#work of compNPP3 data frame
attach(compNPP3)

#add noise level variable
compNPP3$NOISE_LEV<-compNPP3$Noise.Num/compNPP3$Num.Surveys

#create combined9 for 9 or greater surveys
combined9<-subset(compNPP3, Num.Surveys>8)
combined9$NPP<-combined9$npp_Vasc_A  #changes the name of NPP 

#takes residuals from NPP regression
NPPreg<-glm(richness~NPP, family="poisson", data=combined9)
combined9$NPPres<-resid(NPPreg)
attach(combined9)
plot(state, NPPres)

#some regional data also
MWdata<-subset(combined9, region=="MW")
Ndata<-subset(combined9, region=="N")
Sdata<-subset(combined9, region=="S")

#below is unnecessary - these variables are already in NPP3
combined9$PS_ROAD_LEN_300<-combined9$P_ROAD_LEN_300 + combined9$S_ROAD_LEN_300
combined9$PS_ROAD_LEN_600<-combined9$P_ROAD_LEN_600 + combined9$S_ROAD_LEN_600
combined9$PS_ROAD_LEN_1000<-combined9$P_ROAD_LEN_1000 + combined9$S_ROAD_LEN_1000
combined9$PS_ROAD_LEN_5000<-combined9$P_ROAD_LEN_5000 + combined9$S_ROAD_LEN_5000
combined9$PS_ROAD_LEN_10000<-combined9$P_ROAD_LEN_10000 + combined9$S_ROAD_LEN_10000
attach(combined9)

#lm's below for all and for regions
lmtot<-lm(NPPres~NOISE_LEV + Num.Surveys + T_ROAD_LEN_1000 + PROP_AGR_1000 + PROP_DEV_1000 + PROP_FOR_1000, data=combined9)
summary(lmtot)

totMW<-lm(NPPres~NOISE_LEV + Num.Surveys + T_ROAD_LEN_1000 + PROP_AGR_1000 + PROP_DEV_1000 + PROP_FOR_1000, data=MWdata)
summary(totMW)

totN<-lm(NPPres~NOISE_LEV + Num.Surveys + PS_ROAD_LEN_1000 + PROP_AGR_1000 + PROP_DEV_1000 + PROP_FOR_1000, data=Ndata)
summary(totN)

totS<-lm(NPPres~NOISE_LEV + Num.Surveys + T_ROAD_LEN_1000 + PROP_AGR_1000 + PROP_DEV_1000 + PROP_FOR_1000, data=Sdata)
summary(totS)

#single-species models look like this
ANFOhab<-glm(ANFO ~ Num.Surveys + T_ROAD_LEN_1000 + PROP_DEV_1000 + PROP_FOR_5000, family="binomial", data=combined9)
summary(ANFOhab)

ANAMhab<-glm(ANAM ~ Num.Surveys + T_ROAD_LEN_1000 + PROP_DEV_1000 + PROP_FOR_5000 + PROP_AGR_1000, family="binomial", data=combined9)
summary(ANAMhab)

HYCVhab<-glm(sum.HYCV ~ Num.Surveys + T_ROAD_LEN_1000 + PROP_DEV_1000 + PROP_FOR_1000, family="binomial", data=combined9)
summary(HYCVhab)

HYGRhab<-glm(HYGR ~ Num.Surveys + T_ROAD_LEN_1000 + PROP_DEV_1000 + PROP_FOR_5000, family="binomial", data=combined9)
summary(HYGRhab)

HYCIhab<-glm(HYCI ~ Num.Surveys + T_ROAD_LEN_1000 + PROP_DEV_1000 + PROP_FOR_5000 + PROP_AGR_1000, family="binomial", data=combined9)
summary(HYCIhab)

LICAhab<-glm(LICA ~ Num.Surveys + T_ROAD_LEN_1000 + PROP_DEV_1000 + PROP_FOR_5000 + PROP_AGR_1000, family="binomial", data=combined9)
summary(LICAhab)

