Eagle News

Upcoming

Developing a multi-GPU version of Eagle
* looking at distributing GPU-Eagle within singularity.

Aug 2020

Eagle 2.4 uploaded to CRAN.
* Fixed bug in plotting function in OpenGUI
* Improved look of PlotAM
* Added interactive option to PlotAM to give users the option of saving the plot to file.

Julu 2020

Eagle 2.3 uploaded to CRAN.
* Changed gamma parameter in AM function to lambda parameter to be consistent with extBIC parameterisation.
* Added plot function PlotAM. This capability was in the GUI but not as a function.
* Added extra table of summary information to SummaryAM function.
* Fixed bug in plotting function in GUI.

March 2020

Eagle 2.2 uploaded to CRAN.
* Ability to read vcf files added to ReadMarker function
* Revised SummaryAM to also calculate and report allelic effect sizes
* Significant (order of magnitude) improvement in speed to FPR4AM (used for calculating optimal gamma parameter for model building process)
* Changed home screen in OpenGUI app because Eagel workflow has changed.
* Added Bioinformatics citation for Eagle package

Nov 2019

Eagle 2.1.1 hosted on CRAN.
* Fixed bug introduced by last change that would cause ReadMap function to crash.

Nov 2019

Eagle 2.1.0 hosted on CRAN.
* Continued improvement of handling of missing data.
* Better handling of errors in OpenGUI. Previously, app would crash if a file input error was encountered.

Nov 2019

Eagle 2.0.0 hosted on CRAN.
* This is the first of several planned performance improvements. With this version, users should see at least a 50% increase in speed.

Aug 2019

Eagle 1.5.2 hosted on CRAN.
* Minor change to noalias feature in cpp code.

May 2019

Eagle 1.5.1 hosted on CRAN.
* Minor change to GUI. Attempting to make GUI more robust.
* Cleaned up shiny app.R by removing library calls
* Havent been able to solve the mysterious uv_write errors that are written to the R consul when GUI is run. The errors are intermittent and random but have no effect on performance or the analysis.

May 2019

Eagle 1.5.0 hosted on CRAN.
* Significant change made to GUI - a plotting page has been add. Users can now examine the change in score statistic (used for identifying the next "best" SNP to enter the model), across a chromosome or genome. This can be done for each step of the model building process.

April 2019

Eagle 1.4.0 hosted on CRAN.
* Modified SummaryAM function to work with Z matrix.
* Minor changes made to Findings page of GUI.

Febuary 2019

Eagle 1.3.0 hosted on CRAN.
* Fixed missing data issue with FPR4AM where it would crash if the trait contained missing data.
* Added capacity to ReadPheno to accommodate additional read.table arguments such as skip.

November 2018

Eagle 1.2.0 hosted on CRAN.
* Modified FPR4AM so that it will give the best gamma value for a user-defined false positive rate, trait, and analysis model.
* Further developed online R documentation for AM function.

August 2018

Eagle Demo site went live, giving users an opportunity to trial the Eagle GUI on some test data.

August 2018

Eagle 1.1.0 hosted on CRAN.
* fixed memory bug on windows systems.
* added Z matrix functionality to accommodate data where an individual, for a trait, may have multiple measurements.
* replaced problematic tk_choose.files with shinyFiles for improved file browsing.
* changed Makefiles so that Eigen is now row major, doubling the speed.
* added new function FPR4AM to calculate, empirically, the false positive rate (FPR) for a given gamma value for extBIC.

September 2017

Eagle 1.0.3 hosted on CRAN