I'm currently using a basic php code to track my affiliate links on my wp site.

I'm wondering if there is a way to make it so Wordpress can still see what links are being clicked so I can see how links are performing?

I've heard of the Pretty Link plugin but $97 seems a bit much to me just so I can track the number of clicks on my links.

there should be a free wp cloaking plugin around that also counts the number of clicks. try searching for it