setwd("C:/Users/llf44/OneDrive/Documents/ACADEMIA/Graduate School/R Files/Cornell/bee_pathogens/2015-FINAL/science/verified") pathogens<-read.csv("pathogens_2015R.csv") flower<-read.csv("flowers.csv") library(epiR) library(car) #for how many bee species do we have at least one pathogen amplifying? x<-as.data.frame.matrix(table(pathogens$Gen.sp,pathogens$pathogen)) names(x)<-c("absent","present") x$species<-row.names(x) x<-droplevels(subset(x, !species %in% c("Unknown.unknown","Melissodes.Melissodes.sp","Megachile.Megachile.sp","Lasioglossum.Lasioglossum.sp","Hylaeus.Hylaeus.sp","Hoplitis.Hoplitis.sp","Ceratina.Ceratina.sp","Andrena.Andrena.sp"))) y<-droplevels(subset(x, !present==0)) ((30)/46)*100 # percent species that have at least one pathogen #for how many flower species do we have at least one pathogen amplifying? flower$total<-flower$C.b+flower$NosC+flower$Neog flower$pathogen <- pmin(flower$total, 1) table(flower$flower.sp,flower$pathogen) #9/12 = 75% # Is the "host control" primer, which was developed for Apidae, biased by family? table(pathogens$family,pathogens$ap) contable <- array(c(0,33,2,15,2,4,312,28,165,12), dim=c(5,2)) # no differences across families chisq.test(contable) ## In Bees #prevalence of Neogregarines table(pathogens$neo) epi.prev(pos=34, tested=575, se=.95, sp=.95, method = "blaker", units = 100, conf.level = 0.95)$tp #prevalence of N.ceranae table(pathogens$N.c) epi.prev(pos=90, tested=575, se=.95, sp=.95, method = "blaker", units = 100, conf.level = 0.95)$tp #prevalence of Trypanosomes table(pathogens$tryp) epi.prev(pos=154, tested=575, se=.95, sp=.95, method = "blaker", units = 100, conf.level = 0.95)$tp #prevalence of N.bombi table(pathogens$N.b) epi.prev(pos=5, tested=575, se=.95, sp=.95, method = "blaker", units = 100, conf.level = 0.95)$tp #prevalence of any pathogen table(pathogens$pathogen) epi.prev(pos=233, tested=575, se=.95, sp=.95, method = "blaker", units = 100, conf.level = 0.95)$tp ##In Flowers #prevalence of Neogregarines table(flower$Neog) epi.prev(pos=1, tested=81, se=.95, sp=.95, method = "blaker", units = 100, conf.level = 0.95)$tp #prevalence of N.ceranae table(flower$NosC) epi.prev(pos=15, tested=81, se=.95, sp=.95, method = "blaker", units = 100, conf.level = 0.95)$tp #prevalence of Trypanosomes table(flower$C.b) epi.prev(pos=14, tested=81, se=.95, sp=.95, method = "blaker", units = 100, conf.level = 0.95)$tp #prevalence of any pathogen table(flower$pathogen) epi.prev(pos=27, tested=81, se=.95, sp=.95, method = "blaker", units = 100, conf.level = 0.95)$tp #prevalence of N.bombi: 0