library(MCMCglmm) ###### Data: Female & Male Mass in cadmium (ca) diet ###### four regimes: Cad, Salt, Te (Temp), So(Spatial) Cad1_ca<-read.csv(file = "Cad1_mass_cadmium_diet.csv") Cad2_ca<-read.csv(file = "Cad2_mass_cadmium_diet.csv") Cad3_ca<-read.csv(file = "Cad3_mass_cadmium_diet.csv") Cad4_ca<-read.csv(file = "Cad4_mass_cadmium_diet.csv") Cad5_ca<-read.csv(file = "Cad5_mass_cadmium_diet.csv") Salt1_ca<-read.csv(file = "Salt1_mass_cadmium_diet.csv") Salt2_ca<-read.csv(file = "Salt2_mass_cadmium_diet.csv") Salt3_ca<-read.csv(file = "Salt3_mass_cadmium_diet.csv") Salt4_ca<-read.csv(file = "Salt4_mass_cadmium_diet.csv") Salt5_ca<-read.csv(file = "Salt5_mass_cadmium_diet.csv") Te1_ca<-read.csv(file = "Temp1_mass_cadmium_diet.csv") Te2_ca<-read.csv(file = "Temp2_mass_cadmium_diet.csv") Te3_ca<-read.csv(file = "Temp3_mass_cadmium_diet.csv") Te4_ca<-read.csv(file = "Temp4_mass_cadmium_diet.csv") Te5_ca<-read.csv(file = "Temp5_mass_cadmium_diet.csv") So1_ca<-read.csv(file = "Spatial1_mass_cadmium_diet.csv") So2_ca<-read.csv(file = "Spatial2_mass_cadmium_diet.csv") So3_ca<-read.csv(file = "Spatial3_mass_cadmium_diet.csv") So4_ca<-read.csv(file = "Spatial4_mass_cadmium_diet.csv") So5_ca<-read.csv(file = "Spatial5_mass_cadmium_diet.csv") ###### Data: Female & Male Mass in salt diet Cad1_salt<-read.csv(file = "Cad1_mass_salt_diet.csv") Cad2_salt<-read.csv(file = "Cad2_mass_salt_diet.csv") Cad3_salt<-read.csv(file = "Cad3_mass_salt_diet.csv") Cad4_salt<-read.csv(file = "Cad4_mass_salt_diet.csv") Cad5_salt<-read.csv(file = "Cad5_mass_salt_diet.csv") Salt1_salt<-read.csv(file = "Salt1_mass_salt_diet.csv") Salt2_salt<-read.csv(file = "Salt2_mass_salt_diet.csv") Salt3_salt<-read.csv(file = "Salt3_mass_salt_diet.csv") Salt4_salt<-read.csv(file = "Salt4_mass_salt_diet.csv") Salt5_salt<-read.csv(file = "Salt5_mass_salt_diet.csv") So1_salt<-read.csv(file = "Spatial1_mass_salt_diet.csv") So2_salt<-read.csv(file = "Spatial2_mass_salt_diet.csv") So3_salt<-read.csv(file = "Spatial3_mass_salt_diet.csv") So4_salt<-read.csv(file = "Spatial4_mass_salt_diet.csv") So5_salt<-read.csv(file = "Spatial5_mass_salt_diet.csv") Te1_salt<-read.csv(file = "Temp1_mass_salt_diet.csv") Te2_salt<-read.csv(file = "Temp2_mass_salt_diet.csv") Te3_salt<-read.csv(file = "Temp3_mass_salt_diet.csv") Te4_salt<-read.csv(file = "Temp4_mass_salt_diet.csv") Te5_salt<-read.csv(file = "Temp5_mass_salt_diet.csv") ####### Data: Survival in cadmium diet Cad1_ca_Survival<-read.csv(file = "Cad1_survival_cadmium_diet.csv") Cad1_ca_Survival$PresumedDead<-Cad1_ca_Survival$Egg - Cad1_ca_Survival$Adult Cad2_ca_Survival<-read.csv(file = "Cad2_survival_cadmium_diet.csv") Cad2_ca_Survival$PresumedDead<-Cad2_ca_Survival$Egg - Cad2_ca_Survival$Adult Cad3_ca_Survival<-read.csv(file = "Cad3_survival_cadmium_diet.csv") Cad3_ca_Survival$PresumedDead<-Cad3_ca_Survival$Egg - Cad3_ca_Survival$Adult Cad4_ca_Survival<-read.csv(file = "Cad4_survival_cadmium_diet.csv") Cad4_ca_Survival$PresumedDead<-Cad4_ca_Survival$Egg - Cad4_ca_Survival$Adult Cad5_ca_Survival<-read.csv(file = "Cad5_survival_cadmium_diet.csv") Cad5_ca_Survival$PresumedDead<-Cad5_ca_Survival$Egg - Cad5_ca_Survival$Adult Salt1_ca_Survival<-read.csv(file = "Salt1_survival_cadmium_diet.csv") Salt1_ca_Survival$PresumedDead<-Salt1_ca_Survival$Egg - Salt1_ca_Survival$Adult Salt2_ca_Survival<-read.csv(file = "Salt2_survival_cadmium_diet.csv") Salt2_ca_Survival$PresumedDead<-Salt2_ca_Survival$Egg - Salt2_ca_Survival$Adult Salt3_ca_Survival<-read.csv(file = "Salt3_survival_cadmium_diet.csv") Salt3_ca_Survival$PresumedDead<-Salt3_ca_Survival$Egg - Salt3_ca_Survival$Adult Salt4_ca_Survival<-read.csv(file = "Salt4_survival_cadmium_diet.csv") Salt4_ca_Survival$PresumedDead<-Salt4_ca_Survival$Egg - Salt4_ca_Survival$Adult Salt5_ca_Survival<-read.csv(file = "Salt5_survival_cadmium_diet.csv") Salt5_ca_Survival$PresumedDead<-Salt5_ca_Survival$Egg - Salt5_ca_Survival$Adult Te1_ca_Survival<-read.csv(file = "Temp1_survival_cadmium_diet.csv") Te1_ca_Survival$PresumedDead<-Te1_ca_Survival$Egg - Te1_ca_Survival$Adult Te2_ca_Survival<-read.csv(file = "Temp2_survival_cadmium_diet.csv") Te2_ca_Survival$PresumedDead<-Te2_ca_Survival$Egg - Te2_ca_Survival$Adult Te3_ca_Survival<-read.csv(file = "Temp3_survival_cadmium_diet.csv") Te3_ca_Survival$PresumedDead<-Te3_ca_Survival$Egg - Te3_ca_Survival$Adult Te4_ca_Survival<-read.csv(file = "Temp4_survival_cadmium_diet.csv") Te4_ca_Survival$PresumedDead<-Te4_ca_Survival$Egg - Te4_ca_Survival$Adult Te5_ca_Survival<-read.csv(file = "Temp5_survival_cadmium_diet.csv") Te5_ca_Survival$PresumedDead<-Te5_ca_Survival$Egg - Te5_ca_Survival$Adult So1_ca_Survival<-read.csv(file = "Spatial1_survival_cadmium_diet.csv") So1_ca_Survival$PresumedDead<-So1_ca_Survival$Egg - So1_ca_Survival$Adult So2_ca_Survival<-read.csv(file = "Spatial2_survival_cadmium_diet.csv") So2_ca_Survival$PresumedDead<-So2_ca_Survival$Egg - So2_ca_Survival$Adult So3_ca_Survival<-read.csv(file = "Spatial3_survival_cadmium_diet.csv") So3_ca_Survival$PresumedDead<-So3_ca_Survival$Egg - So3_ca_Survival$Adult So4_ca_Survival<-read.csv(file = "Spatial4_survival_cadmium_diet.csv") So4_ca_Survival$PresumedDead<-So4_ca_Survival$Egg - So4_ca_Survival$Adult So5_ca_Survival<-read.csv(file = "Spatial5_survival_cadmium_diet.csv") So5_ca_Survival$PresumedDead<-So5_ca_Survival$Egg - So5_ca_Survival$Adult ####### Data: Survival In Salt Cad1_salt_Survival<-read.csv(file = "Cad1_survival_salt_diet.csv") Cad1_salt_Survival$PresumedDead<-Cad1_salt_Survival$Egg - Cad1_salt_Survival$Adult Cad2_salt_Survival<-read.csv(file = "Cad2_survival_salt_diet.csv") Cad2_salt_Survival$PresumedDead<-Cad2_salt_Survival$Egg - Cad2_salt_Survival$Adult Cad3_salt_Survival<-read.csv(file = "Cad3_survival_salt_diet.csv") Cad3_salt_Survival$PresumedDead<-Cad3_salt_Survival$Egg - Cad3_salt_Survival$Adult Cad4_salt_Survival<-read.csv(file = "Cad4_survival_salt_diet.csv") Cad4_salt_Survival$PresumedDead<-Cad4_salt_Survival$Egg - Cad4_salt_Survival$Adult Cad5_salt_Survival<-read.csv(file = "Cad5_survival_salt_diet.csv") Cad5_salt_Survival$PresumedDead<-Cad5_salt_Survival$Egg - Cad5_salt_Survival$Adult Salt1_salt_Survival<-read.csv(file = "Salt1_survival_salt_diet.csv") Salt1_salt_Survival$PresumedDead<-Salt1_salt_Survival$Egg - Salt1_salt_Survival$Adult Salt2_salt_Survival<-read.csv(file = "Salt2_survival_salt_diet.csv") Salt2_salt_Survival$PresumedDead<-Salt2_salt_Survival$Egg - Salt2_salt_Survival$Adult Salt3_salt_Survival<-read.csv(file = "Salt3_survival_salt_diet.csv") Salt3_salt_Survival$PresumedDead<-Salt3_salt_Survival$Egg - Salt3_salt_Survival$Adult Salt4_salt_Survival<-read.csv(file = "Salt4_survival_salt_diet.csv") Salt4_salt_Survival$PresumedDead<-Salt4_salt_Survival$Egg - Salt4_salt_Survival$Adult Salt5_salt_Survival<-read.csv(file = "Salt5_survival_salt_diet.csv") Salt5_salt_Survival$PresumedDead<-Salt5_salt_Survival$Egg - Salt5_salt_Survival$Adult Te1_salt_Survival<-read.csv(file = "Temp1_survival_salt_diet.csv") Te1_salt_Survival$PresumedDead<-Te1_salt_Survival$Egg - Te1_salt_Survival$Adult Te2_salt_Survival<-read.csv(file = "Temp2_survival_salt_diet.csv") Te2_salt_Survival$PresumedDead<-Te2_salt_Survival$Egg - Te2_salt_Survival$Adult Te3_salt_Survival<-read.csv(file = "Temp3_survival_salt_diet.csv") Te3_salt_Survival$PresumedDead<-Te3_salt_Survival$Egg - Te3_salt_Survival$Adult Te4_salt_Survival<-read.csv(file = "Temp4_survival_salt_diet.csv") Te4_salt_Survival$PresumedDead<-Te4_salt_Survival$Egg - Te4_salt_Survival$Adult