MAPpoly v. 0.4.1 Release Notes

MAPpoly v. 0.4.1 introduces parallelized pairwise analysis to improve computational efficiency. This version integrates RcppParallel, significantly reducing runtime for large datasets while maintaining accuracy and robustness in genetic map construction.

Key Updates in MAPpoly v. 0.4.1

• Parallelized Two-Point Analysis – The pairwise recombination fraction estimation step now leverages multi-core processing, improving computational performance.
• Improved Efficiency – Reduces processing time, particularly for datasets with many markers (>10,000).
• Scalability Enhancements – Optimized for high-performance computing (HPC) environments, enabling more efficient map construction for diploids and autopolyploids
• General Improvements & Bug Fixes – Various refinements to ensure stability and accuracy.

These updates enhance the package's ability to handle large and complex genetic datasets efficiently.

Fix minor bugs

• Added function find_blocks
• Added several utility functions
• Update function filter_individuals
• Update filtering graphics
• Update some color schemes

In this release,

Since version 0.3.0 we:

• Minor modifications to the test functions
• Changed 'smacof' package to suggested

In this release,

Other changes since version 0.3.0 we:

• Added function est_pairwise_rf2 to avoid memory overflow in personal computers when estimating recombination fraction in large number of markers.
• Added Vignette
• Added function 'export_qtlpoly'
• Added function 'filter_individuals'
• Changed the name of function 'calc_homoprob' to 'calc_homologprob'

In this release the suggested packages are used conditionally, following §1.1.3.1 of 'Writing R Extensions'. We also added the flag LazyDataCompression: xz in DESCRIPTION file, following §1.1.6 of 'Writing R Extensions'.

Other changes since version 0.2.1

• Fix minor bugs
• Update documentation
• Update DESCRIPTION file
• Added function plot_GIC

MAPpoly version 0.2.1

This release fixes the error found when checking with "no-long-double" Linux check.

Also it implements the following:

• Added estimation of two-point recombination fraction using genotype probabilities
• Added 'read_fitpoly' function
• New graphical feature in function 'rf_snp_filt'
• Added option to plot large recombination fraction matrix using cell aggregation for a given order
• Added estimation of map distance using the MDSMap package procedure (projects the MDS order onto a single dimension using principal curves)

First CRAN resease