See discrete-time-and-state-Markov.pdf for notes and background information. See the non-missing data form here.
|n - 1 = 0||# observed transitions|
|nd = 0||number of color changes|
|ns = 0||# adjacent samples with same color|
|ŝ = ?||estimate of the switch probability|
Blue trace is full likelihood. Red trace just uses information from adjacent non-missing entries.