Preheat oven to 350 degrees and grease and flour a 9x13 inch baking pan. Set aside.
In a large mixing bowl, combine apples and sugar. Stir in oil, eggs, and vanilla.
In another mixing bowl combine flour, baking powder, baking soda, cinnamon, nutmeg and salt. Add the flour mixture to the apple mixture. Add milk and stir until just combined. Add chopped pecans.
Pour into prepared 9x13 inch pan. Bake for 30-40 minutes or until toothpick comes out clean. Let cool completely.
To make the frosting: Beat the cream cheese until smooth. Add butter and continue to beat until smooth scraping down sides when needed. Add vanilla and brown sugar. Beat for 5 minutes until it is light and fluffy and the sugar has dissolved. Spread evenly on top of the cake. Refrigerate after frosting.