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Overload, Recovery, Adaptation & Reversibility Specificity
When choosing the type of training program to go on, specificity should always be considered. If you are competing in a high level sport or activity, you'll want to make sure that your training program enables you to show the most improvement in that actual activity. It would not make sense to dedicate hours of your time, improving your fitness level, if this did not mean you would perform better when it counts. This is where specificity of a program comes in.
The main factors to consider are overload, recovery, adaptation and reversibility. You will want each one to mirror that of the activity you are doing. If this activity is composed on a short bursts of movement for example, you'll want the overloading stimulus to be high intensity sprints since that will likely give you the most benefits. Going out for an hour long run isn't really going to be all that applicable to your situation.
When training with specificity though, attention really needs to be paid to recovery. Since the majority of your activities are now going to be targeting in on one or two main components of your fitness, you must be providing ample rest to recover from this.
For example, if you are doing sprint sessions along with weight training sessions because your chosen sport is football (which requires short bursts of energy along with a great deal of muscular strength), both of these workouts will place heavy demands on your central nervous system. If you are doing a heavy lifting session three days a week and sprint training three days a week, this may not be enough time to allow for recovery. In this case, you'll want to prioritize which area needs the most work and tone your sessions down in frequency so you can have two to three days off a week.
Lastly, don't completely neglect the importance of cross training as well. On the days you take 'off', you could very well implement some light physical activity that is not in any way related to the sport you are performing (or the type of training you are doing the rest of the week). For example, if you are a track athlete, training hard on the track and in the weight room, on your days off you may want to go for a leisurely swim or a yoga session. This will help to further improve recovery since it will cause more oxygen to move through the muscles and deliver nutrients to help heal any muscle tears.
So when designing your workout program, make sure you keep this key factor in mind.