MANOVA: Multi-factor ANOVA.
In bruceR: Broadly Useful Convenient and Efficient R Functions

MANOVA

R Documentation

Multi-factor ANOVA.

Description

Multi-factor ANOVA (between-subjects, within-subjects, and mixed designs), with and without covariates (ANCOVA).

This function is based on and extends afex::aov_ez(). You only need to specify the data, dependent variable(s), and factors (between-subjects and/or within-subjects). Almost all results you need will be displayed together, including effect sizes (partial \eta^2) and their confidence intervals (CIs). 90% CIs for partial \eta^2 (two-sided) are reported, following Steiger (2004). In addition to partial \eta^2, it also reports generalized \eta^2, following Olejnik & Algina (2003).

How to prepare your data and specify the arguments of MANOVA?

Wide-format data (one person in one row, and repeated measures in multiple columns):

Betweem-subjects design
MANOVA(data=, dv=, between=, ...)

Within-subjects design
MANOVA(data=, dvs=, dvs.pattern=, within=, ...)

Mixed design
MANOVA(data=, dvs=, dvs.pattern=, between=, within=, ...)
Long-format data (one person in multiple rows, and repeated measures in one column):

Betweem-subjects design
(not applicable)

Within-subjects design
MANOVA(data=, subID=, dv=, within=, ...)

Mixed design
MANOVA(data=, subID=, dv=, between=, within=, ...)

Usage

MANOVA(
  data,
  subID = NULL,
  dv = NULL,
  dvs = NULL,
  dvs.pattern = NULL,
  between = NULL,
  within = NULL,
  covariate = NULL,
  ss.type = "III",
  sph.correction = "none",
  aov.include = FALSE,
  digits = 3,
  file = NULL
)

Arguments

`data`	Data frame. Both wide-format and long-format are supported.
`subID`	Subject ID (the column name). Only necessary for long-format data.
`dv`	Dependent variable. For wide-format data, `dv` only can be used for between-subjects designs. For within-subjects and mixed designs, please use `dvs` and `dvs.pattern`. For long-format data, `dv` is the outcome variable.
`dvs`	Repeated measures. Only for wide-format data (within-subjects or mixed designs). Can be: `"start:stop"` to specify the range of variables (sensitive to the order of variables): e.g., `"A1B1:A2B3"` is matched to all variables in the data between `"A1B1"` and `"A2B3"` a character vector to directly specify variables (insensitive to the order of variables): e.g., `c("Cond1", "Cond2", "Cond3")` or `cc("Cond1, Cond2, Cond3")` See `cc` for its usage.
`dvs.pattern`	If you use `dvs`, you should also specify the pattern of variable names using regular expression. Examples: `"Cond(.)"` extracts levels from `"Cond1", "Cond2", "Cond3", ...` You may rename the factor using the `within` argument (e.g., `within="Condition"`) `"X(..)Y(..)"` extracts levels from `"X01Y01", "X02Y02", "XaaYbc", ...` `"X(.+)Y(.+)"` extracts levels from `"X1Y1", "XaYb", "XaY002", ...` Tips on regular expression: `"(.)"` extracts any single character (number, letter, and other symbols) `"(.+)"` extracts >= 1 character(s) `"(.*)"` extracts >= 0 character(s) `"([0-9])"` extracts any single number `"([a-z])"` extracts any single letter More information: Link 1 (in English) and Link 2 (in Chinese)
`between`	Between-subjects factor(s). Multiple variables should be included in a character vector `c()`.
`within`	Within-subjects factor(s). Multiple variables should be included in a character vector `c()`.
`covariate`	Covariates. Multiple variables should be included in a character vector `c()`.
`ss.type`	Type of sums of squares (SS) for ANOVA. Defaults to `"III"`. Possible values are `"II"`, `"III"`, `2`, or `3`.
`sph.correction`	[Only for repeated measures with >= 3 levels] Sphericity correction method for adjusting the degrees of freedom (df) when the sphericity assumption is violated. Defaults to `"none"`. If Mauchly's test of sphericity is significant, you may set it to `"GG"` (Greenhouse-Geisser) or `"HF"` (Huynh-Feldt).
`aov.include`	Include the `aov` object in the returned object? Defaults to `FALSE`, as suggested by `afex::aov_ez()` (please see the `include_aov` argument in this help page, which provides a detailed explanation). If `TRUE`, you should also specify `model.type="univariate"` in `EMMEANS`.
`digits`	Number of decimal places of output. Defaults to `3`.
`file`	File name of MS Word (`.doc`).

