# statgenHTP 1.0.6.1

- 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

# 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

# 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

# statgenHTP 1.0.0