# CHANGES IN RRPP 0.6.1 (Patch Release)

### NEW FEATURES
### OTHER CHANGES
### BUG FIXES
* Refined `manova.update` to have more efficient code and better notes.
* Fixed a bug in `summary.manova.lm.rrpp` that mixed up rows and columns of a matrix of random stats.
* Fixed a bug that eliminated row names for `lm.rrpp` data when converting a vector of data to a matrix.
* Added a step to coerce single-column matrices to vectors in `rrpp.data.frame` to prevent downstream issues.
* Made it possible to use `trajectory.analysis` with univariate response data, omitting vector correlations output.

# CHANGES IN RRPP 0.6.0 (Minor Release)

### NEW FEATURES
* `ordinate` function.
* `summary.ordinate` and `plot.ordinate` S3 functions
* `add.tree` function (for plotting with `plot.ordinate`)

### OTHER CHANGES
* Updated support functions for `lm.rrpp` to provide better flexibility for different formulas.  
* Changed `$LM$data` in `lm.rrpp` to be a model frame rather than a data frame, consistent with `$model` from `lm`.

### BUG FIXES 
* Fixed issue with transformation of dependent variable -- e.g., log(y) -- in formula for lm.rrpp. The bug was a failure to transform the variable(s).

# CHANGES IN RRPP 0.5.2 (Patch Release)

### BUG FIXES 
* Fixed issue with GLS estimation of coefficients in pairwise (used GLS residuals instead of
transformed residuals, by mistake).

# CHANGES IN RRPP 0.5.1 (Patch Release)

### BUG FIXES 
* Fixed data.frame error in lm.rrpp for within-formula transformations (like log or poly).
* Arranged effect.type argument options in lm.rrpp to match anova.lm.rrpp).

# CHANGES IN RRPP 0.5.0 (Minor Release)

### NEW FEATURES
* `prep.lda` A new function to generate arguments for `lda` in the `MASS` library.

### OTHER CHANGES
* `classify` deprecated (in favor of `prep.lda`)
* Changed the ouput structure for lm.rrpp objects.  Either OLS or GLS statistics are returned, not both.  There is no longer differentiation between GLS and weighted stats, as weighted stats are GLS estimated stats.  The difference is obvious with the inclusion of weights or Cov matrix.
* No longer a `verbose` option with `manova.update`.  The function was optimized to provide verbose output without having to slow down computation time.

### BUG FIXES 
* Fixed some issues with linear model weights and offset, throughout many functions.
* Sweeping changes to be CRAN 4.0 compliant



# CHANGES IN RRPP 0.4.3 (Patch Release)

### NEW FEATURES

### OTHER CHANGES

### BUG FIXES 
* Fixed a parallel processing issue with internal function, `SS.iter` (produced incorrect RSS).
* Fixed multi-model anova TSS issue.
* Fixed an issue with the centering of trajectories in `trajectoty.analysis`.
* Fixed an issue for calculating fitted values for GLS in the `lm.rrpp` function.


------

# CHANGES IN RRPP 0.4.2 (Patch Release)

### NEW FEATURES

### OTHER CHANGES
* Added `tol` and `pc.no` arguments to `model.comparison` (were fixed before) so that users have more control of the analysis.

### BUG FIXES 
* Tweaked logL tolerance calculation to be consistent with `prcomp`.
* Tweaked support code for `lm.rrpp` to work better with missing data frames.
* Fixed absolute eigenvalue issue with Cov.proj.
* Added forgotten code from last update to fix non-full rank design matrices.
* Fixed `trajectory.analysis` traj.list issue, to not use grep for sorting trajectories.  (Now lexical ordering of interactions is used.)
* Changed `det` to `determinant` in all needing functions, to use modulus for near-singular matrices
* Fixed bug in `plot.lm.rrpp` (code lines out of order)

------

# CHANGES IN RRPP VERSION 0.4.1 (Patch release)

### NEW FEATURES

### OTHER CHANGES
* Updated source in Description.

### BUG FIXES 
* Fixed univariate data issue with `model.comparison`
* Fixed xlab flexibility issue for regression plots in `plot.procD.lm`
    
------

# CHANGES IN RRPP VERSION 0.4.0 (Minor release)

### NEW FEATURES
* `manova.update` function
* `trajectory.analysis` function
* `reveal.model.designs` function
* New vignette for `ANOVA versus MANOVA in RRPP`

### OTHER CHANGES
* Added a pairwise variance comparison for the `pairwise` function.

### BUG FIXES 
* Tuned F-stat calculations to allow for model-specific residual variances, for multiple terms.
* Updated `procD.lm` to better work with data in the global environment rather than a data frame. 

------

# CHANGES IN RRPP VERSION 0.3.0 (Minor release)

### NEW FEATURES
* Added `print.summary.pairwise`.
* Added `model.comparison` function.
* Added classify function.

### OTHER CHANGES

* Added an update to allow classify to work on univariate data.

### BUG FIXES 

* Tuned criterion for assessing whether generalized inverse should be performed.
* Fixed bug with GLS variance estimation in pairwise.
* Fixed some issues with univariate data for `classify`.
* Fixed some issues with univariate data for `pairwise`.
* Fixed the logL function within model.comparisons for GLS determinants 
    (was returning 0).
* Fixed some issues with the aov.multimodel subfunction of `anova.lm.rrpp`, related to GLS permutations and intercept only models.  
* Added random SS output to aov.multimodel subfunction of `anova.lm.rrpp`, so that it can be called by other functions/packages.
    
------

# CHANGES IN RRPP VERSION 0.2.0 (Minor release)

### NEW FEATURES

* `pairwise function`: allows pairwise comparison of means or slopes for a `lm.rrpp fit`.
* A vignette for using RRPP, which is the same as Appendix S2 in Collyer and Adams 
    (2008). RRPP: An R package for fitting linear models to high-dimensional data using 
    residual randomization. Methods in Ecology and Evolution.  (submitted)

### OTHER CHANGES

* Added multi-model inference capability to `anova.lm.rrpp`
    
### BUG FIXES 

* Fixed issue for `coef.lm.rrpp` tests when type II or type III SS is chosen, to make sure that appropriate coefficients are used.
 
------

# CHANGES IN RRPP VERSION 0.1.0 (Major release)

###	New Release!

###	New features

*	`anova.lm.rrpp.r`
*   `coef.lm.rrpp.r`
*	`lm.rrpp.r`
*	`predict.lm.rrpp.r`
*	`RRPP.support.code.r`
*	`RRPP.utils.r`

* Added a `NEWS.md` file to track changes to the package.
