jlaake/mrds — pull request #1 by dill (2011-10-21 14:47:01+00:00)
Title: Dave's changes - fixes and monotonicity support

First try at pull request, let's hope it doesn't go horribly wrong...

**Superficial changes**:

* The `nonmono` option is now called `mono`, since it was misleading. Now `mono=TRUE` enables monotonicity.
* `strict` is now called `mono.strict`, as above. Default `mono.strict=TRUE`, `mono=FALSE`, so when you turn on monotonicity, you automatically turn on strict monotonicity, does this seem reasonable?

**Internals**:

* Lorenzo's code now in place.
* `Rsolnp` now a required package.
* `summary()` warns that monotonicity was enforced (and specifies if it was strong).
* New element in control, `mono.points`, gives number of points to evaluate the constraints at.
* Added some example tests.
* `testthat` is now a required package.
* At the moment the ones checking equality in parameters of monotonically vs. non-monotonically constrained optimisation fail (but with differences in parameter values in the order of 10^-8).

**Bugs**:

* Removed `standardize=TRUE` in `detect()`, caused divide by zero errors. Need to think about this properly.
* Adjustment terms cause `qqplot.ddf()`, to crash, because of bug in how the cdf is calculated in `cdf.ds()` fixed.