In RPGXP's default battle system, attack (ATK), physical defense (PDEF), and magic defense (MDEF) are solely based on the weapons and armors equipped. The relation of the parameters Strength, Dexterity, Agility, and Intelligence to damage calculation is not very clear.
In calculating damage, the system calculates two values: force and rate. Force is a base damage value, and rate is a multiplier to force; in this case, force is multiplied by rate and divided by 20.
For normal attacks:
Force is increased by attack and decreased by physical defense
Rate increases by strength
For healing skills:
Force is the base amount given in the database
Rate increases depending on strength, dexterity, agility, and intelligence
For damaging skills:
Force is increased by attack and decreased by physical and magical defense
Rate increases depending on strength, dexterity, agility, and intelligence
Multiply force by rate and you get the damage. There are also effects such as element modifiers and critical hit modifiers that modify the damage dealt, as well as a "variance" factor to make the damage fluctuate within a certain range.
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For comparison, RPGVX's battle system is much simpler when it comes to damage calculation. The values Attack, Defense, and Spirit relate directly to the damage dealt and can be increased with weapons and armors. For completeness, I will briefly explain the damage calculation:
For normal attacks:
Damage is 4 times attack minus 2 times defense
For healing skills:
Healing rate is affected by attack and spirit
For damaging skills:
Damage is increased by attacker's attack and spirit and decreased
by opponent's defense and spirit