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I've noticed many skills reference a stack of some sort, but I can't seem to find any reference to the stack. Is it simply a counter? Do the stacks increase ever? Here is an in game example.

Defensive Subroutines. You randomly pick a Subroutine focused on Health or Shields, which grants increased Capacity and Regeneration for the chosen attribute. The catch? You deal reduced damage with all gun types. Upon selecting Subroutine you gain 100 Frag Stacks which decrease over time. When you run out of Frag Stacks, your Subroutine will be replaced with a new one.

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  • "Stacks" in relation to effects is a term that says that an effect "stack on top of" another effect, usually of the same type, instead of replacing it. Such a stack usually comes with a number indicating how many times the effect stack. As an example, an effect might give you +10 health, and stack up to 5 times (usually described on whatever gives that effect). Thus, you can have from +0 (no effect present) up to +50 (5 stacks) health from this effect. So yes, it is usually just a counter. – Lasse V. Karlsen Nov 5 '14 at 9:13
  • As for whether a stack increases or decreases, usually whatever gave an effect increases the number of stacking effects, and usually this is described on whatever gives that effect. Stacks can be decreased, as described on the specific example you give, and why/when is also usually described on whatever gives this effect. – Lasse V. Karlsen Nov 5 '14 at 9:14
  • The term is used in a variety of games, usually games that lend a lot of mechanics from role playing games where I think the term was originally used. Here's an example from the Diablo 3 2.1 Patch Notes. "Conflagrate: Burn damage stacks up to 3 times..." – Lasse V. Karlsen Nov 5 '14 at 9:18
  • The example used in the question is very confusing. In general, stacks of effects work along the lines of @FeralChimp's answer, but Frag Stacks are very different, as discussed here. Also, the question may be considered too broad, because the answer without listing every skill will be "differently". – Orc JMR Apr 24 '15 at 12:46
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Every stack in the game works differently, but there are some aspects in common.

Stacks are gained and accumulate. Each stacks lasts for a while, and then you lose it. You usually get a bonus for each stack. Most stacks will show up on your screen above your experience bar, as you can see in the Nisha screenshot in Chimp's answer. Getting more specific than that requires looking at the specific skill descriptions.

Nisha Example

Feral Chimp has provided a good example of this with Nisha's Order stacks.

There, you can see that the way in which you gain the stacks is spelled out in the skill description:

Every time you take 15% of your maximum health in damage, you gain a stack of Order.

The skill description also says how you lose the stacks (not included in Chimp's answer):

Order stacks are quickly lost when outside combat.

And also what benefit you gain from the stacks:

Based on your number of Order stacks, you have a chance to instantly heal double the damage taken.

and

Heal Chance +1.2% per Order stack.

As well as the maximum number you can have:

Maximum Stacks: 10.

Frag Stacks

All the information you need to answer your question is in the skill description you've provided.

How you gain the stacks:

Upon selecting Subroutine you gain 100 Frag Stacks which decrease over time.

So you get 100 every time a subroutine is selected. This is a bit odd, as most stacks require you to earn them by doing something, such as Nisha's Order stacks which require you to be damaged, or Wilhelm's Rolling Thunder stacks which increase the longer Wolf is active.

How you lose the stacks:

Upon selecting Subroutine you gain 100 Frag Stacks which decrease over time.

These stacks simply decrease over time from 100 to 0. It's basically a countdown. Although other skills in Claptrap's tree allow you to modify the rate at which it counts down, at first you have no control over it.

What the stacks do:

You randomly pick a Subroutine focused on Health or Shields, which grants increased Capacity and Regeneration for the chosen attribute.

These stacks are also unusual in that there is no per-stack bonus. Most stacks give you something per stack, like Nisha's Order stacks which give you a chance to heal per stack, or Wilhelm's Rolling Thunder stacks which give extra Wolf damage per stack. Instead, as long as you have Frag stacks you'll get specific preset bonuses to the randomly chosen attribute: health or shields. The bonuses are also listed in the skill: "Capacity +35% Regeneration 2.5% of Max Attribute / sec. Gun Damage -15%". So if Shields was chosen as your subroutine, you get +35% shield capacity, -15% gun damage, and regenerate 2.5% of your shields per second.

How many you can have:

Upon selecting Subroutine you gain 100 Frag Stacks which decrease over time.

I don't think there's actually a cap on frag stacks, but it might be 100. I'm not really using this tree with my claptrap, except for the one skill you're asking about. Eventually there are skills which let you add to your frag stack total, and it's possible these could push you over 100 stacks. At first though, you can't affect the total, and just get 100 to begin with.

You can see your current frag stack count above your experience bar.

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A couple of examples may help to clarify what Stacks are about. Consider two of Nisha's skills:

  • Order: Every time you take 15% of your maximum health in damage, you gain a stack of Order. The more Order stacks you have accumulated, the greater your chance to instantly heal double the taken damage.

  • Wanted: When an enemy would cause you to gain an Order stack, that enemy gets a Wanted stack. When you damage an enemy who has accumulated one or more Wanted stacks, you do bonus damage to them base on the number of stacks that specific enemy has accumulated, instantly using up the Wanted stacks.

In the screenshot below I've been fighting a pack of lowly Kraggons to show how this works.

  • Above my experience bar you can see 15 Order stacks. This means that at least 15 times, something has damaged me for the equivalent of 15% of my maximum health.

  • By the 4 stars above the Kraggon Immolator's head, you can see that he/she has caused me Order-worthy damage at least 4 times.

Stack Limit/Cap/Max

When I say "at least" above, that's because there's a limit to the number of times an effect can stack. Wanted, for example, is limited to 5 stacks. Sometimes this will be worded as "Wanted can be stacked a maximum of 5 times" or "Wanted has a cap of 5 stacks".

Sometimes other skills will increase a stack limit. Again using Nisha as an example, Order has a limit of 10 stacks, but adding her Rough Rider skill will increase that cap (maximum) by 5.

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depending on the amount of ranks that are available for that particular perk they may increase, if it is the only rank available that they wont increase unless directly affected by a piece of equipment (eg. mod, Oz pack). and essentially yes it is a counter from 100> down, then it would reset as a different effect as described in the perk.

also I should mention that not all stacks work in this way, some you would have to earn (eg,x amount of kills/bullets fired....and so on = x amount of stacks) depending on which character, skill tree ect.

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