library(MAGNAMWAR)

parsed_data <- FormatAfterOrtho('File_S6.txt',format = "groups")

pheno_data <- read.table('File_S5.csv', header = TRUE, sep = ',')
pheno_data[1,]

hist(log(pheno_data$CFU_FLY))
hist(log(pheno_data$CFU_FLY+1))

pheno_data$logCFU <- log(pheno_data$CFU_FLY+1)
mcl_matrix2 <- AnalyzeOrthoMCL(parsed_data, 
						 pheno_data, 
						 model = 'lmeR2ind', 
						 species_name = 'Treat',  
						 resp = 'logCFU', 
						 rndm1 = 'Treat', 
						 rndm2 = 'Expt',
						 princ_coord = 0.5)

WriteMCL(mcl_matrix,"multi-MAGNAMWAS/CFUS_MGWA_PC05.csv")