Bugs in makeLifeTable, dEntropy, and kEntropy about rage

[patrickbarks]

Few more issues:

Applies to dEntropy

1. The final calculation in dEntropy is:

abs(sum(lxmx * log(lxmx)) / sum(lxmx))

When lxmx == 0, the lxmx * log(lxmx) part yields NaN (i.e. 0 * -Inf). To get around this, instances of lxmx == 0 are first converted to 1. This trick works fine in the numerator, because the limit of x * log(x) as x approaches 0 is 0, and correspondingly 1 * log(1) == 0.

But the extra 1s added to lxmx are also getting carried into the denominator (R0 = sum(lxmx)), which is not correct. Suggest editing so that denominator is calculated before 0s are converted to 1s in lxmx.

2. There's a lot of code duplication in the final three blocks that calculate entropy with respect to the different types of reproduction: Fec, Clo, and FecClo. Suggest pulling the duplicated sections into a separate utility function that calculates entropy given vectors lx and fx (where fx is one of mx, cx, or mxcx).

Applies to kEntropy

3. When argument trapeze == TRUE, I think the kEntropy function currently implements the 'midpoint approximation' to a definite integral rather than the 'trapezoidal approximation', as advertised.

Some details on the two approximations below:
http://tutorial.math.lamar.edu/Classes/CalcII/ApproximatingDefIntegrals.aspx
https://www.r-bloggers.com/the-trapezoidal-rule-of-numerical-integration-in-r/

4. The kEntropy function returns NaN if any values of lx are 0 (due to the same log(0) issue described for dEntropy). Suggest adding code to omit late age-classes at/after which survivorship has fallen to 0.