Multiple pairwise comparison for one-way design
Source:R/pairwise-comparisons.R
pairwise_comparisons.RdCalculate parametric, non-parametric, robust, and Bayes Factor pairwise comparisons between group levels with corrections for multiple testing.
Usage
pairwise_comparisons(
data,
x,
y,
subject.id = NULL,
type = "parametric",
paired = FALSE,
var.equal = FALSE,
tr = 0.2,
bf.prior = 0.707,
p.adjust.method = "holm",
digits = 2L,
...
)Arguments
- data
A data frame (or a tibble) from which variables specified are to be taken. Other data types (e.g., matrix,table, array, etc.) will not be accepted. Additionally, grouped data frames from
{dplyr}should be ungrouped before they are entered asdata.- x
The grouping (or independent) variable from
data. In case of a repeated measures or within-subjects design, ifsubject.idargument is not available or not explicitly specified, the function assumes that the data has already been sorted by such an id by the user and creates an internal identifier. So if your data is not sorted, the results can be inaccurate when there are more than two levels inxand there areNAs present. The data is expected to be sorted by user in subject-1,subject-2, ..., pattern.- y
The response (or outcome or dependent) variable from
data.- subject.id
Relevant in case of a repeated measures or within-subjects design (
paired = TRUE, i.e.), it specifies the subject or repeated measures identifier. Important: Note that if this argument isNULL(which is the default), the function assumes that the data has already been sorted by such an id by the user and creates an internal identifier. So if your data is not sorted and you leave this argument unspecified, the results can be inaccurate when there are more than two levels inxand there areNAs present.- type
A character specifying the type of statistical approach:
"parametric""nonparametric""robust""bayes"
You can specify just the initial letter.
- paired
Logical that decides whether the experimental design is repeated measures/within-subjects or between-subjects. The default is
FALSE.- var.equal
a logical variable indicating whether to treat the two variances as being equal. If
TRUEthen the pooled variance is used to estimate the variance otherwise the Welch (or Satterthwaite) approximation to the degrees of freedom is used.- tr
Trim level for the mean when carrying out
robusttests. In case of an error, try reducing the value oftr, which is by default set to0.2. Lowering the value might help.- bf.prior
A number between
0.5and2(default0.707), the prior width to use in calculating Bayes factors and posterior estimates. In addition to numeric arguments, several named values are also recognized:"medium","wide", and"ultrawide", corresponding to r scale values of 1/2, sqrt(2)/2, and 1, respectively. In case of an ANOVA, this value corresponds to scale for fixed effects.- p.adjust.method
Adjustment method for p-values for multiple comparisons. Possible methods are:
"holm"(default),"hochberg","hommel","bonferroni","BH","BY","fdr","none".- digits
Number of digits for rounding or significant figures. May also be
"signif"to return significant figures or"scientific"to return scientific notation. Control the number of digits by adding the value as suffix, e.g.digits = "scientific4"to have scientific notation with 4 decimal places, ordigits = "signif5"for 5 significant figures (see alsosignif()).- ...
Additional arguments passed to other methods.
Value
The returned tibble data frame can contain some or all of the following columns (the exact columns will depend on the statistical test):
statistic: the numeric value of a statisticdf: the numeric value of a parameter being modeled (often degrees of freedom for the test)df.erroranddf: relevant only if the statistic in question has two degrees of freedom (e.g. anova)p.value: the two-sided p-value associated with the observed statisticmethod: the name of the inferential statistical testestimate: estimated value of the effect sizeconf.low: lower bound for the effect size estimateconf.high: upper bound for the effect size estimateconf.level: width of the confidence intervalconf.method: method used to compute confidence intervalconf.distribution: statistical distribution for the effecteffectsize: the name of the effect sizen.obs: number of observationsexpression: pre-formatted expression containing statistical details
For examples, see data frame output vignette.
Pairwise comparison tests
The table below provides summary about:
statistical test carried out for inferential statistics
type of effect size estimate and a measure of uncertainty for this estimate
functions used internally to compute these details
between-subjects
Hypothesis testing
| Type | Equal variance? | Test | p-value adjustment? | Function used |
| Parametric | No | Games-Howell test | Yes | PMCMRplus::gamesHowellTest() |
| Parametric | Yes | Student's t-test | Yes | stats::pairwise.t.test() |
| Non-parametric | No | Dunn test | Yes | PMCMRplus::kwAllPairsDunnTest() |
| Robust | No | Yuen's trimmed means test | Yes | WRS2::lincon() |
| Bayesian | NA | Student's t-test | NA | BayesFactor::ttestBF() |
Effect size estimation
Not supported.
within-subjects
Hypothesis testing
| Type | Test | p-value adjustment? | Function used |
| Parametric | Student's t-test | Yes | stats::pairwise.t.test() |
| Non-parametric | Durbin-Conover test | Yes | PMCMRplus::durbinAllPairsTest() |
| Robust | Yuen's trimmed means test | Yes | WRS2::rmmcp() |
| Bayesian | Student's t-test | NA | BayesFactor::ttestBF() |
Effect size estimation
Not supported.
