The averages you see on the student dashboard (and on the homepage) are based off the total number of times students were present and the total number of opportunities they had to be present. This is true for both class attendance and daily attendance.
For example, the screenshot below shows that class attendance has been logged for 21 students on this day, and 18 of them were present, resulting in an overall percentage of 86%. Hover over the percentage to see the numbers used to calculate the percentage.
For daily attendance, all students are presumed present until marked otherwise. That means that if no one logs any attendance for the day, Schoolrunner will display the daily percentage as 100% (since students can only have one daily record per day; learn more class and daily records here).
This is different than class attendance, where the Schoolrunner system waits to see which courses have attendance taken, and then uses the data generated by teachers to determine the class percentage.
Note that, formerly, the number shown in the average row was an average of the percentages above it. This method was less accurate than the current method of calculation. However, if you want an average of percentages, you can still download an export of your dashboard and average out the percentages in the spreadsheet.