anopafct: ANOPA: analysis of proportions using Anscombe transform.

In ANOPA: Analyses of Proportions using Anscombe Transform

ANOPA: analysis of proportions using Anscombe transform.

Description

The function anopa() performs an ANOPA for designs with up to 4 factors according to the ANOPA framework. See \insertCitelc23;textualANOPA for more.

Usage

anopa(formula = NULL, data = NULL, WSFactors = NULL)

Arguments

formula	A formula with the factors on the left-hand side. See below for writing the formula to match the data format.
data	Dataframe in one of wide, long, or compiled format;
WSFactors	For within-subject designs, provide the factor names and their number of levels. This is expressed as a vector of strings such as "Moment(2)".

Details

Note the following limitations:

1. The main analysis performed by anopa() is currently restricted to three factors in total (between and/or within). Contact the author if you plan to analyze more complex designs.

2. If you have repeated-measure design, the data must be provided in wide or long format. The correlation between successes cannot be assessed once the data are in a compiled format.

3. The data can be given in three formats:

   • wide: In the wide format, there is one line for each participant, and one column for each between-subject factors in the design. In the column(s), the level of the factor is given (as a number, a string, or a factor). For within-subject factors, the columns contains 0 or 1 based on the status of the measurement.

   • long: In the long format, there is an identifier column for each participant, a factor column and a level number for that factor. If there are n participants and m factors, there will be in total n x m lines.

   • compiled: In the compiled format, there are as many lines as there are cells in the design. If there are two factors, with two levels each, there will be 4 lines.

See the vignette vignette("B-DataFormatsForProportions", package = "ANOPA") for more on data format and how to write their formula.

Value

An omnibus analyses of the given proportions. Each factor's significance is assessed, as well as their interactions when there is more than one factor. The results are obtained with summary() or summarize() as usual. If desired, the corrected-only statistics can be presented \insertCitew76ANOPA using corrected(); the uncorrected statistics only are obtained with uncorrected(). For decomposition of the main analyses, follow the main analysis with emProportions(), contrastProportions(), or posthocProportions())

References

\insertAllCited

Examples

# -- FIRST EXAMPLE --
# Basic example using a single between-subject factor design with the data in compiled format. 
# Ficticious data present success (1) or failure (0) of the observation according
# to the state of residency (three levels: Florida, Kentucky or Montana) for 
# 3 possible cells. There are 175 observations (with unequal n, Montana having only)
# 45 observations). 
minimalBSExample
# The data are in compiled format, consequently the data frame has only three lines.
# The complete data frame in wide format would be composed of 175 lines, one per participant.

# The following formula using curly braces is describing this data format
# (note the semicolon to separate the number of successes from the number of observations):
formula <- {s; n} ~ state

# The analysis is performed using the function `anopa()` with a formula and data:
w <- anopa(formula, minimalBSExample) 
summary(w)
# As seen, the proportions of success do not differ across states.

# To see the proportions when the data is in compiled format, simply divide the 
# number of success (s) by the total number of observations (n):
minimalBSExample$s / minimalBSExample$n

# A plot of the proportions with error bars (default 95% confidence intervals) is
# easily obtained with
anopaPlot(w)

# The data can be re-formated into different formats with, 
# e.g., `toRaw()`, `toLong()`, `toWide()`
head(toWide(w))
# In this format, only 1s and 0s are shown, one participant per line.
# See the vignette `DataFormatsForFrequencies` for more.

# -- SECOND EXAMPLE --
# Real-data example using a three-factor design with the data in compiled format:
ArringtonEtAl2002

#  This dataset, shown in compiled format, has three cells missing 
# (e.g., fishes whose location is African, are Detrivore, feeding Nocturnally)
w <- anopa( {s;n} ~ Location * Trophism * Diel, ArringtonEtAl2002 )

# The function `anopa()` generates the missing cells with 0 success over 0 observations.
# Afterwards, cells with missing values are imputed  based on the option:
getOption("ANOPA.zeros")
# where 0.05 is 1/20 of a success over one observations (arcsine transforms allows 
# fractions of success; it remains to be studied what imputation strategy is best...)

# The analysis suggests a main effect of Trophism (type of food ingested)
# but the interaction Trophism by Diel (moment of feeding) is not to be neglected...
summary(w) # or summarize(w)

# The above presents both the uncorrected statistics as well as the corrected
# ones for small samples (Williams, 1976). You can obtain only the uncorrected...
uncorrected(w)

#... or the corrected ones
corrected(w)

# Finally, the data may have repeated measures and still be accessible in a compiled 
# format, as is the case of this short example:
minimalMxExampleCompiled

# As seen, it has one "group" factor (between) and two repeated measures (under the
# "foraging" or "frg" within factor). The groups are unequal, ranging form 16 to 81. 
# Finally, as this is repeated measures, there are correlations in each group
# (generally weak except possibly for the "treatment3" group).

# Such a compiled structure can be provided to anopa() by specifying the 
# repeated measures first (within cbind()), next the number of observation column, 
# and finally, the column containing the measure of correlation (any names can be used):
v <- anopa( {cbind(frg.before,frg.after); Count; uAlpha} ~ group, 
             minimalMxExampleCompiled,
             WSFactors = "foraging(2)")
anopaPlot(v)
summary(v)


# You can also ask easier outputs with:
explain(w)   # human-readable ouptut NOT YET DONE

ANOPA documentation built on Aug. 19, 2025, 1:11 a.m.