Position the shelves in the upper and lower thirds of the oven. Heat the oven to 375°F Line the muffin pans with paper or foil cupcake liners.
Chop apples by hand or place the apples in the work bowl of a food processor fitted with a metal blade and pulse 8-10 times, or until the apples are chopped into 1/4 –inch pieces.
In a medium bowl, thoroughly whisk together the flour, baking powder, cinnamon, nutmeg, baking soda, and salt. Set aside.
In the bowl of an electric mixer fitted with the whip attachment, beat the eggs on medium-high speed until lightened in color, about 2 minutes. Add the brown sugar 1 to 2 tablespoons at a time, taking about 2 minutes, and beat the mixture for 1 minute longer.
Stop the machine and add the honey and vanilla. Turn the mixer on to medium speed and mix to combine. In a small bowl, whisk together the melted butter and oil and pour it into the egg mixture in a steady stream, taking about 1 minute. Add the apples and blend well.
Reduce the mixer speed to medium-low and add the dry ingredients all at once, blending just until incorporated. Fold in the raisins and pecans.
Portion the batter into the prepared pans. Bake for 20 to 25 minutesthe preheated oven, rotating the pans for even browning halfway through.