Stir together first three ingredients; press mixture evenly on bottom and up sides of a 10 inch springform pan. Freeze 20 minutes.
Stir together apples and flour.
Melt 1/4 cup butter; add apple mixture and 1/2 cup brown sugar. Cook, stirring constantly, 3 to 4 minutes or until mixture is thickened. Remove from heat.
Beat cream cheese and remaining 1 1/2 cups brown sugar; add eggs, 1 at a time, beating after each addition. Add vanilla, beat until blended.
Pour half of mixture into prepared crust. Gently spoon apple mixture on top, spreading to within 1 inch of edge.
Spoon remaining cream cheese mixture over apple mixture, starting at outer edge and working toward the center.
Bake at 350 degrees for 1 hour. Turn oven off and let cheesecake stand in oven 30 minutes. Cool on a wire rack. Chill at least 8 hours.
Garnish with toasted chopped pecans.