In brouwern/DRmencia: Data and code to replicate analyses for Latta, Brouwer, et al. 2018. PeerJ.

knitr::opts_chunk$set(echo = TRUE)

Load site persistence df

filename <- "site_persist_cleaned.csv"
filename <- here::here("data-raw",
                  "data-raw-mencia",
                  "mencia_site_persistence",
                  filename)

sp <- read.csv(file = filename)

with(sp,table(wanderer,status,useNA = "always"))

Code site persistence

summary(sp$wanderer)

sp$persistent <- as.character(sp$wanderer)

sp$persistent[is.na(sp$persistent)] <- "not.persist"
sp$persistent <- gsub("W","P",sp$persistent)

summary(factor(sp$persistent))
sp$persistent  <- factor(sp$persistent)

Determine unique individuals

i.unique <- match(unique(sp$band),
                  sp$band)

length(i.unique)
dim(sp)

summary(sp$wanderer)
summary(sp$persistent )

Model site persistence

m1 <- glmer(persistent ~ scale(site.age)*status +
              # (1|ID) +
               (1|year) +
               (1|site) +
               (scale(site.age)|species),
              data = sp[,],
              family = binomial)

m1b <- glmer(persistent ~ 1 +
              # (1|ID) +
               (1|year) +
               (1|site) +
               (scale(site.age)|species:status),
              data = sp[,],
              family = binomial)


summary(m1)
ranef(m1b)

plot site ratio

library(ggplot2)

ggplot(data = sp[,],
       aes(y = as.numeric(persistent)-1,
           x = site.age), 
       color = site,
       group = status) +
  geom_point(aes(color = site)) +
  facet_wrap(~ status) + 
  geom_smooth(method = glm,
              method.args = list(family = "binomial")) +
  ylab("Age ratio")

brouwern/DRmencia documentation built on May 6, 2019, 12:24 p.m.