inst/doc/varequal.R

In varequal: Tests and Measures for Homoscedasticity

## ----include = FALSE----------------------------------------------------------
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

## ----eval=FALSE---------------------------------------------------------------
# install.packages("varequal")

## ----eval=FALSE---------------------------------------------------------------
# if (!require("pak")) install.packages("pak")
# pak::pak("P10911004-NPUST/varequal")

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library(varequal)

# For reproducibility
set.seed(123)

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data("roGFP")

df1 <- roGFP[[1]]

is_var_equal(df1, ro ~ grp)

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is_var_equal(df1, ro ~ grp)

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is_var_equal(df1, ro ~ grp, summary = TRUE)

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check_var_equal(df1, ro ~ grp, method = "LV")

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Levene_test(df1, ro ~ grp)

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check_var_equal(df1, ro ~ grp, method = "BF")

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x <- list(A = rnorm(12), B = rnorm(12), C = rnorm(12))
is_var_equal(x)

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ab <- Ansari_Bradley_test(df1, ro ~ grp)

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bl <- Bartlett_test(df1, ro ~ grp, summary = TRUE)

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mbf <- Brown_Forsythe_test(df1, ro ~ grp)

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bf <- Brown_Forsythe_test(df1, ro ~ grp, method = "BF")

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Brown_Forsythe_test(df1, ro ~ grp, transform = function(x) abs(x - mean(x)))

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fk <- Fligner_Killeen_test(df1, ro ~ grp)

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lg <- Lam_G_test(df1, ro ~ grp)

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Lam_G_test(df1, ro ~ grp, alternative = "two.sided")
Lam_G_test(df1, ro ~ grp, alternative = "greater")
Lam_G_test(df1, ro ~ grp, alternative = "less")

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lv <- Levene_test(df1, ro ~ grp)

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Levene_test(df1, ro ~ grp, transform = function(x) (x - median(x)) ^ 2)

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# Absolute deviations from the mean
Levene_test(df1, ro ~ grp, transform = function(x) abs(x - mean(x)))

# Square-root absolute deviations
Levene_test(df1, ro ~ grp, transform = function(x) sqrt(abs(x - median(x))))

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ob <- O.Brien_test(df1, ro ~ grp)

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om <- O.Neill_Mathews_test(df1, ro ~ grp)

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method <- "FK"
result <- check_var_equal(df1, ro ~ grp, method = method, silent = TRUE)
result

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for (s in 1:5) {
  cat("sensitivity =", s, "\n")
  print(is_var_equal(df1, ro ~ grp, sensitivity = s))
}

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result <- is_var_equal(df1, ro ~ grp, summary = TRUE)
result$is_var_equal
result$summary

## ----fig.width=6--------------------------------------------------------------
text = sprintf("Variance equal: %s", is_var_equal(df1, ro ~ grp))
boxplot(ro ~ grp, 
        data = df1, 
        main = text, 
        horizontal = TRUE, 
        xlab = "Redox index", 
        ylab = "Group")
points(x = df1$ro, 
       y = jitter(as.numeric(df1$grp), amount = 0.15))

## ----fig.width=6--------------------------------------------------------------
data("CYCB1")
df2 <- CYCB1[[2]]
text = sprintf("Variance equal: %s", is_var_equal(df2, cells ~ grp))
boxplot(cells ~ grp,
        data = df2,
        main = text,
        horizontal = TRUE,
        xlab = "Cell number",
        ylab = "Group"
)
points(x = df2$cells, 
       y = jitter(as.numeric(df2$grp), amount = 0.15))

## -----------------------------------------------------------------------------
data("roGFP")
str(roGFP[[1]])

## -----------------------------------------------------------------------------
data("CYCB1")
str(CYCB1[[1]])