- 0.5*sum(x*(log(x)-log(m))) + 0.5*sum(y*(log(y)-log(m)))
    if (is.finite(val)) val else 0
  }

[kshirley]

is.finite() doesn't quite work here, I don't think.

A good test case is

x <- c(0, 0, 0.2, 0.8)
y <- c(0, 0.2, 0, 0.8)

The Jensen Shannon Divergence should return 0 for the first element, and non-zero for the last 3 elements, before summing.

I gotta run right now but I can look at this tonight, should just be a couple line fix.

I think in theory we didn't worry about this because technically with the priors in LDA, you should never have exact zeroes in phi or theta, but we probably should have realized they would occur with rounding! :)

[kshirley]

Ah, the solution above from @dhicks based on @Maren-Eckhoff 's earlier comment works.

Let's just replace log(x/m) with (log(x) - log(m)) and replace log(y/m) with (log(y) - log(m)) in the PR from @dhicks to make it more robust, as suggested in #80

[cpsievert]

Done in c7234d7