BKQualit: Analysis of Qualitative Traits, Segregation and Genetic Linkage

A colour-first toolkit for the analysis of qualitative (categorical) traits in plant breeding and genetics. It tests observed segregation against the classical Mendelian expectations, fitting every standard mono-, di- and trihybrid ratio automatically and ranking them by goodness of fit, with Yates continuity correction and Monte Carlo exact tests for sparse tables. It partitions chi-square across families into pooled and heterogeneity components, so that a poor overall fit can be attributed either to the hypothesised ratio or to variation between families. Genetic linkage is estimated by maximum likelihood from two-locus second filial generation and backcross data, with logarithm of odds scores and likelihood-ratio confidence intervals for the recombination fraction. The package further computes Shannon-Weaver and Simpson diversity for descriptor states used in distinctness, uniformity and stability testing, and performs multiple correspondence analysis and Gower-distance clustering of mixed categorical and quantitative descriptors. Every analysis returns a tidy result object and a publication-ready 'ggplot2' figure. Methods follow Mather (1951, <ISBN:9780416470406>), Allard (1956) <doi:10.3733/hilg.v24n10p235> and Gower (1971) <doi:10.2307/2528823>.

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