# statgenHTP 1.0.9.1

* No user visual changes.

# statgenHTP 1.0.9

* Tests are modified for compatibility with the upcoming version of ggplot2.
* `statgenHTP` no longer imports `reshape2` and `factoextra`.

# statgenHTP 1.0.8

* A small bug in a helper function for `fitSplineHDM()` is fixed. Impact on the results is very minimal.
* Several improvements of the documentation and examples.

# statgenHTP 1.0.7

* For spatial models fitted with SpATS it is now assured that the number of segments used for rows and columns is divisible by the value of nest.div used. This is done to accommodate a minor fix in an upcoming release of SpATS.
* Functions no longer rely on soft-deprecated ggplot2 functions.

# statgenHTP 1.0.6

* The package has been extended by functions for modelling evolution of the genetic signal. This extension consists of functions `fitSplineHDM()` for fitting a hierarchical data model, `predict.psHDM()` for making predictions based on this model, and `plot.psHDM()` for plotting the results. The methods used are described in a new vignette.
* A small bug in `detectSingleOutMaize()` is fixed. Observations with a missing value for one of the involved traits are no longer tagged as outliers.

# statgenHTP 1.0.5

* No user visible changes

# statgenHTP 1.0.4

* The `removeSerieOut()` function now has an extra argument reason allowing for restricting removal of outliers to one or more reason the outliers where tagged.
* The `plot` function for `serieOut` objects now has an extra argument reason allowing for restricting the plotting of outliers to one or more reason the outliers where tagged.
* The `detectSerieOut()` function is now able to handle plotIds with irregular naming, i.e. plotIds starting with a number.
* The results of `estimateSplineParameters()` can now be plotted in a box plot and histogram.
* In the `estimateSplineParameters()` function multiple parameters can now be estimated at once.
* A bug in `detectSerieOut()` that caused slope outliers to be never detected is fixed.
* A bug causing predictions to be made in `fitSpline()` for missing values at the beginning or end of a time course is fixed.
* The `detectSerieOut()` function now checks for number of plotIds per plant in the correct location leading to a more user friendly error message.

# statgenHTP 1.0.3

* No user visible changes

# statgenHTP 1.0.2

* Plotting second derivatives of fitted splines, plotted first derivatives. This is fixed now. 
* The `detectSerieOut()` function now uses an extra criterion for checking if time courses our outlying. See the function documentation and vignettes for a full explanation of this new criterion.
* The parameter `trait` in the `removeSerieOut()` function is renamed to `traits` and now accepts a vector of traits that for which outlier values can be replaced by `NA`.
* Plotting the output of `detectSerieOut()` now has an extra parameter `geno.decomp` to restrict the output to selected levels of the geno.decomp variable in the data.
* Computing the area under the curve in `estimateSplineParameters()` now allows the specification of the time unit used on the x-axis.
* Fitting models using SpATS is now done using the option `centered = TRUE` by default.

# statgenHTP 1.0.1

* No user visible changes

# statgenHTP 1.0.0

* Initial CRAN Release
