Tukey's Honestly Significant Difference (HSD) Post-Hoc Mean Comparison Engine

The `compute_tukey` function executes a high-precision pairwise post-hoc mean separation analysis using Tukey's Honestly Significant Difference framework.

Usage

compute_tukey(
  data,
  trait,
  anova_results,
  total_replications,
  alpha = 0.05,
  reporting_level = 2
)

Arguments

data: A verified data.frame containing the columns Genotype and the phenotypic trait under evaluation.
trait: A single character string specifying the column name of the target trait.
anova_results: A structured list derived from upstream ANOVA layouts.
total_replications: An integer specifying the absolute number of replication blocks (\(r\)).
alpha: A numeric value defining the adjusted family-wise error rate threshold. Defaults to 0.05.
reporting_level: An integer vector flag defining console trace settings. Defaults to 2.

Value

A structured named list of class "list" containing 4 computational components:

tukey_value: The absolute calculated scalar value of Tukey's Honestly Significant Difference threshold.
se_mean: The isolated Standard Error of the treatment mean scalar (\(SE_{\bar{y}}\)).
comparison_matrix: A detailed data frame or NULL layout reserved for pairwise lines differences.
ranked_means: A structured data frame containing sorted treatment means and significance group letters (Tukey_Letters).

Author

Faheem Khan (2022ag94@uaf.edu.pk)

Examples

data(gv_data, package = "AgriDataTools")
reps <- length(unique(gv_data$Replication))

model_fit <- aov(PH ~ Genotype + Replication, data = gv_data)
anova_summary <- summary(model_fit)[[1]]

mock_anova <- list(
  anova_table = data.frame(
    Source = c("Genotype", "Replication", "Error"),
    Df = anova_summary$Df,
    MS = anova_summary$`Mean Sq`,
    stringsAsFactors = FALSE
  )
)

tukey_output <- compute_tukey(
  data = gv_data,
  trait = "PH",
  anova_results = mock_anova,
  total_replications = reps
)
print(tukey_output$ranked_means)
#>    Genotype      Mean Tukey_Letters
#> 1       G16 103.66667             a
#> 2        G7 100.83333            ab
#> 3        G3 100.66667           abc
#> 4       G25  99.66667          abcd
#> 5       G27  99.66667          abcd
#> 6        G9  99.16667          abcd
#> 7        G2  97.50000         abcde
#> 8       G20  97.30000         abcde
#> 9       G11  96.66667        abcdef
#> 10      G13  96.33333        abcdef
#> 11      G18  95.33333        bcdefg
#> 12      G14  95.00000       bcdefgh
#> 13      G23  95.00000       bcdefgh
#> 14       G5  94.33333       bcdefgh
#> 15      G29  93.66667       bcdefgh
#> 16      G31  93.66667       bcdefgh
#> 17      G33  93.50000       bcdefgh
#> 18      G21  93.33333       bcdefgh
#> 19       G1  92.66667       cdefghi
#> 20      G22  92.66667       cdefghi
#> 21      G38  92.66667       cdefghi
#> 22      G26  92.33333       defghij
#> 23       G8  92.00000       defghij
#> 24      G15  91.83333       defghij
#> 25      G17  91.66667       defghij
#> 26      G30  91.66667       defghij
#> 27      G40  91.66667       defghij
#> 28      G37  91.00000        efghij
#> 29      G24  90.50000        efghij
#> 30       G4  90.50000        efghij
#> 31       G6  89.83333        efghij
#> 32      G39  89.66667        efghij
#> 33      G32  89.00000         fghij
#> 34      G36  89.00000         fghij
#> 35      G19  87.66667          ghij
#> 36      G12  87.33333          ghij
#> 37      G34  87.33333          ghij
#> 38      G10  87.00000           hij
#> 39      G28  84.83333            ij
#> 40      G35  84.33333             j