References
For more, see: https://indrajeetpatil.github.io/ggstatsplot/articles/web_only/pairwise.html
Examples
# for reproducibility
set.seed(123)
library(statsExpressions)
#------------------- between-subjects design ----------------------------
# parametric
# if `var.equal = TRUE`, then Student's t-test will be run
pairwise_comparisons(
data = mtcars,
x = cyl,
y = wt,
type = "parametric",
var.equal = TRUE,
paired = FALSE,
p.adjust.method = "none"
)
#> # A tibble: 3 × 6
#> group1 group2 p.value p.adjust.method test expression
#> <chr> <chr> <dbl> <chr> <chr> <list>
#> 1 4 6 0.0106 None Student's t <language>
#> 2 4 8 0.000000207 None Student's t <language>
#> 3 6 8 0.00516 None Student's t <language>
# if `var.equal = FALSE`, then Games-Howell test will be run
pairwise_comparisons(
data = mtcars,
x = cyl,
y = wt,
type = "parametric",
var.equal = FALSE,
paired = FALSE,
p.adjust.method = "bonferroni"
)
#> # A tibble: 3 × 9
#> group1 group2 statistic p.value alternative distribution p.adjust.method
#> <chr> <chr> <dbl> <dbl> <chr> <chr> <chr>
#> 1 4 6 5.39 0.0125 two.sided q Bonferroni
#> 2 4 8 9.11 0.0000124 two.sided q Bonferroni
#> 3 6 8 5.12 0.0148 two.sided q Bonferroni
#> test expression
#> <chr> <list>
#> 1 Games-Howell <language>
#> 2 Games-Howell <language>
#> 3 Games-Howell <language>
# non-parametric (Dunn test)
pairwise_comparisons(
data = mtcars,
x = cyl,
y = wt,
type = "nonparametric",
paired = FALSE,
p.adjust.method = "none"
)
#> # A tibble: 3 × 9
#> group1 group2 statistic p.value alternative distribution p.adjust.method
#> <chr> <chr> <dbl> <dbl> <chr> <chr> <chr>
#> 1 4 6 1.84 0.0663 two.sided z None
#> 2 4 8 4.76 0.00000198 two.sided z None
#> 3 6 8 2.22 0.0263 two.sided z None
#> test expression
#> <chr> <list>
#> 1 Dunn <language>
#> 2 Dunn <language>
#> 3 Dunn <language>
# robust (Yuen's trimmed means *t*-test)
pairwise_comparisons(
data = mtcars,
x = cyl,
y = wt,
type = "robust",
paired = FALSE,
p.adjust.method = "fdr"
)
#> # A tibble: 3 × 10
#> group1 group2 estimate conf.level conf.low conf.high p.value p.adjust.method
#> <chr> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <chr>
#> 1 4 6 -0.909 0.95 -1.64 -0.173 0.00872 FDR
#> 2 4 8 -1.62 0.95 -2.50 -0.746 0.000549 FDR
#> 3 6 8 -0.713 0.95 -1.58 0.155 0.0438 FDR
#> test expression
#> <chr> <list>
#> 1 Yuen's trimmed means <language>
#> 2 Yuen's trimmed means <language>
#> 3 Yuen's trimmed means <language>
# Bayes Factor (Student's *t*-test)
pairwise_comparisons(
data = mtcars,
x = cyl,
y = wt,
type = "bayes",
paired = FALSE
)
#> # A tibble: 3 × 18
#> group1 group2 term effectsize estimate conf.level conf.low
#> <chr> <chr> <chr> <chr> <dbl> <dbl> <dbl>
#> 1 4 6 Difference Bayesian t-test -0.686 0.95 -1.22
#> 2 4 8 Difference Bayesian t-test -1.63 0.95 -2.21
#> 3 6 8 Difference Bayesian t-test -0.715 0.95 -1.36
#> conf.high pd prior.distribution prior.location prior.scale bf10
#> <dbl> <dbl> <chr> <dbl> <dbl> <dbl>
#> 1 -0.157 0.992 cauchy 0 0.707 11.4
#> 2 -1.01 1 cauchy 0 0.707 5222.
