#####Yoshioka et al. Development of a camera trap for perching dragonflies: a new tool for freshwater environmental assessment.
#####Supplemental Code S2
#####This code was executed using R version 4.0.0 (https://www.R-project.org/).

####Validation by time-laps camera monitoring

###Fisher's exact test
#The one sided test with the alternative hypothesis that the ratio of true posives to false negatives in the field site is higher than that in the pond site. 
fisher.test(matrix(c(1,0,8,4),ncol=2,byrow=T),alternative="greater")


####Comparison with the dragonfly census

###The first analysis

##camera detection 

#Field vs Pond 
pd1<-chisq.test(c(15,50),simulate.p.value = TRUE, B = 1000000,set.seed(0))$p.value
#Pond vs Rooftop
pd2<-chisq.test(c(50,0),simulate.p.value = TRUE, B = 1000000,set.seed(0))$p.value
#Field vs Rooftop
pd3<-chisq.test(c(15,0),simulate.p.value = TRUE, B = 1000000,set.seed(0))$p.value

#P-value adjustment by Holm's method
pd<-c(pd1,pd2,pd3)
adjpd<-pd*rank(-1*pd)
#adjusted p-values for Field vs Pond, Pond vs Rooftop, and Field vs Rooftop
adjpd

##census observation

#Field vs Pond 
po1<-chisq.test(c(35,21),simulate.p.value = TRUE, B = 1000000,set.seed(0))$p.value
#Pond vs Rooftop 
po2<-chisq.test(c(21,8),simulate.p.value = TRUE, B = 1000000,set.seed(0))$p.value
#Field vs Rooftop
po3<-chisq.test(c(35,8),simulate.p.value = TRUE, B = 1000000,set.seed(0))$p.value

#P-value adjustment by Holm's method
po<-c(po1,po2,po3)
adjpo<-po*rank(-1*po)
#adjusted p-values for Field vs Pond, Pond vs Rooftop, and Field vs Rooftop
adjpo

###The second analysis

##In advance, the package glmmTMB should be installed from https://cran.r-project.org/  

##Package loading
library(glmmTMB)

##Data loading

#census observation for 10 min
obs<-c(10,10,0,9,6,0,8,10,0,0,3,0,3,4,0,1,0,0)
#Camera detection for 3 hours
detect<-c(0,0,0,0,15,0,15,35,0,0,0,0,0,0,0,0,0,0)
#Site ID "F":field, "P":pond, "R":rooftop
site<-c("F","F","F","F","F","F","P","P","P","P","P","P","R","R","R","R","R","R")
#date ID "a":21th October, "b":22th October
date<-c("a","a","a","b","b","b","a","a","a","b","b","b","a","a","a","b","b","b")
#time period ID 1:9:00-12:00,2:12:00-15:00,3:15:00-18:00
time<-c(1,2,3,1,2,3,1,2,3,1,2,3,1,2,3,1,2,3)

##GLMM

#Whether the camera detection reflect census observation
summary(glmmTMB(detect~obs+(1|site)+(1|date)+(1|time),family="nbinom1"))

#Whether the census observation reflect camera detection
summary(glmmTMB(obs~detect+(1|site)+(1|date)+(1|time),family="nbinom1"))