Details

If observations are not uniquely identified in user-defined long-format data, the function takes averages across those multiple observations for each case. In technical details, it specifies fun_aggregate=mean in afex::aov_ez() and values_fn=mean in tidyr::pivot_wider().

Value

A result object (list) returned by afex::aov_ez(), along with several other elements: between, within, data.wide, data.long.

Interaction Plot

You can save the returned object and use the emmeans::emmip() function to create an interaction plot (based on the fitted model and a formula specification). For usage, please see the help page of emmeans::emmip(). It returns an object of class ggplot, which can be easily modified and saved using ggplot2 syntax.

References

Olejnik, S., & Algina, J. (2003). Generalized eta and omega squared statistics: Measures of effect size for some common research designs. Psychological Methods, 8(4), 434–447.

Steiger, J. H. (2004). Beyond the F test: Effect size confidence intervals and tests of close fit in the analysis of variance and contrast analysis. Psychological Methods, 9(2), 164–182.

Examples

#### Between-Subjects Design ####

between.1
MANOVA(between.1, dv="SCORE", between="A")

between.2
MANOVA(between.2, dv="SCORE", between=c("A", "B"))

between.3
MANOVA(between.3, dv="SCORE", between=c("A", "B", "C"))

## How to create an interaction plot using `emmeans::emmip()`?
## See help page for its usage: ?emmeans::emmip()
m = MANOVA(between.2, dv="SCORE", between=c("A", "B"))
emmip(m, ~ A | B, CIs=TRUE)
emmip(m, ~ B | A, CIs=TRUE)
emmip(m, B ~ A, CIs=TRUE)
emmip(m, A ~ B, CIs=TRUE)


#### Within-Subjects Design ####

within.1
MANOVA(within.1, dvs="A1:A4", dvs.pattern="A(.)",
       within="A")
## the same:
MANOVA(within.1, dvs=c("A1", "A2", "A3", "A4"), dvs.pattern="A(.)",
       within="MyFactor")  # renamed the within-subjects factor

within.2
MANOVA(within.2, dvs="A1B1:A2B3", dvs.pattern="A(.)B(.)",
       within=c("A", "B"))

within.3
MANOVA(within.3, dvs="A1B1C1:A2B2C2", dvs.pattern="A(.)B(.)C(.)",
       within=c("A", "B", "C"))


#### Mixed Design ####

mixed.2_1b1w
MANOVA(mixed.2_1b1w, dvs="B1:B3", dvs.pattern="B(.)",
       between="A", within="B")
MANOVA(mixed.2_1b1w, dvs="B1:B3", dvs.pattern="B(.)",
       between="A", within="B", sph.correction="GG")

mixed.3_1b2w
MANOVA(mixed.3_1b2w, dvs="B1C1:B2C2", dvs.pattern="B(.)C(.)",
       between="A", within=c("B", "C"))

mixed.3_2b1w
MANOVA(mixed.3_2b1w, dvs="B1:B2", dvs.pattern="B(.)",
       between=c("A", "C"), within="B")


#### Other Examples ####

data.new = mixed.3_1b2w
names(data.new) = c("Group", "Cond_01", "Cond_02", "Cond_03", "Cond_04")
MANOVA(data.new,
       dvs="Cond_01:Cond_04",
       dvs.pattern="Cond_(..)",
       between="Group",
       within="Condition")  # rename the factor

# ?afex::obk.long
MANOVA(afex::obk.long,
       subID="id",
       dv="value",
       between=c("treatment", "gender"),
       within=c("phase", "hour"),
       cov="age",
       sph.correction="GG")

bruceR documentation built on June 22, 2024, 12:26 p.m.