Preheat oven to 350 degrees and prepare a muffin tin with paper liners.
In a large bowl, whisk together oil, melted butter, honey, white sugar and brown sugar. Add in eggs and vanilla, and continue to whisk together until smooth.
Combine dry ingredients: flour, baking soda, baking powder, salt, cinnamon and nutmeg.
Add the dry mixture to the wet ingredients and mix until fully combined.
Fold in the shredded carrots and pecans (use a food processor for small, uniform pieces).
Drop the batter into the lined muffin tins, filling each one about ¾ of the way full.
Bake at 350 degrees for 25 minutes; remove the oven and cool completely on a wire rack.
While the cupcakes are cooking and cooling, prepare the frosting. Combine the softened cream cheese and butter with vanilla extract, cinnamon, salt, and powdered sugar in a bowl. Use an electric mixture to beat the ingredients together until smooth.
Ice the cooled cupcakes with the cream cheese frosting and decorate with sprinkles.