gghistostats

Indrajeet Patil

2020-03-22

Source: vignettes/web_only/gghistostats.Rmd

The function ggstatsplot::gghistostats can be used for data exploration and to provide an easy way to make publication-ready histograms with appropriate and selected statistical details embedded in the plot itself. In this vignette we will explore several examples of how to use it.

Some instances where you would want to use gghistostats-

  • to inspect distribution of a continuous variable
  • to test if the mean of a sample variable is different from a specified value (population parameter)

Distribution of a sample with gghistostats

Let’s begin with a very simple example from the psych package (psych::sat.act), a sample of 700 self-reported scores on the SAT Verbal, SAT Quantitative and ACT tests. ACT composite scores may range from 1 - 36. National norms have a mean of 20.

# loading needed libraries
library(ggstatsplot)
library(psych)
library(dplyr)

# looking at the structure of the data using glimpse
dplyr::glimpse(x = psych::sat.act)
#> Observations: 700
#> Variables: 6
#> $ gender    <int> 2, 2, 2, 1, 1, 1, 2, 1, 2, 2, 1, 2, 1, 2, 2, 2, 2, 2, 1, ...
#> $ education <int> 3, 3, 3, 4, 2, 5, 5, 3, 4, 5, 3, 4, 4, 4, 3, 4, 3, 4, 4, ...
#> $ age       <int> 19, 23, 20, 27, 33, 26, 30, 19, 23, 40, 23, 34, 32, 41, 2...
#> $ ACT       <int> 24, 35, 21, 26, 31, 28, 36, 22, 22, 35, 32, 29, 21, 35, 2...
#> $ SATV      <int> 500, 600, 480, 550, 600, 640, 610, 520, 400, 730, 760, 71...
#> $ SATQ      <int> 500, 500, 470, 520, 550, 640, 500, 560, 600, 800, 710, 60...

To get a simple histogram with no statistics and no special information. gghistostats will by default choose a binwidth max(x) - min(x) / sqrt(N). You should always check this value and explore multiple widths to find the best to illustrate the stories in your data since histograms are sensitive to binwidth.

ggstatsplot::gghistostats(
  data = psych::sat.act, # data from which variable is to be taken
  x = ACT, # numeric variable
  results.subtitle = FALSE, # don't run statistical tests
  messages = FALSE, # turn off messages
  xlab = "ACT Score", # x-axis label
  title = "Distribution of ACT Scores", # title for the plot
  subtitle = "N = 700", # subtitle for the plot
  caption = "Data courtesy of: SAPA project (https://sapa-project.org)", # caption for the plot
  centrality.k = 1 # show 1 decimal places for centrality label
)

Statistical analysis with gghistostats

The authors note that “the score means are higher than national norms suggesting both self selection for people taking on line personality and ability tests and a self reporting bias in scores.” Let’s display the national norms (labeled as “Test”) and test (using results.subtitle = TRUE) the hypothesis that our sample mean is the same as our national population mean of 20 using a parametric one sample t-test (type = "p"). To demonstrate some of the options available we’ll also:

  1. Change the overall theme with ggtheme = ggthemes::theme_tufte()
  2. Make the histogram bars a different color with bar.fill = "#D55E00"
  3. Plot proportions on the y axes with bar.measure = "proportion"
  4. Turn messages on to receive additional diagnostic information with messages = TRUE
  5. Compute information about the Bayes Factor (bf.message = TRUE, see below)
ggstatsplot::gghistostats(
  data = psych::sat.act, # data from which variable is to be taken
  x = ACT, # numeric variable
  results.subtitle = TRUE, # run statistical tests
  messages = TRUE, # turn on messages
  bar.measure = "proportion", # proportions
  xlab = "ACT Score", # x-axis label
  title = "Distribution of ACT Scores", # title for the plot
  type = "p", # one sample t-test
  bf.message = TRUE, # display Bayes method results
  ggtheme = ggthemes::theme_tufte(), # changing default theme
  bar.fill = "#D55E00", # change fill color
  normal.curve = TRUE, # disply a normal distribution curve
  normal.curve.color = "black",
  test.value = 20, # test value
  test.value.line = TRUE, # show a vertical line at `test.value`
  caption = "Data courtesy of: SAPA project (https://sapa-project.org)", # caption for the plot
  centrality.k = 1 # show 1 decimal places for centrality label
)
#> Note: Shapiro-Wilk Normality Test for ACT Score: p-value = < 0.001