LICLhab<-glm(LICL ~ Num.Surveys + T_ROAD_LEN_1000 + PROP_DEV_1000 + PROP_FOR_5000 + PROP_AGR_1000, family="binomial", data=combined9)
summary(LICLhab)

LIPAhab<-glm(LIPA ~ Num.Surveys + T_ROAD_LEN_1000 + PROP_DEV_1000 + PROP_FOR_5000 + PROP_AGR_1000, family="binomial", data=combined9)
summary(LIPAhab)

LISPhab<-glm(LISP ~ Num.Surveys + PROP_DEV_1000 + PROP_FOR_5000 + PROP_AGR_1000, family="binomial", data=combined9)
summary(LISPhab)

LISYhab<-glm(LISY ~ Num.Surveys + T_ROAD_LEN_1000 + PROP_DEV_1000 + PROP_FOR_1000 + PROP_AGR_1000, family="binomial", data=compNOMN)
summary(LISYhab)

#this added the subset of wetland data but there's not a lot of these
combwet<-merge(combined9, revisedareas, by="route")
attach(combwet)

cor.test(NPPres, Area300, use="pairwise.complete.obs")
cor.test(NPPres, Area600, use="pairwise.complete.obs")
cor.test(NPPres, Area1000, use="pairwise.complete.obs")
cor.test(NPPres, Area5000, use="pairwise.complete.obs")
cor.test(NPPres, Area10000, use="pairwise.complete.obs")

cor(Area300, Area1000, use="pairwise.complete.obs")
cor(Area300, Area10000, use="pairwise.complete.obs")
cor(Area1000, Area10000, use="pairwise.complete.obs")

attach(combined9)
plot(state, richness, xlab="state", ylab="richness")
plot(state, NPPres, xlab="state", ylab="richness")


attach(combined9)
cor.test(NPPres, T_ROAD_LEN_300, use="pairwise.complete.obs")
cor.test(NPPres, T_ROAD_LEN_600, use="pairwise.complete.obs")
cor.test(NPPres, T_ROAD_LEN_1000, use="pairwise.complete.obs")
cor.test(NPPres, T_ROAD_LEN_5000, use="pairwise.complete.obs")
cor.test(NPPres, T_ROAD_LEN_10000, use="pairwise.complete.obs")

cor.test(NPPres, PROP_DEV_300, use="pairwise.complete.obs")
cor.test(NPPres, PROP_DEV_600, use="pairwise.complete.obs")
cor.test(NPPres, PROP_DEV_1000, use="pairwise.complete.obs")
cor.test(NPPres, PROP_DEV_5000, use="pairwise.complete.obs")
cor.test(NPPres, PROP_DEV_10000, use="pairwise.complete.obs")

cor.test(NPPres, PROP_FOR_300, use="pairwise.complete.obs")
cor.test(NPPres, PROP_FOR_600, use="pairwise.complete.obs")
cor.test(NPPres, PROP_FOR_1000, use="pairwise.complete.obs")
cor.test(NPPres, PROP_FOR_5000, use="pairwise.complete.obs")
cor.test(NPPres, PROP_FOR_10000, use="pairwise.complete.obs")

cor.test(NPPres, PROP_AGR_300, use="pairwise.complete.obs")
cor.test(NPPres, PROP_AGR_600, use="pairwise.complete.obs")
cor.test(NPPres, PROP_AGR_1000, use="pairwise.complete.obs")
cor.test(NPPres, PROP_AGR_5000, use="pairwise.complete.obs")
cor.test(NPPres, PROP_AGR_10000, use="pairwise.complete.obs")

attach(combined9)
cor.test(NPPres, WET_CONNECT, use="pairwise.complete.obs")
cor.test(NPPres, TOTAL_CONNECT, use="pairwise.complete.obs") 

plot(region, PROP_AGR_1000)
plot(region, T_ROAD_LEN_1000)
plot(region, PROP_FOR_1000)
plot(region, PROP_DEV_1000)