Performs McNemar chi-squared test to compare paired proportions.
Wrappers around the R base function mcnemar.test(), but
provide pairwise comparisons between multiple groups
mcnemar_test(x, y = NULL, correct = TRUE)
pairwise_mcnemar_test(
data,
formula,
type = c("mcnemar", "exact"),
correct = TRUE,
p.adjust.method = "bonferroni"
)either a two-dimensional contingency table in matrix form, or a factor object.
a factor object; ignored if x is a matrix.
a logical indicating whether to apply continuity correction when computing the test statistic.
a data frame containing the variables in the formula.
a formula of the form a ~ b | c, where a is the
outcome variable name; b is the within-subjects factor variables; and c
(factor) is the column name containing individuals/subjects identifier.
Should be unique per individual.
type of statistical tests used for pairwise comparisons. Allowed
values are one of c("mcnemar", "exact").
method to adjust p values for multiple comparisons. Used when pairwise comparisons are performed. Allowed values include "holm", "hochberg", "hommel", "bonferroni", "BH", "BY", "fdr", "none". If you don't want to adjust the p value (not recommended), use p.adjust.method = "none".
return a data frame with the following columns:
n: the number of participants.
statistic: the value of McNemar's statistic.
df the
degrees of freedom of the approximate chi-squared distribution of the test
statistic.
p: p-value.
p.adj: the adjusted
p-value.
method: the used statistical test.
p.signif: the significance level of p-values.
The returned object has an attribute called args, which is a list holding the test arguments.
mcnemar_test(): performs McNemar's chi-squared test for comparing two
paired proportions
pairwise_mcnemar_test(): performs pairwise McNemar's chi-squared test between
multiple groups. Could be used for post-hoc tests following a significant Cochran's Q test.
# Comparing two paired proportions
#%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
# Data: frequencies of smokers before and after interventions
xtab <- as.table(
rbind(c(25, 6), c(21,10))
)
dimnames(xtab) <- list(
before = c("non.smoker", "smoker"),
after = c("non.smoker", "smoker")
)
xtab
#> after
#> before non.smoker smoker
#> non.smoker 25 6
#> smoker 21 10
# Compare the proportion of smokers
mcnemar_test(xtab)
#> # A tibble: 1 × 6
#> n statistic df p p.signif method
#> * <dbl> <dbl> <dbl> <dbl> <chr> <chr>
#> 1 62 7.26 1 0.00705 ** McNemar test
# Comparing multiple related proportions
# %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
# Generate a demo data
mydata <- data.frame(
outcome = c(0,1,1,0,0,1,0,1,1,1,1,1,0,0,1,1,0,1,0,1,1,0,0,1,0,1,1,0,0,1),
treatment = gl(3,1,30,labels=LETTERS[1:3]),
participant = gl(10,3,labels=letters[1:10])
)
mydata$outcome <- factor(
mydata$outcome, levels = c(1, 0),
labels = c("success", "failure")
)
# Cross-tabulation
xtabs(~outcome + treatment, mydata)
#> treatment
#> outcome A B C
#> success 2 5 10
#> failure 8 5 0
# Compare the proportion of success between treatments
cochran_qtest(mydata, outcome ~ treatment|participant)
#> # A tibble: 1 × 6
#> .y. n statistic df p method
#> * <chr> <int> <dbl> <dbl> <dbl> <chr>
#> 1 outcome 10 10.9 2 0.00432 Cochran's Q test
# pairwise comparisons between groups
pairwise_mcnemar_test(mydata, outcome ~ treatment|participant)
#> # A tibble: 3 × 6
#> group1 group2 p p.adj p.adj.signif method
#> * <chr> <chr> <dbl> <dbl> <chr> <chr>
#> 1 A B 0.371 1 ns McNemar test
#> 2 A C 0.0133 0.0399 * McNemar test
#> 3 B C 0.0736 0.221 ns McNemar test