Te5_salt_Survival<-read.csv(file = "Temp5_survival_salt_diet.csv") Te5_salt_Survival$PresumedDead<-Te5_salt_Survival$Egg - Te5_salt_Survival$Adult So1_salt_Survival<-read.csv(file = "Spatial1_survival_salt_diet.csv") So1_salt_Survival$PresumedDead<-So1_salt_Survival$Egg - So1_salt_Survival$Adult So2_salt_Survival<-read.csv(file = "Spatial2_survival_salt_diet.csv") So2_salt_Survival$PresumedDead<-So2_salt_Survival$Egg - So2_salt_Survival$Adult So3_salt_Survival<-read.csv(file = "Spatial3_survival_salt_diet.csv") So3_salt_Survival$PresumedDead<-So3_salt_Survival$Egg - So3_salt_Survival$Adult So4_salt_Survival<-read.csv(file = "Spatial4_survival_salt_diet.csv") So4_salt_Survival$PresumedDead<-So4_salt_Survival$Egg - So4_salt_Survival$Adult So5_salt_Survival<-read.csv(file = "Spatial5_survival_salt_diet.csv") So5_salt_Survival$PresumedDead<-So5_salt_Survival$Egg - So5_salt_Survival$Adult ### Hadfield's "Course Notes" p. 25 uses ### list(V = 1e-16, n = -2) ### as uniformative prior for variance prior_UninformativeVar <- list(R = list(V = 10^-16, nu = -2), G = list(G1 = list(V = 10^-16, nu = -2))) UseThis_burnin<-10^4 UseThis_nitt<-5*10^7 UseThis_thin<-50 # ############# MCMCglmm Survival(Surv) in cadmium diet # MCMCglmm_Cad1_ca_Surv <-MCMCglmm(cbind(Adult, PresumedDead) ~ 1, random = ~Sire, family = "multinomial2", data = Cad1_ca_Survival, prior=prior_UninformativeVar, thin = UseThis_thin, nitt = UseThis_nitt, burnin = UseThis_burnin, verbose = FALSE) MCMCglmm_Cad2_ca_Surv <-MCMCglmm(cbind(Adult, PresumedDead) ~ 1, random = ~Sire, family = "multinomial2", data = Cad2_ca_Survival, prior=prior_UninformativeVar, thin = UseThis_thin, nitt = UseThis_nitt, burnin = UseThis_burnin, verbose = FALSE) MCMCglmm_Cad3_ca_Surv <-MCMCglmm(cbind(Adult, PresumedDead) ~ 1, random = ~Sire, family = "multinomial2", data = Cad3_ca_Survival, prior=prior_UninformativeVar, thin = UseThis_thin, nitt = UseThis_nitt, burnin = UseThis_burnin, verbose = FALSE) MCMCglmm_Cad4_ca_Surv <-MCMCglmm(cbind(Adult, PresumedDead) ~ 1, random = ~Sire, family = "multinomial2", data = Cad4_ca_Survival, prior=prior_UninformativeVar, thin = UseThis_thin, nitt = UseThis_nitt, burnin = UseThis_burnin, verbose = FALSE) MCMCglmm_Cad5_ca_Surv <-MCMCglmm(cbind(Adult, PresumedDead) ~ 1, random = ~Sire, family = "multinomial2", data = Cad5_ca_Survival, prior=prior_UninformativeVar, thin = UseThis_thin, nitt = UseThis_nitt, burnin = UseThis_burnin, verbose = FALSE) # MCMCglmm_Salt1_ca_Surv <-MCMCglmm(cbind(Adult, PresumedDead) ~ 1, random = ~Sire, family = "multinomial2", data = Salt1_ca_Survival, prior=prior_UninformativeVar, thin = UseThis_thin, nitt = UseThis_nitt, burnin = UseThis_burnin, verbose = FALSE) # ##adjusted data set to remove rows with missing data that bugger MCMCglmm MCMCglmm_Salt2_ca_Surv <-MCMCglmm(cbind(Adult, PresumedDead) ~ 1, random = ~Sire, family = "multinomial2", data = Salt2_ca_Survival[!is.na(Na2_Ca_Survival$Egg),], prior=prior_UninformativeVar, thin = UseThis_thin, nitt = UseThis_nitt, burnin = UseThis_burnin, verbose = FALSE) MCMCglmm_Salt3_ca_Surv <-MCMCglmm(cbind(Adult, PresumedDead) ~ 1, random = ~Sire, family = "multinomial2", data = Salt3_ca_Survival, prior=prior_UninformativeVar, thin = UseThis_thin, nitt = UseThis_nitt, burnin = UseThis_burnin, verbose = FALSE) MCMCglmm_Salt4_ca_Surv <-MCMCglmm(cbind(Adult, PresumedDead) ~ 1, random = ~Sire, family = "multinomial2", data = Salt4_ca_Survival, prior=prior_UninformativeVar, thin = UseThis_thin, nitt = UseThis_nitt, burnin = UseThis_burnin, verbose = FALSE) MCMCglmm_Salt5_ca_Surv <-MCMCglmm(cbind(Adult, PresumedDead) ~ 1, random = ~Sire, family = "multinomial2", data = Salt5_ca_Survival, prior=prior_UninformativeVar, thin = UseThis_thin, nitt = UseThis_nitt, burnin = UseThis_burnin, verbose = FALSE) # MCMCglmm_Te1_ca_Surv <-MCMCglmm(cbind(Adult, PresumedDead) ~ 1, random = ~Sire, family = "multinomial2", data = Te1_ca_Survival, prior=prior_UninformativeVar, thin = UseThis_thin, nitt = UseThis_nitt, burnin = UseThis_burnin, verbose = FALSE) # ##adjusted data set to remove rows with missing data that bugger MCMCglmm MCMCglmm_Te2_ca_Surv <-MCMCglmm(cbind(Adult, PresumedDead) ~ 1, random = ~Sire, family = "multinomial2", data = Te2_ca_Survival[!is.na(Te2_Ca_Survival$Egg),], prior=prior_UninformativeVar, thin = UseThis_thin, nitt = UseThis_nitt, burnin = UseThis_burnin, verbose = FALSE) MCMCglmm_Te3_ca_Surv <-MCMCglmm(cbind(Adult, PresumedDead) ~ 1, random = ~Sire, family = "multinomial2", data = Te3_ca_Survival, prior=prior_UninformativeVar, thin = UseThis_thin, nitt = UseThis_nitt, burnin = UseThis_burnin, verbose = FALSE) MCMCglmm_Te4_ca_Surv <-MCMCglmm(cbind(Adult, PresumedDead) ~ 1, random = ~Sire, family = "multinomial2", data = Te4_ca_Survival, prior=prior_UninformativeVar, thin = UseThis_thin, nitt = UseThis_nitt, burnin = UseThis_burnin, verbose = FALSE) MCMCglmm_Te5_ca_Surv <-MCMCglmm(cbind(Adult, PresumedDead) ~ 1, random = ~Sire, family = "multinomial2", data =Te5_ca_Survival, prior=prior_UninformativeVar, thin = UseThis_thin, nitt = UseThis_nitt, burnin = UseThis_burnin, verbose = FALSE) # MCMCglmm_So1_ca_Surv <-MCMCglmm(cbind(Adult, PresumedDead) ~ 1, random = ~Sire, family = "multinomial2", data = So1_ca_Survival, prior=prior_UninformativeVar, thin = UseThis_thin, nitt = UseThis_nitt, burnin = UseThis_burnin, verbose = FALSE) # ##adjusted data set to remove rows with missing data that bugger MCMCglmm MCMCglmm_So2_ca_Surv <-MCMCglmm(cbind(Adult, PresumedDead) ~ 1, random = ~Sire, family = "multinomial2", data = So2_ca_Survival[!is.na(So2_Ca_Survival$Egg),], prior=prior_UninformativeVar, thin = UseThis_thin, nitt = UseThis_nitt, burnin = UseThis_burnin, verbose = FALSE) MCMCglmm_So3_ca_Surv <-MCMCglmm(cbind(Adult, PresumedDead) ~ 1, random = ~Sire, family = "multinomial2", data = So3_ca_Survival, prior=prior_UninformativeVar, thin = UseThis_thin, nitt = UseThis_nitt, burnin = UseThis_burnin, verbose = FALSE) MCMCglmm_So4_ca_Surv <-MCMCglmm(cbind(Adult, PresumedDead) ~ 1, random = ~Sire, family = "multinomial2", data = So4_ca_Survival, prior=prior_UninformativeVar, thin = UseThis_thin, nitt = UseThis_nitt, burnin = UseThis_burnin, verbose = FALSE) MCMCglmm_So5_ca_Surv <-MCMCglmm(cbind(Adult, PresumedDead) ~ 1, random = ~Sire, family = "multinomial2", data = So5_ca_Survival, prior=prior_UninformativeVar, thin = UseThis_thin, nitt = UseThis_nitt, burnin = UseThis_burnin, verbose = FALSE) # # save(MCMCglmm_Cad1_ca_Surv, MCMCglmm_Cad2_ca_Surv, MCMCglmm_Cad3_ca_Surv, MCMCglmm_Cad4_ca_Surv, MCMCglmm_Cad5_ca_Surv, MCMCglmm_Salt1_ca_Surv, MCMCglmm_Salt2_ca_Surv, MCMCglmm_Salt3_ca_Surv, MCMCglmm_Salt4_ca_Surv, MCMCglmm_Salt5_ca_Surv, MCMCglmm_Te1_ca_Surv, MCMCglmm_Te2_ca_Surv, MCMCglmm_Te3_ca_Surv, MCMCglmm_Te4_ca_Surv, MCMCglmm_Te5_ca_Surv, MCMCglmm_So1_ca_Surv, MCMCglmm_So2_ca_Surv, MCMCglmm_So3_ca_Surv, MCMCglmm_So4_ca_Surv, MCMCglmm_So5_ca_Surv, file = "MCMCglmmModels_Surv_cadmium_diet.Rdata") # ########### MCMCglmm Survival (Surv) in salt diet # MCMCglmm_Cad1_salt_Surv <-MCMCglmm(cbind(Adult, PresumedDead) ~ 1, random = ~Sire, family = "multinomial2", data = Cad1_salt_Survival, prior=prior_UninformativeVar, thin = UseThis_thin, nitt = UseThis_nitt, burnin = UseThis_burnin, verbose = FALSE) MCMCglmm_Cad2_salt_Surv <-MCMCglmm(cbind(Adult, PresumedDead) ~ 1, random = ~Sire, family = "multinomial2", data = Cad2_salt_Survival, prior=prior_UninformativeVar, thin = UseThis_thin, nitt = UseThis_nitt, burnin = UseThis_burnin, verbose = FALSE) MCMCglmm_Cad3_salt_Surv <-MCMCglmm(cbind(Adult, PresumedDead) ~ 1, random = ~Sire, family = "multinomial2", data = Cad3_salt_Survival, prior=prior_UninformativeVar, thin = UseThis_thin, nitt = UseThis_nitt, burnin = UseThis_burnin, verbose = FALSE) MCMCglmm_Cad4_salt_Surv <-MCMCglmm(cbind(Adult, PresumedDead) ~ 1, random = ~Sire, family = "multinomial2", data = Cad4_salt_Survival, prior=prior_UninformativeVar, thin = UseThis_thin, nitt = UseThis_nitt, burnin = UseThis_burnin, verbose = FALSE) MCMCglmm_Cad5_salt_Surv <-MCMCglmm(cbind(Adult, PresumedDead) ~ 1, random = ~Sire, family = "multinomial2", data = Cad5_salt_Survival, prior=prior_UninformativeVar, thin = UseThis_thin, nitt = UseThis_nitt, burnin = UseThis_burnin, verbose = FALSE) # MCMCglmm_Salt1_salt_Surv <-MCMCglmm(cbind(Adult, PresumedDead) ~ 1, random = ~Sire, family = "multinomial2", data = Salt1_salt_Survival, prior=prior_UninformativeVar, thin = UseThis_thin, nitt = UseThis_nitt, burnin = UseThis_burnin, verbose = FALSE) # ##adjusted data set to remove rows with missing data that bugger MCMCglmm MCMCglmm_Salt2_salt_Surv <-MCMCglmm(cbind(Adult, PresumedDead) ~ 1, random = ~Sire, family = "multinomial2", data = Salt2_salt_Survival[!is.na(Na2_Salt_Survival$Egg),], prior=prior_UninformativeVar, thin = UseThis_thin, nitt = UseThis_nitt, burnin = UseThis_burnin, verbose = FALSE) MCMCglmm_Salt3_salt_Surv <-MCMCglmm(cbind(Adult, PresumedDead) ~ 1, random = ~Sire, family = "multinomial2", data = Salt3_salt_Survival, prior=prior_UninformativeVar, thin = UseThis_thin, nitt = UseThis_nitt, burnin = UseThis_burnin, verbose = FALSE) MCMCglmm_Salt4_salt_Surv <-MCMCglmm(cbind(Adult, PresumedDead) ~ 1, random = ~Sire, family = "multinomial2", data = Salt4_salt_Survival, prior=prior_UninformativeVar, thin = UseThis_thin, nitt = UseThis_nitt, burnin = UseThis_burnin, verbose = FALSE) MCMCglmm_Salt5_salt_Surv <-MCMCglmm(cbind(Adult, PresumedDead) ~ 1, random = ~Sire, family = "multinomial2", data = Salt5_salt_Survival, prior=prior_UninformativeVar, thin = UseThis_thin, nitt = UseThis_nitt, burnin = UseThis_burnin, verbose = FALSE) # MCMCglmm_Te1_salt_Surv <-MCMCglmm(cbind(Adult, PresumedDead) ~ 1, random = ~Sire, family = "multinomial2", data = Te1_salt_Survival, prior=prior_UninformativeVar, thin = UseThis_thin, nitt = UseThis_nitt, burnin = UseThis_burnin, verbose = FALSE) # ##adjusted data set to remove rows with missing data that bugger MCMCglmm MCMCglmm_Te2_salt_Surv <-MCMCglmm(cbind(Adult, PresumedDead) ~ 1, random = ~Sire, family = "multinomial2", data = Te2_salt_Survival[!is.na(Te2_Salt_Survival$Egg),], prior=prior_UninformativeVar, thin = UseThis_thin, nitt = UseThis_nitt, burnin = UseThis_burnin, verbose = FALSE) MCMCglmm_Te3_salt_Surv <-MCMCglmm(cbind(Adult, PresumedDead) ~ 1, random = ~Sire, family = "multinomial2", data = Te3_salt_Survival, prior=prior_UninformativeVar, thin = UseThis_thin, nitt = UseThis_nitt, burnin = UseThis_burnin, verbose = FALSE) MCMCglmm_Te4_salt_Surv <-MCMCglmm(cbind(Adult, PresumedDead) ~ 1, random = ~Sire, family = "multinomial2", data = Te4_salt_Survival, prior=prior_UninformativeVar, thin = UseThis_thin, nitt = UseThis_nitt, burnin = UseThis_burnin, verbose = FALSE) MCMCglmm_Te5_salt_Surv <-MCMCglmm(cbind(Adult, PresumedDead) ~ 1, random = ~Sire, family = "multinomial2", data =Te5_salt_Survival, prior=prior_UninformativeVar, thin = UseThis_thin, nitt = UseThis_nitt, burnin = UseThis_burnin, verbose = FALSE) # MCMCglmm_So1_salt_Surv <-MCMCglmm(cbind(Adult, PresumedDead) ~ 1, random = ~Sire, family = "multinomial2", data = So1_salt_Survival, prior=prior_UninformativeVar, thin = UseThis_thin, nitt = UseThis_nitt, burnin = UseThis_burnin, verbose = FALSE) # ##adjusted data set to remove rows