gghistostats computed Bayes Factors to quantify the likelihood of the research (BF10) and the null hypothesis (BF01). In our current example, the Bayes Factor value provides very strong evidence (Kass and Rafferty, 1995) in favor of the research hypothesis: these ACT scores are much higher than the national average. The log(Bayes factor) of 492.5 means the odds are 7.54e+213:1 that this sample is different.

Grouped analysis with grouped_gghistostats

What if we want to do the same analysis separately for each gender? ggstatsplot provides a special helper function for such instances: grouped_gghistostats. This is merely a wrapper function around ggstatsplot::combine_plots. It applies gghistostats across all levels of a specified grouping variable and then combines the individual plots into a single plot. Note that the grouping variable can be anything: conditions in a given study, groups in a study sample, different studies, etc.

Let’s see how we can use this function to apply gghistostats to accomplish our task.

ggstatsplot::grouped_gghistostats(
  # arguments relevant for ggstatsplot::gghistostats
  data = psych::sat.act, # same dataset
  x = ACT, # same outcome variable
  xlab = "ACT Score",
  grouping.var = gender, # grouping variable males = 1, females = 2
  title.prefix = "Gender", # prefix for the fixed title
  k = 1, # number of decimal places in results
  type = "r", # robust test: one-sample percentile bootstrap
  test.value = 20, # test value against which sample mean is to be compared
  test.value.line = TRUE, # show a vertical line at `test.value`
  bar.measure = "density", # density
  centrality.parameter = "median", # plotting centrality parameter
  centrality.line.args = list(color = "#D55E00"), 
  centrality.label.args = list(color = "#D55E00"),
  test.value.line.args = list(color = "#009E73"),
  test.value.label.args = list(color = "#009E73"),
  messages = FALSE, # turn off messages
  ggtheme = ggthemes::theme_stata(), # changing default theme
  ggstatsplot.layer = FALSE, # turn off ggstatsplot theme layer
  # arguments relevant for ggstatsplot::combine_plots
  title.text = "Distribution of ACT scores across genders",
  caption.text = "Data courtesy of: SAPA project (https://sapa-project.org)",
  plotgrid.args = list(
    nrow = 2,
    ncol = 1,
    labels = c("Male", "Female")
  )
)

As can be seen from these plots, the mean value is much higher than the national norm. Additionally, we see the benefits of plotting this data separately for each gender. We can see the differences in distributions.

Grouped analysis with purrr

Although this is a quick and dirty way to explore a large amount of data with minimal effort, it does come with an important limitation: reduced flexibility. For example, if we wanted to add, let’s say, a separate test.value argument for each gender, this is not possible with grouped_gghistostats. For cases like these, or to run separate kinds of tests (robust for some, parametric for other, while Bayesian for some other levels of the group) it would be better to use purrr.

See the associated vignette here: https://indrajeetpatil.github.io/ggstatsplot/articles/web_only/purrr_examples.html

Summary of tests

Following tests are carried out for each type of analyses-

Type Test
Parametric One-sample Student’s t-test
Non-parametric One-sample Wilcoxon test
Robust One-sample percentile bootstrap
Bayes Factor One-sample Student’s t-test

Following effect sizes (and confidence intervals/CI) are available for each type of test-

Type Effect size CI?
Parametric Cohen’s d, Hedge’s g (central-and noncentral-t distribution based) Yes
Non-parametric r (computed as \(Z/\sqrt{N_{obs}}\)) Yes
Robust \(M_{robust}\) (Robust location measure) Yes
Bayes Factor No No

Effect size interpretation

To see how the effect sizes displayed in these tests can be interpreted, see: https://indrajeetpatil.github.io/ggstatsplot/articles/web_only/effsize_interpretation.html

Suggestions

If you find any bugs or have any suggestions/remarks, please file an issue on GitHub: https://github.com/IndrajeetPatil/ggstatsplot/issues