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Changelog

Source: NEWS.md

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

CRAN release: 2021-09-15

  • No user visible changes

statgenHTP 1.0.4

CRAN release: 2021-08-20

  • 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

CRAN release: 2021-06-18

  • No user visible changes

statgenHTP 1.0.2

CRAN release: 2021-06-10

  • 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

CRAN release: 2021-03-09

  • No user visible changes

statgenHTP 1.0.0

CRAN release: 2021-03-05

  • Initial CRAN Release