This file documents updates and changes in package ordinal since version
2010.03-04

March 04 2010:

- First version of the package is created.

2010-04-06:

- removing class "clm.fit" from results of finalizeRho.
- moving offset computations from logLik and gradient funtions to
  newRho function.
- Bug fixed in grad.lambda
- checks and warning messages added to profile.clm
- a warning is now given if the profile fits do not converge
- profile.clm has grown the argument 'stepWarn', which gives a
  warning if the no. profile steps in each direction (up or down) is
  less than stepWarn (default 8), which indicates that the profile is
  unreliable.
- Bug in loglog-link for clmm fits fixed.
- Missing values are handled better in clm and clmm.
- clmm has grown an argument 'sdFixed' which assigns a fixed value of
  the standard deviation of the random effects. Optimization is
  performed with respect to the remaining parameters.
- profile.clmm, confint.profile.clmm and plot.profile.clmm are now
  available. Profiling is restricted to the standard deviation
  parameter of the random effects.
- control.clm and control.clmm now handles the control parameters.

2010-05-06:

- allowing the formulas to be constructed outside clm and clmm
  (the formulas are evaluated in the parent frame before the variable
  names are extracted)

2010-05-17:

- Better evaluation in case of non-standard formula usage allowing
  e.g. clm(data$y ~ data$x).
- Better handling of ill-defined variance-covariance matrix of the
  parameters in summary methods for clm and clmm objects.

2010-06-12:

- Standard Gauss-Hermite quadrature is now available via the nAGQ
  argument to clmm.
- Core functions implemented in C for speed. This includes all link
  functions, update of the conditional modes of the random effects,
  adaptive Gauss-Hermite quadrature and standard, i.e. non-adaptive
  Gauss-Hermite quadrature. Select R or C implementation via the
  argument doFit to clmm.
- Bug in random effects estimates and their conditional modes
  corrected. 

2010-07-06:

- Bug in predict when 'newdata' was supplied is now corrected.

2010-07-23:

- Better descriptions of random effect estimates and fitted values in
  the clmm help page.

2010-10-22:

- Updated help page for predict.clm/clmm.

2010-12-13:

- Bug in predict.clm corrected for models with nominal effects and
  newdata supplied (thanks to Simon Blomberg for the bug report).

2011-04-21:

- Better message from summary.clmm when Hess = FALSE
- endpoint thresholds are now closer to infinity. This is due to a bug
  report from Ioannis Kosmidis (March 30, 2011); the model estimates
  weren't right with very large scale effects. Tests are added to
  testCLM.R 
- gradTol in clm.control now defaults to 1e-5 rather than 1e-4.
  convTol is retained at 1e-4, so we are asking for closer convergence
  than we require.
- getGnll no longer returns Inf if !all(pr > 0)
- link utility functions are moved from clm.R to linkUtils.R
- extensive testing for NaN-specials in C-code for the link functions
  is added. 
- details section added to clmm.control.Rd with comment about using
  "central" gradients with the ucminf optimizer.
- examples updated in confint.Rd

2012-01-19:

- Changed evaluation of formula in clm to make clm more forgiving for
  evaluation inside other functions.

2012-05-09:

- Updated evaluation of formula in clmm, cf. resent update of clm.

2012-05-22:

- Better evaluation of fitted probabilities. This should reduce the
  occurance of the "sqrt(phi2) : NaNs produced" error message.
- Improved evaluation of control parameters in clmm using the new
  function getCtrlArgs.
- Better warning if intercept is attempted removed in clmm.

2012-05-23:

- Adding useMatrix argument to clmm.control
- Using getFitted in clm
- Implementing getFittedC in C and updating C code for fit.clmm.ssr
  with better and faster evaluation of fitted values   
- Introduction of links.h, links.c and get_fitted.c in /src

2012-05-29:

- Correcting formula interpretation in clm to allow for really long
  formulas.
- Better evaluation of control arguments in clmm (adjustment of
  getCtrlAgs).
- Adding clmm.control.R to ./test

2012-09-10:
- Computing Newton step in clm with solve() rather than
  .Call("La_dgesv", ...) to accomodate changes in R base. 

2012-09-11:
- Using globalVariables() conditional on getRversion() >= '2.15.1'.