knitr::opts_chunk$set(echo = TRUE)

Load Mencia site persistence data

library(here)


fi <- here::here("data-raw",
           "data-raw-aceitillar_96-02",
           "aceit_site_persist_clean.csv")
aceitillar.sp <- read.csv(fi)

Create month columns

#aceitillar.sp$date.cap.orig
aceitillar.sp$yr <- lubridate::year(aceitillar.sp$date.cap.orig)
aceitillar.sp$mo <- lubridate::month(aceitillar.sp$date.cap.orig)
aceitillar.sp$mo2 <- lubridate::month(aceitillar.sp$date.cap.orig,
                                      label = T,
                                      abbr = T)
aceitillar.sp$mo2 <- gsub("Jan","J",aceitillar.sp$mo2)
aceitillar.sp$mo2 <- gsub("Nov","N",aceitillar.sp$mo2)
aceitillar.sp$mo2 <- gsub("Mar","M",aceitillar.sp$mo2)
aceitillar.sp$mo2 <- gsub("Feb","M",aceitillar.sp$mo2) #Feb is nominally Mach

summary(factor(aceitillar.sp$mo2))

Construct names of columns w/t capture/ resight info

aceit.col.1st.cap <- with(aceitillar.sp,paste(mo2,yr,sep = "."))

aceit.col.1st.cap <- gsub("20","",aceit.col.1st.cap)
aceit.col.1st.cap <- gsub("19","",aceit.col.1st.cap)


#add column to main datafram
aceitillar.sp$yr.mo.1st.cap <-aceit.col.1st.cap

Note

There are 132 records of birds 1st capture in birds 1st capture in march of 2001 in the sp dataframe no march records for 99, 00, or 02 as originally implied by data structure

which(aceitillar.sp$yr.mo.1st.cap == "M.99")
which(aceitillar.sp$yr.mo.1st.cap == "M.00")
length(which(aceitillar.sp$yr.mo.1st.cap == "M.01")) #132
which(aceitillar.sp$yr.mo.1st.cap == "M.02")

Convert alpha codes to nmber

j.cols <- grep("[NDJFM]",names(aceitillar.sp))
for(i in 1:length(j.cols)){
 aceitillar.sp[,j.cols[i]]  <- as.character(aceitillar.sp[,j.cols[i]]  )
  aceitillar.sp[,j.cols[i]] <- gsub("C","1",aceitillar.sp[,j.cols[i]])
  aceitillar.sp[,j.cols[i]] <- gsub("CS","1",aceitillar.sp[,j.cols[i]])
  aceitillar.sp[,j.cols[i]] <- gsub("CC","1",aceitillar.sp[,j.cols[i]])
  aceitillar.sp[,j.cols[i]] <- as.numeric(aceitillar.sp[,j.cols[i]])
}

summary(aceitillar.sp[,j.cols])
head(aceitillar.sp[,j.cols])

Code 1st time captured

length(col.1st.cap)

for(i in 1:length(aceit.col.1st.cap)){
 # print(i)

  #March 2001 birds - skip
  if(aceit.col.1st.cap[i] == "M.01"){next} 
  j <- which(names(aceitillar.sp) == aceit.col.1st.cap[i])

  #print(j)


  aceitillar.sp[i,j] <- -1


}

Check that it worked

length(which(aceitillar.sp$N.96 == -1))
length(which(aceitillar.sp$yr == 1996 & aceitillar.sp$mo == 11))
head(aceitillar.sp[,j.cols])

Determine site persistence

aceitillar.sp$recapYN <- NA
aceitillar.sp$num.rc.rs <- NA
for(i in 1:dim(aceitillar.sp)){

  aceitillar.sp$num.rc.rs[i] <-length(which(aceitillar.sp[i,j.cols] > 0))

}

hist(aceitillar.sp$num.rc.rs)
aceitillar.sp$recapYN <- ifelse(aceitillar.sp$num.rc.rs > 0, "sp","not.sp")

Look at ratio of caps to recaps

with(aceitillar.sp, table(spp.code, recapYN) )

summary(factor(aceitillar.sp$stat))

aceitillar.sp$stat  <- as.character(aceitillar.sp$stat )
aceitillar.sp$stat.MvsR <- ifelse(aceitillar.sp$stat == "RE","R",aceitillar.sp$stat)
i.1st.cap.96.N <- which(aceitillar.sp$N.96 == -1)
i.1st.cap.96.all <- which(aceitillar.sp$N.96 == -1 |
                          aceitillar.sp$J.97 == -1 |
                          aceitillar.sp$M.97 == -1)
length(i.1st.cap.96.N)
length(i.1st.cap.96.all)
# 
# summary(factor(aceitillar.sp[i.1st.cap.96.all,"yr.mo.1st.cap"]))
# summary(factor(aceitillar.sp[i.1st.cap.96.all,"recapYN"]))
# summary(factor(aceitillar.sp[i.1st.cap.96.all,"spp.code"]))
# summary(factor(aceitillar.sp[i.1st.cap.96.all,"spp.code"]))

m.sp.aceitillar <- bglmer(recapYN ~ 1 + stat.MvsR  +
                        (1|spp.code) +
                        (1|yr.mo.1st.cap), 
                   family = binomial,
                   data = aceitillar.sp[i.1st.cap.96.all,])
summary(m.sp.aceitillar)

m.sp.mencia.means <- bglmer(recapYN ~ -1 + stat.MvsR + 
                        (1|spp.code), 
                   family = binomial,
                   data = aceitillar.sp[i.1st.cap.96.all,])
summary(m.sp.mencia.means)


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