`superb`

`superb`

Many studies collect data that are categorized according to one or
some factors. For example, it is possible to categorize a sample of
college students based on their gender and on their projects after
college is finished (go to university, get a job, etc.). Here, there are
two “factors”: gender and plans post studies. The measure for each
participant is in which of the “cells” the participant is categorized.
Typically, the data are summarized as *frequencies*, that is, the
*count* of participants in each of the various combinations of
the factor levels. For two classification factors, the data are said to
be two-way classfication data, or to form a contingency table. Nothing
prevent from having more than 2 factors, e.g., a three-way
classification data.

Although frequencies are often given in a table, these tables provides very little insight with regards to trends. It is far more adviseable to illustrate the frequencies using a plot showing the count in each levels of the factors. However, to be truly informative, such a plot should be accompanied with error bars such as the confidence interval. Herein, we show how this can be done.

We adopted an approach based on the pivot method developed by Clopper & Pearson (1934). This method is given in an analytic form in Leemis & Trivedi (1996). Such confidence intervals are commonly non-symmetrical around the estimate; they are also exact or conservative, in which case the length of the interval tends to be too long when the frequencies are small (Chen, 1990).

Given the total sample size \(N\) in
all the cells, each observed frequency \(n\) in a given cell is used to get lower
and upper confidence bounds around the proportion \(\hat{p}=n/N\) with the formula: \[
\hat{\pi}_{\,\text{low}}=\left(
1+\frac{N-n+1}{n F_{1-\alpha/2}(2n,2(N-n+1)}
\right)^{-1}
< \hat{\pi} <
\left(
1+\frac{N-n}{(n+1) F_{\alpha/2}(2(n+1),2(N-x)}
\right)^{-1}
=\hat{\pi}_{\,\text{high}}
\] in which \(F_{q}\) denotes
the \(100\;q\)% quantile of an \(F\) distribution and $1-$ the desired
coverage of the interval, often 95%. The interval \[
\{n_{\,\text{low}}, n_{\,\text{high}} \} = N \, \times\, \{
\hat{\pi}_{\,\text{low}}, \hat{\pi}_{\,\text{high}} \}
\] is then used as a \(100
(1-\alpha)\)% confidence interval of the observed frequency \(n\) which can be used to compare one
frequency to an expected or theoretical frequency. Such an unadjusted
confidence interval is termed a *stand-alone confidence interval*
(Cousineau, Goulet, & Harding,
2021).

As more commonly, we wish to compare an observed frequency to another
observed frequency, a *difference-adjusted* confidence interval
is sought. To obtain a difference-adjusted confidence interval, it is
required to multiply the interval width by 2, \[
n_{\,\text{low}}^* = 2(n-n_{\,\text{low}})+n
\] \[
n_{\,\text{high}}^* = 2(n_{\,\text{high}}-n)+n
\] where the asterisk denotes difference-adjusted confidence
interval limits. Thus, the interval

\[
\{ n^*_{\,\text{low}}, n^*_{\,\text{high}} \}
\] is the *difference-adjusted* \(100 (1-\alpha)\)% confidence interval (Baguley, 2012). The difference-adjusted
confidence intervals allow comparing the frequencies pairwise rather
than to a theoretical frequency.

The reason for the multiplication by 2 is two-fold. First, to obtain a difference-adjusted confidence interval (CI), it is necessary to multiply the CI width by \(\sqrt{2}\) (under the assumption of homogeneous variance). Second, as the total must necessarily be equal to \(N\), the observed frequencies are correlated and this correlation equals \(-1 / (C-1)\) where \(C\) is the number of class. As this CI is meant for pair-wise comparisons, \(C\) is replaced by 2 in this formula, resulting in a second, correlation-based, correction of \(\sqrt{1-r} = \sqrt{1 - (-1/(2-1))} = \sqrt{2}\). As usual, both corrections to the CI width are multiplicative.

To illustrate the method on a real data set, we enter the data set found in Light & Margolin (1971). The data counts the number of teenagers based (first factor) on their gender an on (second factor) their educational vocation (the type of studies they want to complete in the future). The sample is composed of 617 teens. To generate the dataset, we use the following:

```
<- data.frame(
dta vocation = factor(unlist(lapply(c("Secondary","Vocational","Teacher","Gymnasium","University"), function(p) rep(p,2))),
levels = c("Secondary","Vocational","Teacher","Gymnasium","University")),
gender = factor(rep(c("Boys","Girls"),5), levels=c("Boys","Girls")),
obsfreq = c(62,61,121,149,26,41,33,20,84,20)
)
```

The function `factor`

uses the argument
`levels`

to specify the order in which the items are to be
plotted; otherwise, the default order is alphabetic order.

If you have the data in a file, it is actually a lot more easier to import the file!

Here are the data *in extenso*:

` dta`

```
## vocation gender obsfreq
## 1 Secondary Boys 62
## 2 Secondary Girls 61
## 3 Vocational Boys 121
## 4 Vocational Girls 149
## 5 Teacher Boys 26
## 6 Teacher Girls 41
## 7 Gymnasium Boys 33
## 8 Gymnasium Girls 20
## 9 University Boys 84
## 10 University Girls 20
```

To have a quick-and-dirty plot, just display the raw counts with no error bars

```
library(superb)
library(ggplot2)
<- superbPlot(
plt1
dta,BSFactors = c("vocation","gender"),
variables = "obsfreq", # name of the column with the counts
statistic = "identity", # the raw data as is
errorbar = "none", # no error bars
# the following is for the look of the plot
plotStyle = "line", # style of the plot
lineParams = list( size = 1.0) # thicker lines as well
) plt1
```

First, we need the summary function that computes the frequency. This is actually the datum stored in the data frame, so there is nothing to compute.

