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cwad - Connectivity-Weighted Allocation and Comparison of Field-Plot Designs

A reproducible mixed-model toolkit for plant-breeding trial design. It evaluates any replication allocation under a known genetic relationship (kinship) matrix using one common linear-mixed-model engine on genotype means. Crucially, allocation and analysis model are crossed rather than confounded: every allocation can be scored both with and without kinship, so the precision gain attributable to a design can be separated from the gain attributable to the kinship-based analysis adopted alongside it. It computes A-optimal, connectivity-aware allocations via rank-1 Sherman-Morrison updates, and provides Monte-Carlo stress tests for outlier shrinkage and kinship mis-specification, each with a matched control arm.

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3.70 score 1 stars

BKBreed - Colourful Biometrical Analysis for Plant Breeding and Genetics

A compact, colour-first toolkit for the analysis of plant breeding and genetics field experiments. It provides analysis of variance for the randomised block design (RBD) and factorial RBD, a check-anchored intra-block analysis for augmented alpha-lattice designs, and the core biometrical-genetics workflow used in crop improvement: estimation of genetic variability (genotypic and phenotypic coefficients of variation, broad-sense heritability, expected genetic advance), genotypic and phenotypic correlation, path-coefficient analysis, line x tester and Griffing diallel combining-ability analysis (general combining ability and specific combining ability), Mahalanobis D-square genetic-divergence analysis with Tocher and hierarchical clustering, and genotype-by-environment stability analysis (Eberhart-Russell regression and the additive main effects and multiplicative interaction (AMMI) model). Methods follow Griffing (1956) <doi:10.1071/BI9560463> and Eberhart and Russell (1966) <doi:10.2135/cropsci1966.0011183X000600010011x>. Every analysis returns a tidy result object and a publication-ready 'ggplot2' figure using a bespoke high-contrast colour system.

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3.18 score 1 stars 3 scripts 314 downloads

BKMutate - Statistical Analysis of Induced Mutagenesis Experiments in Crop Plants

A colour-first toolkit for the statistical analysis of induced mutagenesis experiments in crop plants. It fits dose-response models to physical and chemical mutagen data and estimates the median lethal and growth-reduction doses (LD50, GR50) with confidence intervals obtained from Fieller's theorem; quantifies first-generation biological damage (lethality, injury and pollen sterility); and estimates mutagenic effectiveness and mutagenic efficiency. Effectiveness and efficiency are conventionally reported as point estimates only; this package treats them as functions of binomial proportions and supplies interval estimates by the delta method on the logarithmic scale and by the nonparametric bootstrap. It further provides chlorophyll mutation spectrum analysis with tests of homogeneity and diversity, generalised linear models for second-generation mutant counts with formal assessment of overdispersion, and formal comparison of mutagens including relative biological effectiveness. Every analysis returns a tidy result object and a publication-ready 'ggplot2' figure. Methods follow Konzak et al. (1965, ISBN:9789201150653), Fieller (1954) <doi:10.1111/j.2517-6161.1954.tb00159.x> and Katz et al. (1978) <doi:10.2307/2530610>.

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3.00 score 1 stars 269 downloads

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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3.00 score 1 stars 288 downloads

BKVerify - Consistency Auditing of Reported Plant Breeding Statistics

Audits published or draft plant breeding tables for internal arithmetic consistency. Analysis of variance tables, precision statistics and genetic variability parameters are jointly over-determined by exact algebraic identities; 'BKVerify' recomputes every derivable quantity using rounding-interval arithmetic and reports a value as inconsistent only when no combination of values inside the reported rounding intervals can satisfy the identity. The package deliberately restricts itself to relationships that hold irrespective of which variance-component definition an author adopted, so that flagged results reflect arithmetic inconsistency rather than methodological disagreement. Implemented checks cover analysis of variance internal structure, coefficient of variation, standard error of mean and critical difference, the genetic advance identity of Johnson, Robinson and Comstock (1955) <doi:10.2134/agronj1955.00021962004700070009x>, the relation between genotypic and phenotypic coefficients of variation and broad-sense heritability, and admissibility of reported correlation matrices.

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2.70 score 1 stars 303 downloads