PokéBase - Pokémon Q&A
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I'm not sure about this. But if you reset the game you won't close the game. So does the game keep on count on that?
And does the shiny be under 4096 at all if you just encounter them without resetting?

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Encounter rate is static. The game will always make a 1/4069 Pokemon shiny. You're probably thinking of the likelihood that you'd get a shiny and how it changes every time you don't. And to that, yes, every time you reset and don't get a shiny, the percentage likelihood that you will increases. The more you do something, the more likely you are to get the result you want.

I don't really know how else to explain it. The game doesn't increase the rate you'd get a shiny every time you don't, it's always the same number just like it is to say win at a casino. But just mathematically the more you do something the better your outcomes are likely to be
Shininess is random, so it's like flipping a coin. If you want heads and flip it twice, then there's still a chance that you get no heads, right?

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No. Think about it like rolling a die. Statistically, there's a 1/6 chance that you'll roll a specific number, but that doesn't necessarily mean that, after six rolls, you will get that roll. The same thing applies to encountering a shiny Pokemon. If you roll a die with 4096 sides, it's very possible to both roll a 4096 before rolling 4096 times or to roll a 4096 after rolling 4096 times.

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I don't get anything. Blame my language, but I don't know what "a die" is :/
a die is the singular for dice
Fun fact: 'dice' is acceptable as the singular nowadays :)
https://en.oxforddictionaries.com/definition/dice
"Historically, dice is the plural of die, but in modern standard English dice is both the singular and the plural"
The more you know... (Shooting star)
Sounds like language laziness to me.