Vets will generally give the medication as a liquid and will provide you with a syringe. You can either scruff the rat and inject the medicine directly into their mouths or you can just mix it with a bit of baby food and they generally will lap it up.
Rats have very delicate respitory systems and require adequate ventilation regardless of the substrate, so if your enclosures don't allow for that, consider finding a way to add more. As as been mentioned already, pine and cedar are not good for rats. They both will contribute to respitory issues and pine can cause a rise in liver enzymes in rodents.
http://www.ratfanclub.org/litters.html has more info on it.
Rats are very prone to RI's and they usually recover very well if treated early enough, so I'm keeping my fingers crossed that your girl will be OK.
Good luck!
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