#TRUE PREVALENCE library("epiR") #Apis all viruses epi.prev(pos = 114, tested = 237, method = "blaker", conf.level = 0.95, sp = 1 ,se = 0.95) #Bombus all viruses epi.prev(pos = 97, tested = 453, method = "blaker", conf.level = 0.95, sp = 1 ,se = 0.95) #Apis single viruses #bqcv epi.prev(pos = 33, tested = 237, method = "blaker", conf.level = 0.95, sp = 1 ,se = 0.95) #dwv epi.prev(pos = 82, tested = 237, method = "blaker", conf.level = 0.95, sp = 1 ,se = 0.95) #abpv epi.prev(pos = 11, tested = 237, method = "blaker", conf.level = 0.95, sp = 1 ,se = 0.95) #sbpv epi.prev(pos = 5, tested = 237, method = "blaker", conf.level = 0.95, sp = 1 ,se = 0.95) #sbv epi.prev(pos = 4, tested = 237, method = "blaker", conf.level = 0.95, sp = 1 ,se = 0.95) #Bombus single viruses #bqcv epi.prev(pos = 25, tested = 453, method = "blaker", conf.level = 0.95, sp = 1 ,se = 0.95) #dwv epi.prev(pos = 14, tested = 453, method = "blaker", conf.level = 0.95, sp = 1 ,se = 0.95) #abpv epi.prev(pos = 48, tested = 453, method = "blaker", conf.level = 0.95, sp = 1 ,se = 0.95) #sbpv epi.prev(pos = 21, tested = 453, method = "blaker", conf.level = 0.95, sp = 1 ,se = 0.95) #sbv epi.prev(pos = 4, tested = 453, method = "blaker", conf.level = 0.95, sp = 1 ,se = 0.95) #B. hortorum #bqcv epi.prev(pos = 3, tested = 30, method = "blaker", conf.level = 0.95, sp = 1 ,se = 0.95) #dwv epi.prev(pos = 0, tested = 30, method = "blaker", conf.level = 0.95, sp = 1 ,se = 0.95) #abpv epi.prev(pos = 1, tested = 30, method = "blaker", conf.level = 0.95, sp = 1 ,se = 0.95) #sbpv epi.prev(pos = 10, tested = 30, method = "blaker", conf.level = 0.95, sp = 1 ,se = 0.95) #sbv epi.prev(pos = 0, tested = 30, method = "blaker", conf.level = 0.95, sp = 1 ,se = 0.95) #B. lapidarius #bqcv epi.prev(pos = 11, tested = 169, method = "blaker", conf.level = 0.95, sp = 1 ,se = 0.95) #dwv epi.prev(pos = 4, tested = 169, method = "blaker", conf.level = 0.95, sp = 1 ,se = 0.95) #abpv epi.prev(pos = 34, tested = 169, method = "blaker", conf.level = 0.95, sp = 1 ,se = 0.95) #sbpv epi.prev(pos = 1, tested = 169, method = "blaker", conf.level = 0.95, sp = 1 ,se = 0.95) #sbv epi.prev(pos = 0, tested = 169, method = "blaker", conf.level = 0.95, sp = 1 ,se = 0.95) #B. lucorum #bqcv epi.prev(pos = 2, tested = 89, method = "blaker", conf.level = 0.95, sp = 1 ,se = 0.95) #dwv epi.prev(pos = 3, tested = 89, method = "blaker", conf.level = 0.95, sp = 1 ,se = 0.95) #abpv epi.prev(pos = 2, tested = 89, method = "blaker", conf.level = 0.95, sp = 1 ,se = 0.95) #sbpv epi.prev(pos = 3, tested = 89, method = "blaker", conf.level = 0.95, sp = 1 ,se = 0.95) #sbv epi.prev(pos = 0, tested = 89, method = "blaker", conf.level = 0.95, sp = 1 ,se = 0.95) #B. pascuorum #bqcv epi.prev(pos = 3, tested = 55, method = "blaker", conf.level = 0.95, sp = 1 ,se = 0.95) #dwv epi.prev(pos = 0, tested = 55, method = "blaker", conf.level = 0.95, sp = 1 ,se = 0.95) #abpv epi.prev(pos = 1, tested = 55, method = "blaker", conf.level = 0.95, sp = 1 ,se = 0.95) #sbpv epi.prev(pos = 1, tested = 55, method = "blaker", conf.level = 0.95, sp = 1 ,se = 0.95) #sbv epi.prev(pos = 0, tested = 55, method = "blaker", conf.level = 0.95, sp = 1 ,se = 0.95) #B. terrestris #bqcv epi.prev(pos = 5, tested = 92, method = "blaker", conf.level = 0.95, sp = 1 ,se = 0.95) #dwv epi.prev(pos = 6, tested = 92, method = "blaker", conf.level = 0.95, sp = 1 ,se = 0.95) #abpv epi.prev(pos = 9, tested = 92, method = "blaker", conf.level = 0.95, sp = 1 ,se = 0.95) #sbpv epi.prev(pos = 6, tested = 92, method = "blaker", conf.level = 0.95, sp = 1 ,se = 0.95) #sbv epi.prev(pos = 3, tested = 92, method = "blaker", conf.level = 0.95, sp = 1 ,se = 0.95) #TEST OF PROPORTIONS: #Apis vs Bombus ALL infected <- c(114, 98) total <- c(237, 453) prop.test(infected,total, alternative=c("two.sided"), conf.level = 0.95) #Apis vs Bombus bqcv infected <- c(33, 25) total <- c(237, 453) prop.test(infected,non_infected, alternative=c("two.sided"), conf.level = 0.95) #Apis vs Bombus dwv infected <- c(82, 14) total <- c(237, 453) prop.test(infected,non_infected, alternative=c("two.sided"), conf.level = 0.95) #Apis vs Bombus abpv infected <- c(11, 48) total <- c(237, 453) prop.test(infected,non_infected, alternative=c("two.sided"), conf.level = 0.95) #Apis vs Bombus sbpv infected <- c(5, 21) total <- c(237, 453) prop.test(infected,non_infected, alternative=c("two.sided"), conf.level = 0.95) #Apis vs Bombus sbv infected <- c(4, 4) total <- c(237, 453) prop.test(infected,non_infected, alternative=c("two.sided"), conf.level = 0.95) #KOLMOGOROV-SMIRNOV TESTS bb_bqcv <- c(0, 5, 3, 1, 0, 0, 0, 0) hb_bqcv <- c(1, 7, 5, 2, 1, 1, 0, 0) ks.test(bb_bqcv, hb_bqcv) bb_dwv <- c(2, 1, 5, 0, 0, 0, 0, 0) hb_dwv <- c(1, 5, 3, 4, 1, 1, 15, 15) ks.test(bb_dwv, hb_dwv) #OB vs EXP CO-INFECTION CHI SQ #Apis M <- as.table(rbind(c(123, 95, 17, 2), c(123, 98, 15, 1))) dimnames(M) <- list(group = c("O","E"), infection = c("0","1","2","3")) (Xsq <- chisq.test(M)) #Bombus M <- as.table(rbind(c(355, 83, 13, 1), c(358, 90, 5, 0))) dimnames(M) <- list(group = c("O","E"), infection = c("0","1","2","3")) (Xsq <- chisq.test(M))