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>.
Documentation:
Downloads:
Linking:
Please use the canonical form
https://CRAN.R-project.org/package=BKQualit
to link to this page.