In my experience it is true that in nonlinear periodization, because there is not much distinction between training phases, it can be difficult to time a peak accurately. Also, because high-intensity training never ceases, there is greater risk of overtraining.
For example, Brad Hudson, who favors nonlinear periodization, blames Dathan Ritzenhein’s disappointing debut marathon (11th at New York City in 2006) partly on a mistimed peak; Ritz was killing his workouts three weeks out, but turned stale between that time and race day. I believe that perhaps the most influential factor in determining the degree of effectiveness of linear versus nonlinear periodization for the individual runner is psychological. On a purely physiological level, either method can be customized to suit the needs of any given runner.
But individual runners tend to have strong preferences for one or the other system. Generally, the Lydiard approach works best for runners who like to ease into their training and put off until late in the training cycle the great suffering needed to achieve peak fitness. A nonlinear approach works best for those who like to see and feel steady improvement throughout the training cycle. Think about which approach better suits your psychology in this regard, and start there.
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