From the documentation for fplot:
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fplot(fun,limits,tol) plots fun using the relative error tolerance tol (the default is 2e-3, i.e., 0.2 percent accuracy).
. . .
fplot uses adaptive step control to produce a representative graph, concentrating its evaluation in regions where the function's rate of change is the greatest.
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It seems to me that a tolerance of 1E-6 would require more steps — and therefore more time to execute — than a tolerance of 1E-2.