`<- function(x) x[1] count `

Second, we need an initalizer that will fetch the total sample size \(N\) and dump it in the global environment for later use:

```
<- function(df) {
init.count <<- sum(df$DV)
totalcount }
```

Third and lastly, we compute the confidence interval limits using Clopper & Pearson (1934) approach using the Leemis & Trivedi (1996) analytic expression:

```
<- function(n, gamma=0.95) {
CI.count <- totalcount
N
# Clopper & Pearson CI from Leemis & Trivedi, 1996
<- (1+(N-n+1)/((n+0)*qf(1/2-gamma/2,2*(n+0),2*(N-n+1))))^(-1)
plow <- (1+(N-n+0)/((n+1)*qf(1/2+gamma/2,2*(n+1),2*(N-n+0))))^(-1)
phig
# convert to CI on counts
<- totalcount * plow
nlow <- totalcount * phig
nhig
# increase width for difference- and correlation-adjustments
2 * c( nlow[1]-n[1], nhig[1]-n[1] ) + n[1]
}
```

This is it! All the statistical functions needed to make the plot are in place.

```
<- superbPlot(
plt2
dta,BSFactors = c("vocation","gender"),
variables = "obsfreq",
statistic = "count", # the function defined above
errorbar = "CI", # its CI define above
# the following is for the look of the plot
plotStyle = "line", # style of the plot
errorbarParams = list( width =0.5, size=0.75 ),# have thicker error bars
lineParams = list( size = 1.0) # thicker lines as well
)
```

`## superb::FYI: Running initializer init.count`

```
## Warning in (function (mapping = NULL, data = NULL, stat = "identity", position =
## "identity", : Ignoring unknown parameters: `size`
```

` plt2`

The plot is drab so let’s add some ornaments to it:

```
<- list(
ornate xlab("Educational vocation"), # label on the x-axis
ylab("Observed frequency"), # label on the y-axis
theme_bw(base_size = 16), # black and white theme
scale_x_discrete(guide = guide_axis(n.dodge = 2)) # unalign labels
# etc. anything accepted by ggplots can be added.
)<- plt2 + ornate
plt3 plt3
```

If you look at the plot, it becomes readily apparent that the boys and the girls had (in the 1960s) the same educational aspirations. The only exception is with regards to attending university where girls where fewer to have this aspiration.

Now return to the data listed above, and tell me if you had noticed
that. *Most certainly not*. Tables are terribly inefficient tools
to convey trends whereas plots are ideal to that end. When combined with
a decent measure of error (here, the confidence interval), it is fairly
easy to decide if the trends are reliable or accidental.

The plot with *difference-adjusted* confidence interval is a
very reliable tool to make inference-by-eye. In doubt however, go run
the exact test. In the present case, we performed an ANOFA (Analysis of
Frequency tAble; Laurencelle & Cousineau
(submitted)). It shows that the interaction is highly
significant; subsequent simple effect analyses show that this is indeed
the university aspiration that triggered that interaction.

ANOFA table:

\(G\) | df | \(G_{corrected}\) | \(p\) | |
---|---|---|---|---|

Total | 266.8894 | 9 | ||

Aspiration (A) | 215.0163 | 4 | 214.6684 | < 0.0001 |

Gender (B) | 1.9865 | 1 | 1.9849 | 0.1589 |

A \(\times\) B | 49.8867 | 4 | 49.5554 | < 0.0001 |

Decomposition of the interaction and the Aspiration effects:

Simple effect | \(G\) | df | \(G_{corrected}\) | \(p\) |
---|---|---|---|---|

Gender within Secondary school | 0.0081 | 1 | 0.0081 | 0.9282 |

Gender within Vocational training | 2.9089 | 1 | 2.9078 | 0.0881 |

Gender within Teacher college | 3.3868 | 1 | 3.3855 | 0.0658 |

Gender within Gymnasium | 3.2214 | 1 | 3.2201 | 0.0727 |

Gender within University | 42.3478 | 1 | 42.3307 | <0.0001 |

Frequencies, a.k.a. counts, can be displayed with appropriate confidence intervals without any problem. They are just another regular dependent variable in the researcher’s toolkit.

Baguley, T. (2012). Calculating and graphing within-subject confidence
intervals for ANOVA. *Behavior Research Methods*, *44*,
158–175. https://doi.org/10.3758/s13428-011-0123-7

Chen, H. (1990). The accuracy of approximate intervals for a binomial
parameter. *Journal of the American Statistical Association*,
*85*, 514–518. https://doi.org/10.2307/2289792

Clopper, C. J., & Pearson, E. S. (1934). The use of confidence or
fiducial limits illustrated in the case of the binomial.
*Biometrika*, *26*, 404–413. https://doi.org/10.1093/biomet/26.4.404

Cousineau, D., Goulet, M.-A., & Harding, B. (2021). Summary plots
with adjusted error bars: The superb framework with an implementation in
R. *Advances in Methods and Practices in Psychological
Science*, *4*, 1–18. https://doi.org/10.1177/25152459211035109

Laurencelle, L., & Cousineau, D. (submitted). Analysis of frequency
tables using ANOFA. *Submitted*.

Leemis, L. M., & Trivedi, K. S. (1996). A comparison of approximate
interval estimators for the bernoulli parameter. *The American
Statistician*, *50*(1), 63–68.

Light, R. J., & Margolin, B. H. (1971). An analysis of variance for
categorical data. *Journal of the American Statistical
Association*, *66*, 534–544. https://doi.org/10.1080/01621459.1971.10482297