Game1.js

PS.keyDown = function (key, shift, ctrl, options) {
    "use strict";

    // p was pressed - pause the game
    if (key === 112) {
        GAME.paused = !GAME.paused // flip the state, if it was paused, it's unpaused after this
        PS.debug("Game is now paused: " + GAME.paused);
        // not sure how PS works. I suspect you don't want to stop the timer here, but instead want to do that in code that is higher up
        // i would iamgine the game controller would have access to the timer properties
    }

    // r was pressed, restart the game
    if (key === 114) {
        GAME.ending = true;
        // again, I prefer not to call game-engine related functions down here. let the thing controlling the game know that the user
        // wants to restart the game, and then let it figure out how to do that
    }
}

// then, elswhere, in your rendering code:

// I don't know the interface, this is just a pseudocode-like example
GAME.renderingCode = function() {
    // the order you hit these conditionals about game state matters - keep that in  mind
    if (GAME.restarting) {
        GameSetup();
        return;
    }

    if (GAME.paused) {
        PS.timerStop(sTimerID);
    }
}