knitr::opts_chunk$set( collapse = TRUE, comment = "#>" )
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
- 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
Let's begin with a very simple example from the
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)
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
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
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
- Change the overall theme with
ggtheme = ggthemes::theme_tufte()
- Make the histogram bars a different color with
bar.fill = "#D55E00"
- Plot proportions on the y axes with
bar.measure = "proportion"
- Turn messages on to receive additional diagnostic information with
messages = TRUE
- 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 )
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
What if we want to do the same analysis separately for each gender? In
that case, we will have to either write a
for loop or use
purrr, none of
which seem like an exciting prospect.
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
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 robust.estimator = "mom", # changing the robust estimator used 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.para = "median", # plotting centrality parameter centrality.color = "#D55E00", # color for centrality line and label test.value.color = "#009E73", # color for test line and label 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)", 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
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
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
See the associated vignette here: https://indrajeetpatil.github.io/ggstatsplot/articles/web_only/purrr_examples.html
If you find any bugs or have any suggestions/remarks, please file an issue on GitHub: https://github.com/IndrajeetPatil/ggstatsplot/issues