######################## ## Code to generate decay curves for probaility of water after boards are puuled ## habitat value decay as function of days since boards pulled setwd("C:/water") ## look at probabaility of being >0 cm depth as function of ays since boards pulled (dsp) vdp<-read.csv("water_decay.csv",header=T) names(vdp) vdp$depind<-ifelse(vdp$waterrev.cm>0|vdp$pflood>0|psat>0,1,0) ## get rid of survey prior to board pull vdp<-subset(vdp,vdp$daysince>=0) ## get date boards pulled vdp$bp<-vdp$jdate.surv-vdp$daysince library(gamm4) library(ggplot2) unique(vdp$bp) wdm1b<-gamm4(depind~s(daysince,k=10), random=~(1|field) , family=binomial, data=vdp) summary(wdm1b$mer) decay = data.frame(daysince=seq(0,max(vdp$daysince),1), prop.hab=0) decay$prop.flooded = predict(wdm1b$gam, decay, type='response') preddecay = as.data.frame(predict(wdm1b$gam, decay, type='link', se.fit=T)) decay$lcl = plogis(preddecay$fit-2*preddecay$se.fit) decay$ucl = plogis(preddecay$fit+2*preddecay$se.fit) write.csv(decay,"decay.csv")