Todo

New argument focus for Different Singular Value Partitionings, including GH, JK, SQRT, HJ.

New function ggbiplot() function using ggplot2 graphics to draw the biplot.

Average Environment Coordinate

Bootstrap testing for PCs (Forkman 2019 paper)

Bootstrap conf int

gge 1.5 (20 Jul 2020)

• Please use gge(data,formula) instead of gge(formula,data).

• New argument ggb=TRUE to request construction of GGB biplot.

gge 1.4 (15 May 2018)

• Use cex.gen=0 to omit genotype names.

• On some Windows machines, library(rgl) crashes R, perhaps because of a DLL conflict with Windows. Removed @import rgl so that rgl is not loaded by default, and now biplot3d uses calls like rgl::text3d.

gge 1.3 (14 Dec 2017)

• The nipals() function using C++ code has been removed.

• The rnipals() function has been removed.

• The gge package now imports the nipals package, which is new.

gge 1.2 (25 May 2017)

• New function nipals() for finding principal components using C++. Code from pcaMethods package.

• New function rnipals() for finding principal components in R.

• New function biplot3d() to draw 3d biplots using rgl package.

• Modifed main, subtitle, xlab, ylab arguments to allow removal.

• Changed title argument to main for consistency with other packages.

• Now using testthat and covr packages.

• Added package logo on github.

gge 1.1 (8 Oct 2016)

• Added zoom.gen and zoom.env arguments to biplot() for M.Zoric.

• Moved tests to tests/gge_tests.R

gge 1.0 (14 Dec 2015)

• Package gge is split off from agridat package.

• Added origin, hull arguments to biplot().

gge 0.1 (2013)

• Added gge() to agridat package.

gge 0.0 (May 2004)

• Created function gge() to fit and plot GGE biplots.

A history of NIPALS functions

1. 2007. Created nipals() based on pcaMethods::nipalsPca(). Modified the function for faster execution and submitted a patch back to pcaMethods.
2. 2010. Henning Redestig created a C++ version of NIPALS for the pcaMethods package.
3. 2017. The gge::nipals() R function is re-named rnipals(), and a new nipals() function is created, based on the C++ code in pcaMethods. Released gge version 1.2.
4. 2017. Discovered that mixOmics::nipals() is a pure R function that is faster than the C++ version, so gge::nipals() was re-written into a pure R function. The C++ version was removed from the gge package.
5. The gge::nipals function is moved to a new package, nipals::nipals. The function is optimized for performance, improved to better handle missing values and to orthogonalize the principal components.