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1.dataclean-lokern.R
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### GKR Preliminary Data Analysis
library(ggplot2)
library(plyr)
library(tidyr)
#######
# 1. Load and clean data
#######
### Load all Lokern data
lokern <- read.csv("../Data/Lokern/lokern-trap-data.csv")
#######
# 2. Visualize prelim results (total captured at each site, movement, body weight,
# repro success)
#######
# Plot unique inidividual results by species from 2015
unique.lokern.15 <- subset(lokern, type == "N")
n.plot <- ggplot(unique.lokern, aes(factor(plot)))
n.plot + geom_bar() + facet_wrap(~species)
# Plot unique inidividual results by species from 2016
unique.lokern <- subset(lokern, type == "N")
n.16.plot <- ggplot(unique.lokern, aes(factor(plot)))
n.16.plot + geom_bar() + facet_wrap(~species)
sum.15 <- as.data.frame.matrix(table(unique.lokern$plot, unique.lokern$species))
sum.15$plot <- row.names(sum.15)
sum.15$year <- rep(2015, nrow(sum.15))
sum.16 <- as.data.frame.matrix(table(unique.lokern$plot, unique.lokern$species))
sum.16$plot <- row.names(sum.16)
sum.16$year <- rep(2016, nrow(sum.16))
ses.recaps <- subset(lokern, type == "S")
## See if anyone moved
gkr.2015 <- subset(lokern, species == "DIIN")
gkr.2016 <- subset(lokern, species == "DIIN")
for(i in unique(ses.recaps$left.ear)){
cur.gkr <- subset(lokern, left.ear == i)
cur.gkr.16 <- subset(lokern, left.ear == i)
print(paste("Left Ear:", i, "2015 Plots:", unique(cur.gkr$plot), "2016 Plots:",
unique(cur.gkr.16$plot)))
}
#######
# 3. Create unique capture histories for export
#######
# 2015
all.cap.hist.15 <- NULL
for(i in unique(gkr.2015$left.ear)){
cur.gkr <- subset(gkr.2015, left.ear == i)
cur.trap.hist <- NULL
for(j in 1:5){
if(j %in% unique(cur.gkr$night)){
cur.trap.hist <- paste(cur.trap.hist, "1", sep="")
} else {
cur.trap.hist <- paste(cur.trap.hist, "0", sep="")
}
}
cur.rat <- data.frame(unique(cur.gkr$plot), i, cur.trap.hist)
all.cap.hist.15 <- rbind(all.cap.hist.15, cur.rat)
}
colnames(all.cap.hist.15) <- c("plot", "indiv", "hist")
# Generate table of counts of different recapture histories for 2015
#sum.cap.hist.15 <- count(all.cap.hist.15$plot, all.cap.hist.15$hist)
temp <- as.data.frame.matrix(table(all.cap.hist.15$hist, all.cap.hist.15$plot))
temp$cap.hist <- row.names(temp)
#sum.hist.15 <- gather(temp, cap.hist, site, IVC:P89E)
#colnames(sum.hist.15) <- c("cap.hist", "site", "num")
#spread.hist <- spread(sum.hist.15, site, num)
mark.inp <- data.frame(temp$cap.hist, temp[,1:6])
# alternate attempts at creating a summary table
#sum.hist.16 <- gather(temp, cap.hist, site, IVC:P89E)
#colnames(sum.hist.16) <- c("cap.hist", "site", "num")
# Save output
mark.out.15 <- apply(mark.inp, 1, paste, collapse=" ")
mark.out.15 <- paste(mark.out.15, ";", sep="")
fileconn <- file("../Analysis/cnpa15.inp")
writeLines(mark.out.15, fileconn)
close(fileconn)
# 2016
all.cap.hist.16 <- NULL
for(i in unique(gkr.2016$left.ear)){
cur.gkr <- subset(gkr.2016, left.ear == i)
cur.trap.hist <- NULL
for(j in 1:5){
if(j %in% unique(cur.gkr$night)){
cur.trap.hist <- paste(cur.trap.hist, "1", sep="")
} else {
cur.trap.hist <- paste(cur.trap.hist, "0", sep="")
}
}
cur.rat <- data.frame(unique(cur.gkr$plot), i, cur.trap.hist)
all.cap.hist.16 <- rbind(all.cap.hist.16, cur.rat)
}
colnames(all.cap.hist.16) <- c("plot", "indiv", "hist")
# Generate table of counts of different recapture histories for 2016
temp <- as.data.frame.matrix(table(all.cap.hist.16$hist, all.cap.hist.16$plot))
temp$cap.hist <- row.names(temp)
mark.inp <- data.frame(temp$cap.hist, temp[,1:6])
# alternate attempts at creating a summary table
#sum.hist.16 <- gather(temp, cap.hist, site, IVC:P89E)
#colnames(sum.hist.16) <- c("cap.hist", "site", "num")
# Save output
mark.out.16 <- apply(mark.inp, 1, paste, collapse=" ")
mark.out.16 <- paste(mark.out.16, ";", sep="")
fileconn <- file("../Analysis/cnpa16.inp")
writeLines(mark.out.16, fileconn)
close(fileconn)
## Create Robust Design Capture History
gkr.16.temp <- data.frame(gkr.2016$date, gkr.2016$night, gkr.2016$plot,
gkr.2016$trap, gkr.2016$left.ear)
gkr.16.temp$ses <- rep(2, nrow(gkr.16.temp))
colnames(gkr.16.temp) <- c("date", "night", "plot", "trap", "left.ear", "session")
gkr.15.temp <- data.frame(gkr.2015$date, gkr.2015$night, gkr.2015$plot,
gkr.2015$trap, gkr.2015$left.ear)
gkr.15.temp$ses <- rep(1, nrow(gkr.15.temp))
colnames(gkr.15.temp) <- c("date", "night", "plot", "trap", "left.ear", "session")
combined.data <- rbind(gkr.15.temp, gkr.16.temp)
comb.cap.hist <- NULL
for(i in unique(combined.data$left.ear)){
cur.gkr <- subset(combined.data, left.ear == i)
cur.trap.hist <- NULL
cur.ses <- subset(cur.gkr, session==1)
for(j in 1:5){
if(j %in% unique(cur.ses$night)){
cur.trap.hist <- paste(cur.trap.hist, "1", sep="")
} else {
cur.trap.hist <- paste(cur.trap.hist, "0", sep="")
}
}
cur.ses <- subset(cur.gkr, session==2)
for(j in 1:5){
if(j %in% unique(cur.ses$night)){
cur.trap.hist <- paste(cur.trap.hist, "1", sep="")
} else {
cur.trap.hist <- paste(cur.trap.hist, "0", sep="")
}
}
cur.rat <- data.frame(unique(cur.gkr$plot), i, cur.trap.hist)
comb.cap.hist <- rbind(comb.cap.hist, cur.rat)
}
colnames(comb.cap.hist) <- c("plot", "indiv", "hist")
temp <- as.data.frame.matrix(table(comb.cap.hist$hist, comb.cap.hist$plot))
temp$cap.hist <- row.names(temp)
mark.inp <- data.frame(temp$cap.hist, temp[,1:6])
# Save output
mark.out.comb <- apply(mark.inp, 1, paste, collapse=" ")
mark.out.comb <- paste(mark.out.comb, ";", sep="")
fileconn <- file("../Analysis/cnpa-robust.inp")
writeLines(mark.out.comb, fileconn)
close(fileconn)