NEWS.md

In statgenHTP: High Throughput Phenotyping (HTP) Data Analysis

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

• 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

statgenHTP documentation built on April 14, 2023, 9:12 a.m.