#> 3 -0.0910 0.987 cauchy 0 0.707 5.36
#> conf.method log_e_bf10 n.obs expression test
#> <chr> <dbl> <int> <list> <chr>
#> 1 ETI 2.44 18 <language> Student's t
#> 2 ETI 8.56 25 <language> Student's t
#> 3 ETI 1.68 21 <language> Student's t
#------------------- within-subjects design ----------------------------
# parametric (Student's *t*-test)
pairwise_comparisons(
data = bugs_long,
x = condition,
y = desire,
subject.id = subject,
type = "parametric",
paired = TRUE,
p.adjust.method = "BH"
)
#> # A tibble: 6 × 6
#> group1 group2 p.value p.adjust.method test expression
#> <chr> <chr> <dbl> <chr> <chr> <list>
#> 1 HDHF HDLF 1.06e- 3 FDR Student's t <language>
#> 2 HDHF LDHF 7.02e- 2 FDR Student's t <language>
#> 3 HDHF LDLF 3.95e-12 FDR Student's t <language>
#> 4 HDLF LDHF 6.74e- 2 FDR Student's t <language>
#> 5 HDLF LDLF 1.99e- 3 FDR Student's t <language>
#> 6 LDHF LDLF 6.66e- 9 FDR Student's t <language>
# non-parametric (Durbin-Conover test)
pairwise_comparisons(
data = bugs_long,
x = condition,
y = desire,
subject.id = subject,
type = "nonparametric",
paired = TRUE,
p.adjust.method = "BY"
)
#> # A tibble: 6 × 9
#> group1 group2 statistic p.value alternative distribution p.adjust.method
#> <chr> <chr> <dbl> <dbl> <chr> <chr> <chr>
#> 1 HDHF HDLF 4.78 1.44e- 5 two.sided t BY
#> 2 HDHF LDHF 2.44 4.47e- 2 two.sided t BY
#> 3 HDHF LDLF 8.01 5.45e-13 two.sided t BY
#> 4 HDLF LDHF 2.34 4.96e- 2 two.sided t BY
#> 5 HDLF LDLF 3.23 5.05e- 3 two.sided t BY
#> 6 LDHF LDLF 5.57 4.64e- 7 two.sided t BY
#> test expression
#> <chr> <list>
#> 1 Durbin-Conover <language>
#> 2 Durbin-Conover <language>
#> 3 Durbin-Conover <language>
#> 4 Durbin-Conover <language>
#> 5 Durbin-Conover <language>
#> 6 Durbin-Conover <language>
# robust (Yuen's trimmed means t-test)
pairwise_comparisons(
data = bugs_long,
x = condition,
y = desire,
subject.id = subject,
type = "robust",
paired = TRUE,
p.adjust.method = "hommel"
)
#> # A tibble: 6 × 11
#> group1 group2 estimate conf.level conf.low conf.high p.value p.crit
#> <chr> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
#> 1 HDHF HDLF 1.03 0.95 0.140 1.92 0.00999 0.0127
#> 2 HDHF LDHF 0.454 0.95 -0.104 1.01 0.0520 0.025
#> 3 HDHF LDLF 1.95 0.95 1.09 2.82 0.000000564 0.00851
#> 4 HDLF LDHF -0.676 0.95 -1.61 0.256 0.0520 0.05
#> 5 HDLF LDLF 0.889 0.95 0.0244 1.75 0.0203 0.0169
#> 6 LDHF LDLF 1.35 0.95 0.560 2.14 0.000102 0.0102
#> p.adjust.method test expression
#> <chr> <chr> <list>
#> 1 Hommel Yuen's trimmed means <language>
#> 2 Hommel Yuen's trimmed means <language>
#> 3 Hommel Yuen's trimmed means <language>
#> 4 Hommel Yuen's trimmed means <language>
#> 5 Hommel Yuen's trimmed means <language>
#> 6 Hommel Yuen's trimmed means <language>
# Bayes Factor (Student's *t*-test)
pairwise_comparisons(
data = bugs_long,
x = condition,
y = desire,
subject.id = subject,
type = "bayes",
paired = TRUE
)
#> # A tibble: 6 × 18
#> group1 group2 term effectsize estimate conf.level conf.low
#> <chr> <chr> <chr> <chr> <dbl> <dbl> <dbl>
#> 1 HDHF HDLF Difference Bayesian t-test 1.10 0.95 0.491
#> 2 HDHF LDHF Difference Bayesian t-test 0.455 0.95 -0.0483
#> 3 HDHF LDLF Difference Bayesian t-test 2.13 0.95 1.62
#> 4 HDLF LDHF Difference Bayesian t-test -0.661 0.95 -1.32
#> 5 HDLF LDLF Difference Bayesian t-test 0.991 0.95 0.369
#> 6 LDHF LDLF Difference Bayesian t-test 1.65 0.95 1.14
#> conf.high pd prior.distribution prior.location prior.scale bf10
#> <dbl> <dbl> <chr> <dbl> <dbl> <dbl>
#> 1 1.76 1.00 cauchy 0 0.707 4.16e+ 1
#> 2 0.955 0.962 cauchy 0 0.707 5.83e- 1
#> 3 2.63 1 cauchy 0 0.707 1.20e+10
#> 4 0.0315 0.97 cauchy 0 0.707 6.98e- 1
#> 5 1.57 0.999 cauchy 0 0.707 1.81e+ 1
#> 6 2.15 1 cauchy 0 0.707 4.81e+ 6
#> conf.method log_e_bf10 n.obs expression test
#> <chr> <dbl> <int> <list> <chr>
#> 1 ETI 3.73 88 <language> Student's t
#> 2 ETI -0.539 88 <language> Student's t
#> 3 ETI 23.2 88 <language> Student's t
#> 4 ETI -0.359 88 <language> Student's t
#> 5 ETI 2.90 88 <language> Student's t
#> 6 ETI 15.4 88 <language> Student's t