1. A method of automating a process for conditioning or rehabilitating a subject utilizing an aerobic exercise training protocol based on an aerobic threshold method of exercise training performed on a polyarticular aerobic exercise device, comprising the steps of: (a) creating a first polyarticular aerobic exercise protocol and storing said first protocol on a transportable memory device, said first protocol using a target exercise intensity (workrate) as the controlling variable, wherein the intensity and duration are related to at least one parameter selected from maximum aerobic capacity (VO.sub.2 max) and anaerobic threshold (AT) of the subject; (b) creating a first monitoring protocol and storing said first monitoring protocol on said memory device, said first monitoring protocol being dedicated to operate during performance of said first aerobic exercise protocol and further defining monitoring and sampling intervals for obtaining real-time data from the subject indicative of non-controlling physiological variables selected from oxygen consumption (VO.sub.2), carbon dioxide production (VCO.sub.2), ventilation (VE), heart rate (HR) and blood pressure (BP) and optionally psychological variables selected from the rate of perceived exertion (RPE) and compliance with the exercise protocol during each such repetitive execution of the exercise protocol; (c) transferring the transportable memory device to an aerobic exercise device, said device being automated for operation by the transportable memory device, said device including means for measuring actual power delivered by the subject and controlling the level of subject input power required to achieve said target intensity in an automated manner; (d) wherein the subject reproduces the exercise protocol using said aerobic exercise device through at least a first program, a program comprising repetitive execution of said first aerobic exercise protocol in a series of successive sessions; (e) obtaining real-time data of one or more of said non-controlling physiological variables according to said first monitoring protocol during each repetitive execution of said first aerobic exercise protocol; (f) optionally monitoring non-controlling psychological variables during execution of said first aerobic exercise protocol according to said first monitoring protocol; (g) wherein said real-time data obtained in accordance with said monitoring protocol remains independent from the operation of said exercise device; (h) causing selected real-time data obtained to be stored in said memory device according to said first monitoring protocol; and (i) using changes in one or more measured non-controlling physiological and psychological variables observed over the course of said several sessions of said first program based on data stored in said memory device to evaluate progressive effectiveness of the protocol.