with missing data that bugger MCMCglmm MCMCglmm_So2_salt_Surv <-MCMCglmm(cbind(Adult, PresumedDead) ~ 1, random = ~Sire, family = "multinomial2", data = So2_salt_Survival[!is.na(So2_Salt_Survival$Egg),], prior=prior_UninformativeVar, thin = UseThis_thin, nitt = UseThis_nitt, burnin = UseThis_burnin, verbose = FALSE) MCMCglmm_So3_salt_Surv <-MCMCglmm(cbind(Adult, PresumedDead) ~ 1, random = ~Sire, family = "multinomial2", data = So3_salt_Survival, prior=prior_UninformativeVar, thin = UseThis_thin, nitt = UseThis_nitt, burnin = UseThis_burnin, verbose = FALSE) MCMCglmm_So4_salt_Surv <-MCMCglmm(cbind(Adult, PresumedDead) ~ 1, random = ~Sire, family = "multinomial2", data = So4_salt_Survival, prior=prior_UninformativeVar, thin = UseThis_thin, nitt = UseThis_nitt, burnin = UseThis_burnin, verbose = FALSE) MCMCglmm_So5_salt_Surv <-MCMCglmm(cbind(Adult, PresumedDead) ~ 1, random = ~Sire, family = "multinomial2", data = So5_salt_Survival, prior=prior_UninformativeVar, thin = UseThis_thin, nitt = UseThis_nitt, burnin = UseThis_burnin, verbose = FALSE) # save(MCMCglmm_Cad1_salt_Surv, MCMCglmm_Cad2_salt_Surv, MCMCglmm_Cad3_salt_Surv, MCMCglmm_Cad4_salt_Surv, MCMCglmm_Cad5_salt_Surv, MCMCglmm_Salt1_salt_Surv, MCMCglmm_Salt2_salt_Surv, MCMCglmm_Salt3_salt_Surv, MCMCglmm_Salt4_salt_Surv, MCMCglmm_Salt5_salt_Surv, MCMCglmm_Te1_salt_Surv, MCMCglmm_Te2_salt_Surv, MCMCglmm_Te3_salt_Surv, MCMCglmm_Te4_salt_Surv, MCMCglmm_Te5_salt_Surv, MCMCglmm_So1_salt_Surv, MCMCglmm_So2_salt_Surv, MCMCglmm_So3_salt_Surv, MCMCglmm_So4_salt_Surv, MCMCglmm_So5_salt_Surv, file = "MCMCglmmModels_Surv_salt_diet.Rdata") # # ##### # ######### MCMCglmm Female Mass (F) in salt diet # MCMCglmm_Cad1_salt_F <-MCMCglmm(Female_Mass ~ 1, random = ~Sire, family = "gaussian", data = Cad1_salt, prior=prior_UninformativeVar, thin = UseThis_thin, nitt = UseThis_nitt, burnin = UseThis_burnin, verbose = FALSE) MCMCglmm_Cad2_salt_F <-MCMCglmm(Female_Mass ~ 1, random = ~Sire, family = "gaussian", data = Cad2_salt, prior=prior_UninformativeVar, thin = UseThis_thin, nitt = UseThis_nitt, burnin = UseThis_burnin, verbose = FALSE) MCMCglmm_Cad3_salt_F <-MCMCglmm(Female_Mass ~ 1, random = ~Sire, family = "gaussian", data = Cad3_salt, prior=prior_UninformativeVar, thin = UseThis_thin, nitt = UseThis_nitt, burnin = UseThis_burnin, verbose = FALSE) MCMCglmm_Cad4_salt_F <-MCMCglmm(Female_Mass ~ 1, random = ~Sire, family = "gaussian", data = Cad4_salt, prior=prior_UninformativeVar, thin = UseThis_thin, nitt = UseThis_nitt, burnin = UseThis_burnin, verbose = FALSE) MCMCglmm_Cad5_salt_F <-MCMCglmm(Female_Mass ~ 1, random = ~Sire, family = "gaussian", data = Cad5_salt, prior=prior_UninformativeVar, thin = UseThis_thin, nitt = UseThis_nitt, burnin = UseThis_burnin, verbose = FALSE) # # MCMCglmm_Salt1_salt_F <-MCMCglmm(Female_Mass ~ 1, random = ~Sire, family = "gaussian", data = Salt1_salt, prior=prior_UninformativeVar, thin = UseThis_thin, nitt = UseThis_nitt, burnin = UseThis_burnin, verbose = FALSE) MCMCglmm_Salt2_salt_F <-MCMCglmm(Female_Mass ~ 1, random = ~Sire, family = "gaussian", data = Salt2_salt, prior=prior_UninformativeVar, thin = UseThis_thin, nitt = UseThis_nitt, burnin = UseThis_burnin, verbose = FALSE) MCMCglmm_Salt3_salt_F <-MCMCglmm(Female_Mass ~ 1, random = ~Sire, family = "gaussian", data = Salt3_salt, prior=prior_UninformativeVar, thin = UseThis_thin, nitt = UseThis_nitt, burnin = UseThis_burnin, verbose = FALSE) MCMCglmm_Salt4_salt_F <-MCMCglmm(Female_Mass ~ 1, random = ~Sire, family = "gaussian", data = Salt4_salt, prior=prior_UninformativeVar, thin = UseThis_thin, nitt = UseThis_nitt, burnin = UseThis_burnin, verbose = FALSE) MCMCglmm_Salt5_salt_F <-MCMCglmm(Female_Mass ~ 1, random = ~Sire, family = "gaussian", data = Salt5_salt, prior=prior_UninformativeVar, thin = UseThis_thin, nitt = UseThis_nitt, burnin = UseThis_burnin, verbose = FALSE) # # MCMCglmm_Te1_salt_F <-MCMCglmm(Female_Mass ~ 1, random = ~Sire, family = "gaussian", data = Te1_salt, prior=prior_UninformativeVar, thin = UseThis_thin, nitt = UseThis_nitt, burnin = UseThis_burnin, verbose = FALSE) MCMCglmm_Te2_salt_F <-MCMCglmm(Female_Mass ~ 1, random = ~Sire, family = "gaussian", data = Te2_salt, prior=prior_UninformativeVar, thin = UseThis_thin, nitt = UseThis_nitt, burnin = UseThis_burnin, verbose = FALSE) MCMCglmm_Te3_salt_F <-MCMCglmm(Female_Mass ~ 1, random = ~Sire, family = "gaussian", data = Te3_salt, prior=prior_UninformativeVar, thin = UseThis_thin, nitt = UseThis_nitt, burnin = UseThis_burnin, verbose = FALSE) MCMCglmm_Te4_salt_F <-MCMCglmm(Female_Mass ~ 1, random = ~Sire, family = "gaussian", data = Te4_salt, prior=prior_UninformativeVar, thin = UseThis_thin, nitt = UseThis_nitt, burnin = UseThis_burnin, verbose = FALSE) MCMCglmm_Te5_salt_F <-MCMCglmm(Female_Mass ~ 1, random = ~Sire, family = "gaussian", data =Te5_salt, prior=prior_UninformativeVar, thin = UseThis_thin, nitt = UseThis_nitt, burnin = UseThis_burnin, verbose = FALSE) # # MCMCglmm_So1_salt_F <-MCMCglmm(Female_Mass ~ 1, random = ~Sire, family = "gaussian", data = So1_salt, prior=prior_UninformativeVar, thin = UseThis_thin, nitt = UseThis_nitt, burnin = UseThis_burnin, verbose = FALSE) MCMCglmm_So2_salt_F <-MCMCglmm(Female_Mass ~ 1, random = ~Sire, family = "gaussian", data = So2_salt, prior=prior_UninformativeVar, thin = UseThis_thin, nitt = UseThis_nitt, burnin = UseThis_burnin, verbose = FALSE) MCMCglmm_So3_salt_F <-MCMCglmm(Female_Mass ~ 1, random = ~Sire, family = "gaussian", data = So3_salt, prior=prior_UninformativeVar, thin = UseThis_thin, nitt = UseThis_nitt, burnin = UseThis_burnin, verbose = FALSE) MCMCglmm_So4_salt_F <-MCMCglmm(Female_Mass ~ 1, random = ~Sire, family = "gaussian", data = So4_salt, prior=prior_UninformativeVar, thin = UseThis_thin, nitt = UseThis_nitt, burnin = UseThis_burnin, verbose = FALSE) MCMCglmm_So5_salt_F <-MCMCglmm(Female_Mass ~ 1, random = ~Sire, family = "gaussian", data = So5_salt, prior=prior_UninformativeVar, thin = UseThis_thin, nitt = UseThis_nitt, burnin = UseThis_burnin, verbose = FALSE) # # save(MCMCglmm_Cad1_salt_F, MCMCglmm_Cad2_salt_F, MCMCglmm_Cad3_salt_F, MCMCglmm_Cad4_salt_F, MCMCglmm_Cad5_salt_F, MCMCglmm_Salt1_salt_F, MCMCglmm_Salt2_salt_F, MCMCglmm_Salt3_salt_F, MCMCglmm_salt4_Salt_F, MCMCglmm_salt5_Salt_F, MCMCglmm_Te1_salt_F, MCMCglmm_Te2_salt_F, MCMCglmm_Te3_salt_F, MCMCglmm_Te4_salt_F, MCMCglmm_Te5_salt_F, MCMCglmm_So1_salt_F, MCMCglmm_So2_salt_F, MCMCglmm_So3_salt_F, MCMCglmm_So4_salt_F, MCMCglmm_So5_salt_F, file = "MCMCglmmModels_F_salt_diet.Rdata") # ####### MCMCglmm Male Mass (M) in cadmium diet (ca) MCMCglmm_Cad1_ca_M <-MCMCglmm(Male_Mass ~ 1, random = ~Sire, family = "gaussian", data = Cad1_ca, prior=prior_UninformativeVar, thin = UseThis_thin, nitt = UseThis_nitt, burnin = UseThis_burnin, verbose = FALSE) MCMCglmm_Cad2_ca_M <-MCMCglmm(Male_Mass ~ 1, random = ~Sire, family = "gaussian", data = Cad2_ca, prior=prior_UninformativeVar, thin = UseThis_thin, nitt = UseThis_nitt, burnin = UseThis_burnin, verbose = FALSE) MCMCglmm_Cad3_ca_M <-MCMCglmm(Male_Mass ~ 1, random = ~Sire, family = "gaussian", data = Cad3_ca, prior=prior_UninformativeVar, thin = UseThis_thin, nitt = UseThis_nitt, burnin = UseThis_burnin, verbose = FALSE) MCMCglmm_Cad4_ca_M <-MCMCglmm(Male_Mass ~ 1, random = ~Sire, family = "gaussian", data = Cad4_ca, prior=prior_UninformativeVar, thin = UseThis_thin, nitt = UseThis_nitt, burnin = UseThis_burnin, verbose = FALSE) MCMCglmm_Cad5_ca_M <-MCMCglmm(Male_Mass ~ 1, random = ~Sire, family = "gaussian", data = Cad5_ca, prior=prior_UninformativeVar, thin = UseThis_thin, nitt = UseThis_nitt, burnin = UseThis_burnin, verbose = FALSE) MCMCglmm_Salt1_ca_M <-MCMCglmm(Male_Mass ~ 1, random = ~Sire, family = "gaussian", data = Salt1_ca, prior=prior_UninformativeVar, thin = UseThis_thin, nitt = UseThis_nitt, burnin = UseThis_burnin, verbose = FALSE) MCMCglmm_Salt2_ca_M <-MCMCglmm(Male_Mass ~ 1, random = ~Sire, family = "gaussian", data = Salt2_ca, prior=prior_UninformativeVar, thin = UseThis_thin, nitt = UseThis_nitt, burnin = UseThis_burnin, verbose = FALSE) MCMCglmm_Salt3_ca_M <-MCMCglmm(Male_Mass ~ 1, random = ~Sire, family = "gaussian", data = Salt3_ca, prior=prior_UninformativeVar, thin = UseThis_thin, nitt = UseThis_nitt, burnin = UseThis_burnin, verbose = FALSE) MCMCglmm_Salt4_ca_M <-MCMCglmm(Male_Mass ~ 1, random = ~Sire, family = "gaussian", data = Salt4_ca, prior=prior_UninformativeVar, thin = UseThis_thin, nitt = UseThis_nitt, burnin = UseThis_burnin, verbose = FALSE) MCMCglmm_Salt5_ca_M <-MCMCglmm(Male_Mass ~ 1, random = ~Sire, family = "gaussian", data = Salt5_ca, prior=prior_UninformativeVar, thin = UseThis_thin, nitt = UseThis_nitt, burnin = UseThis_burnin, verbose = FALSE) MCMCglmm_Te1_ca_M <-MCMCglmm(Male_Mass ~ 1, random = ~Sire, family = "gaussian", data = Te1_ca, prior=prior_UninformativeVar, thin = UseThis_thin, nitt = UseThis_nitt, burnin = UseThis_burnin, verbose = FALSE) MCMCglmm_Te2_ca_M <-MCMCglmm(Male_Mass ~ 1, random = ~Sire, family = "gaussian", data = Te2_ca, prior=prior_UninformativeVar, thin = UseThis_thin, nitt = UseThis_nitt, burnin = UseThis_burnin, verbose = FALSE) MCMCglmm_Te3_ca_M <-MCMCglmm(Male_Mass ~ 1, random = ~Sire, family = "gaussian", data = Te3_ca, prior=prior_UninformativeVar, thin = UseThis_thin, nitt = UseThis_nitt, burnin = UseThis_burnin, verbose = FALSE) MCMCglmm_Te4_ca_M <-MCMCglmm(Male_Mass ~ 1, random = ~Sire, family = "gaussian", data = Te4_ca, prior=prior_UninformativeVar, thin = UseThis_thin, nitt = UseThis_nitt, burnin = UseThis_burnin, verbose = FALSE) MCMCglmm_Te5_ca_M <-MCMCglmm(Male_Mass ~ 1, random = ~Sire, family = "gaussian", data =Te5_ca, prior=prior_UninformativeVar, thin = UseThis_thin, nitt = UseThis_nitt, burnin = UseThis_burnin, verbose = FALSE) MCMCglmm_So1_ca_M <-MCMCglmm(Male_Mass ~ 1, random = ~Sire, family = "gaussian", data = So1_ca, prior=prior_UninformativeVar, thin = UseThis_thin, nitt = UseThis_nitt, burnin = UseThis_burnin, verbose = FALSE) MCMCglmm_So2_ca_M <-MCMCglmm(Male_Mass ~ 1, random = ~Sire, family = "gaussian", data = So2_ca, prior=prior_UninformativeVar, thin = UseThis_thin, nitt = UseThis_nitt, burnin = UseThis_burnin, verbose = FALSE) MCMCglmm_So3_ca_M <-MCMCglmm(Male_Mass ~ 1, random = ~Sire, family = "gaussian", data = So3_ca, prior=prior_UninformativeVar, thin = UseThis_thin, nitt = UseThis_nitt, burnin = UseThis_burnin, verbose = FALSE) MCMCglmm_So4_ca_M <-MCMCglmm(Male_Mass ~ 1, random = ~Sire, family = "gaussian", data = So4_ca, prior=prior_UninformativeVar, thin = UseThis_thin, nitt = UseThis_nitt, burnin = UseThis_burnin, verbose = FALSE) MCMCglmm_So5_ca_M <-MCMCglmm(Male_Mass ~ 1, random = ~Sire, family = "gaussian", data = So5_ca, prior=prior_UninformativeVar, thin = UseThis_thin, nitt = UseThis_nitt, burnin = UseThis_burnin, verbose = FALSE) save(MCMCglmm_Cad1_ca_M, MCMCglmm_Cad2_ca_M, MCMCglmm_Cad3_ca_M, MCMCglmm_Cad4_ca_M, MCMCglmm_Cad5_ca_M, MCMCglmm_Salt1_ca_M, MCMCglmm_Salt2_ca_M, MCMCglmm_Salt3_ca_M, MCMCglmm_Salt4_ca_M, MCMCglmm_Salt5_ca_M, MCMCglmm_Te1_ca_M, MCMCglmm_Te2_ca_M, MCMCglmm_Te3_ca_M, MCMCglmm_Te4_ca_M, MCMCglmm_Te5_ca_M, MCMCglmm_So1_ca_M, MCMCglmm_So2_ca_M, MCMCglmm_So3_ca_M, MCMCglmm_So4_ca_M, MCMCglmm_So5_ca_M,file = "MCMCglmmModels_M_cadmium_diet.Rdata")