Heart Rate
Unlike pace, heart rate is a direct indicator of exercise intensity. The higher your heart rate climbs during running, the harder your body is working. Heart rate monitors are especially effective as tools to hold runners back from running harder than they should. When runners are given a heart rate "ceiling" for a given workout, they usually respect it, whereas when they are given a pace target, they often try to "beat" it.
Each runner's heart responds differently to exercise. For one runner, the intensity level known as the ventilatory threshold (where talking becomes difficult) might correspond to a heart rate of 150 beats per minute (bpm), whereas for another runner the same threshold may occur at 160 bpm. To train effectively by heart rate you need to establish target heart rate zones that are tailored to your fitness level.
The traditional way to do this is to perform some kind of heart rate assessment test, use the results to calculate custom heart rate zones, and program these zones into a heart rate monitor. This process can be a bit of a hassle and has prevented many runners from using heart rate monitors. Recently however, new devices have been developed to automate these calculations. Look for products such as PEAR Mobile.
The simplest way to benefit from the use of a conventional heart rate monitor is as follows: Warm up and then run as far as you can in 30 minutes. Note your average heart rate during the last 10 minutes of the time trial. This is your approximate lactate threshold heart rate. Multiply this heart rate by 0.89. Keep your heart rate at or below the resulting number in all runs that are intended as easy runs.
For example, if your average heart rate in the last 10 minutes of your time trial is 160 bpm, do your easy runs at a heart rate of (160 x 0.89 =) 142 bpm or below.
More: Breaking Down Your Target Heart Rate
Perceived Effort
Perceived effort is essentially how hard a running effort feels. The advantage of perceived effort relative to other intensity metrics is that it's a global indicator that encompasses all of the physiological factors that determine exercise intensity.
The main disadvantage of perceived effort is that it's subjective and therefore can be unreliable. For example, research has shown that most recreational runners believe they're running at a low intensity (below the ventilatory threshold) when in fact they're running at a moderate intensity.
It's important to be mindful of perceived effort every time you run. When properly interpreted, perceived effort is the best indicator of your body's overall status and limitations.
Any given pace or heart rate will not feel the same in every run. If you feel much worse than normal one day at a familiar pace or heart rate, this is a reliable sign that something is off physically or psychologically and you should probably slow down. On the other hand, if you feel exceptionally good in a workout, it may be beneficial to push beyond your target pace or heart rate provided it's a workout that is supposed to be challenging.
More: When Does Running Get Easier for Beginners
The Right Mix
Now let's put everything together: Use pace to monitor and control your intensity in harder workouts where performance matters, but ignore pace in easy runs. With heart rate monitoring it's just the opposite: Use heart rate ceilings to ensure that your easy runs are truly easy. Finally, be mindful of your perceived effort in every run and use it to overrule pace or heart rate data.
More: 4 Steps to Your Perfect Pace
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