rm(list=ls()) #remove previous variable assignments # load libraries library(surveillance) # read in data; 4 colonies removed for analysis for quality control purposes data <- read.csv("Data.csv", header=T) data$Initial_lesion_severity <- relevel(data$Initial_lesion_severity, "Low", "Moderate", "High") # jitter infected and removed times data$tI <- jitter(data$Infected) data$tR <- jitter(data$Removed) # format data for analysis using twinSIR # tI = time (in days) until individual showed disease signs from start of monitoring (jittered) epi1 <- as.epidata(data, t0 = 0, tI.col = "tI", tR.col = "tR", id.col = "Focal_colony_number", coords.cols = c("Longitude", "Latitude"), f = list( # Euclidean distances equal to 0,1,5,10,15,20,50 meters touching = function(u) u == 0, oneM = function(u) u <= 6.324555e-06, fiveM = function(u) u <= 3.162278e-05, tenM = function(u) u <= 6.324555e-05, fifteenM = function(u) u <= 9.486833e-05, twentyM = function(u) u <= 0.0001264911, fiftyM = function(u) u <= 0.0003162277 )) # compare different models by changing covariates in model below and then compare AIC values bestModel <- twinSIR(~Size+Initial_lesion_severity+fifteenM, data = epi1) bestModel summary(bestModel)