add rodents stuff

[SBWeinstein]

1. egg infectivity cut off- 4 month
2. incorporating trophic transmission model
3. mean, aggregation of rodent worms- mouse
4. assume adult raccoons get rodent every other month or so, only if over 4 months
5. 25% of rodent worms establish in raccoons
6. how important are rodents- keep egg worms and rodent worm matrices separate, then add together for total worm matrix. worms senecse similarily (separate but equal)

[SBWeinstein]

worms in peromyscus at COPR data saved as peromyscus_bpdata.csv in shared IBM model dropbox folder

mu (abundance)=3.49, size (aggregation)=0.22

require(bbmle) mice<-pero$Bp negbin<-function(mu, size){ -sum(dnbinom(mice, mu=mu, size=size, log=TRUE)) } m4<-mle2(negbin, start=list(mu=3, size=.5))

[mqwilber]

Split worm matrices into rodents and non rodents. Might have slowed things down a little bit. See commit 29414d9 for code without the worm arrays separated.