Jitter is computed as a standard deviation of all ping values measured up to the given time. A more representative value is therefore indicated at the end of the measurement.
Download and upload are measured by transferring blocks of data by HTTP requests. The bandwidth is computed from HTTP payload data transferred (without HTTP and lower layer headers). The graph shows an arithmetic mean of all values measured up to the given time. A more representative value for large file transfers is therefore indicated at the end of the measurement.
The final number indicated in gauges is an average value for all pings and a value at the end of the measurement for the other characteristics.
Original speedtest source code can be obtained at GitHub.