knitr::opts_chunk$set(echo = TRUE)
aceitillar.sp$site <- "Aceitillar" j.cols <- c("recapYN","stat.MvsR","spp.code","yr.mo.1st.cap","site") both.sp <- rbind(aceitillar.sp[i.1st.cap.96.all,j.cols], mencia.sp[i.1st.cap.03.all, j.cols])
Order sites
both.sp$site <- as.character(both.sp$site) both.sp$site <- factor(both.sp$site, levels = c("La Cueva","La Caoba","Morelia","El Corral", "Aceitillar"))
Code Month of capture
both.sp$yr.mo.1st.cap <- as.character(both.sp$yr.mo.1st.cap) both.sp$yr.mo.1st.cap[grep("N",both.sp$yr.mo.1st.cap)] <- "N" both.sp$yr.mo.1st.cap[grep("J",both.sp$yr.mo.1st.cap)] <- "J" both.sp$yr.mo.1st.cap[grep("[FM]",both.sp$yr.mo.1st.cap)] <- "F" #March is nominally Feb
both.sp$yr.mo.1st.cap <- factor(both.sp$yr.mo.1st.cap) both.sp$stat.MvsR <- factor(both.sp$stat.MvsR) summary(both.sp) with(both.sp, table(stat.MvsR,site)) with(both.sp, table(stat.MvsR,yr.mo.1st.cap)) with(both.sp, table(site,yr.mo.1st.cap))
net_hrs <- read.csv(file = "./data/net_hours.csv")[,1:5] net_hrs$site <- factor(net_hrs$site, levels = c("La Cueva","La Caoba","Morelia","El Corral", "Aceitillar")) i.nethrs.use <- which(net_hrs$year %in% c("1996-1997","2003-2004")) net_hrs4sp <- net_hrs[i.nethrs.use,] dim(net_hrs4sp)
both.sp2 <- merge(both.sp,net_hrs4sp,all = T) dim(both.sp) dim(both.sp2) both.sp <- both.sp2
save(both.sp,file = "./data/sp_individual.RData")
sp.cast <- dcast(data = both.sp, formula = site + stat.MvsR + spp.code + yr.mo.1st.cap ~ recapYN, value.var = "recapYN", fun.aggregate = length) with(sp.cast, which(sp == 0 & not.sp == 0)) sp.cast$i <- 1:dim(sp.cast)[1]
save(sp.cast,file = "./data/sp_binomial.RData")
m.binomial <- glmer(cbind(sp,not.sp) ~ site*stat.MvsR + (1|i) + (1|spp.code) + (1|yr.mo.1st.cap), #offset = log(net.hours), family=binomial, data = sp.cast) summary(m.binomial)
m.binomial.means <- glmer(cbind(sp,not.sp) ~ -1 + site:stat.MvsR + (1|i) + (1|spp.code) + (1|yr.mo.1st.cap), #offset = log(net.hours), family=binomial, data = sp.cast)
summary(m.binomial.means)
Intial methods: With the pasture migrant site persistence increased from 0.44 at the youngest abandoned pasture to 0.62 at the oldest, but dropped to 0.15 at the mature forest site. This resulted in an overall significant negative quadratic trend (z = -4.2, p < 0.001). For resident species site persistence declined significantly overall (z = -2.6, p = 0.009) from the youngest pasture (0.38) to the mature forest (0.13), though persistence was hightest in the oldest pasture (0.43).
invlogit(fixef(m.binomial.means))
Create contrast matrix
contrst.mat.10lev <- rbind("Mig-linear" = c(-2,-1, 0, 1, 2, 0, 0, 0, 0, 0), "Mig-quad" = c(+2,-1,-2,-1,+2, 0, 0, 0, 0, 0), #"Mig-brk" = c(-2, 0, 1, 2, -1, 0, 0, 0, 0, 0), "Res-linear" = c( 0, 0, 0, 0, 0,-2,-1, 0, 1, 2), "Res-quad" = c( 0, 0, 0, 0, 0,+2,-1,-2,-1,+2))
Run multcomp
mult.comp.working <- glht(m.binomial.means ,linfct =contrst.mat.10lev ,alternative = c("two.sided")) mult.comp.summary <- summary(mult.comp.working ,test = adjusted(type = "none"))
m.both.sp <- glmer(recapYN ~ 1 + log(net.hours)+ #(1|spp.code) + (1|yr.mo.1st.cap), #offset = log(net.hours), family=binomial(link="cloglog"), data = both.sp) summary(m.both.sp)
m.both.sp.means <- bglmer(recapYN ~ -1 + site:stat.MvsR + (1|spp.code) + (1|yr.mo.1st.cap), family = binomial, data = both.sp) summary(m.both.sp.means)
Create contrast matrix
Need to set up for interaction
contrst.mat <- rbind("Linear" = c( -2,-1, 0, 1, 2), "Quad" = c(+2,-1,-2,-1,+2))
Run multcomp
mult.comp.working.spp.rich <- glht(m.anova.spp.rich.means ,linfct =contrst.mat ,alternative = c("two.sided")) mult.comp.summary.spp.rich <- summary(mult.comp.working.spp.rich ,test = adjusted(type = "none"))
Mult comp output
mult.comp.summary.spp.rich
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