yarrr | An R package for conducting all sorts of R piratery | Development Tools library

If you’re ever curious about what’s going on with a package, I would encourage you to have a quick look through the github. It may be a little overwhelming at first, but you can learn quite a bit by reviewing what others have done.

Looking at the yarrr github, we can see in line 750 the package calculates confidence intervals using a t-interval. You are calculating the 95% confidence interval using a z-interval. The methods are different, so we’ll get different results. For smaller sample sizes (less than 30 as a general rule), t-intervals are more appropriate.

The z-interval assumes we know the population standard error. For smaller sample sizes, you can imagine our estimates are going to be pretty varied and the standard deviation of the sample may not be representative of the population. The confidence intervals that result don’t account for this extra uncertainty and so they don’t have enough coverage to truly be a 95% confidence interval as we're violating the assumption that the population standard error is known.

Let’s do the calculation with your example data just to see the difference and make sure we are matching the package.

mar and title are easy ways to do this. Mar changes spacing of a plot and title sets a title:

The values of each theme in the pirateplot package can be found inside the pirateplot_function.R, in the source code.

Take a look at the source code on GitHub - the themes start at line 833.

For ggplot you could do the same, or call the function without the (), e.g. theme_classic gives you