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Input_90-92(pre-epidem).R
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# ------------ INPUT FILE for the PRE_EPIDEMIC period 1990-1992------------
# Equivalent to Table 1 in the main text
# Demographic states were abbreviated as cubs (C), subadults (SA), breeders (B) or non-breeders (NB),
# social states as high status (H) or low status (L) and infection states as susceptible (S), infected (I) or recovered (R).
###--------- SURVIVAL PROBABILITIES
# CUBS
phiCLS <- 0.861674646 # Survival of Cub, Low-ranking & Susceptible
phiCLI <- 0.622810147 # Survival of Cub, Low-ranking & Infected
phiCLR <- 0 # Survival of Cub, Low-ranking & Recovered (equals to 0 because 0 recovered cub in CMR datasets)
phiCHS <- 0.900786935 # Survival of Cub, High-ranking & Susceptible
phiCHI <- 0.786418457 # Survival of Cub, High-ranking & Infected
phiCHR <- 0 # Survival of Cub, High-ranking & Recovered
# SUBADULTS
phiSLS <- 0.899696769 # Survival of Subadult, Low-ranking & Susceptible
phiSLI <- 0.691349361 # Survival of Subadut, Low-ranking & Infected
phiSLR <- 0.691349361 # Survival of Subadut, Low-ranking & Recovered
phiSHS <- 0.969186164 # Survival of Subadult, High-ranking & Susceptible
phiSHI <- 0.691349361 # Survival of Subadult, High-ranking & Infected
phiSHR <- 0.691349361 # Survival of Subadult, High-ranking & Recovered
# BREEDERS
phiBLS <- 0.946610295 # Survival of Breeder, Low-ranking & Susceptible
phiBLI <- 0.946610295 # Survival of Breeder, Low-ranking & Infected
phiBLR <- 0.946610295 # Survival of Breeder, Low-ranking & Recovered
phiBHS <- 0.946610295 # Survival of Breeder, High-ranking & Susceptible
phiBHI <- 0.946610295 # Survival of Breeder, High-ranking & Infected
phiBHR <- 0.946610295 # Survival of Breeder, High-ranking & Recovered
# NON-BREEDERS
phiNBLS <- 0.863473071 # Survival of Non-Breeder, Low-ranking & Susceptible
phiNBLI <- 0.863473071 # Survival of Non-Breeder, Low-ranking & Infected
phiNBLR <- 0.863473071 # Survival of Non-Breeder, Low-ranking & Recovered
phiNBHS <- 0.863473071 # Survival of Non-Breeder, High-ranking & Susceptible
phiNBHI <- 0.863473071 # Survival of Non-Breeder, High-ranking & Infected
phiNBHR <- 0.863473071 # Survival of Non-Breeder, High-ranking & Recovered
### -----FECUNDITY (equal to 1 as all females in the Breeder state reproduce)
fLS <- 1 # fecundity of Low-Ranking & Susceptible
fLI <- 1 # fecundity of Low-Ranking & Infected
fLR <- 1 # fecundity of Low-Ranking & Recovered
fHS <- 1 # fecundity of High-Ranking & Susceptible
fHI <- 1 # fecundity of High-Ranking & Infected
fHR <- 1 # fecundity of High-Ranking & Recovered
###---------------- SEX RATIO & LITTER SIZE
ls <- 1.53 # Average litter size (see Supplementary Information 2)
sr <- 0.52 # Sex-ratio at birth (see Supplementary Information 2)
###-----------------STATE TRANSITION PROBABILITIES
# SOCIAL STATES
rLL.S <- 0.974790382 # Probability of staying Low-ranking for Susceptible females
rLL.I <- 0.974790382 # Probability of staying Low-ranking for Infected females
rLL.R <- 0.974790382 # Probability of staying Low-ranking for Recovered females
rHH.S <- 0.939695149 # Probability of staying High-ranking for Susceptible females
rHH.I <- 0.939695149 # Probability of staying High-ranking for Infected females
rHH.R <- 0.939695149 # Probability of staying High-ranking for Recovered females
# INFECTION STATES
betaCL <- 0.454504272 # Probability of transition from S to I for Low-ranking Cubs
betaCH <- 0.233491397 # Probability of transition from S to I for High-ranking Cubs
betaSL <- 0.021071825 # Probability of transition from S to I for Low-ranking Subadults
betaSH <- 0.095583371 # Probability of transition from S to I for High-ranking Subadults
betaADL <- 0.021071825 # Probability of transition from S to I for Low-ranking Adults (Breeders&Non-Breeders)
betaADH <- 0.095583371 # Probability of transition from S to I for High-ranking Adults (Breeders&Non-Breeders)
# DEMOGRAPHIC states (i.e. accounts for recruitment)
bSL <- 0.01002621 # Probability of transition that Low-ranking Subadults become Breeders
bBL <- 0.452045588 # Probability of transition that Low-ranking Breeders become Breeders
bNBL <- 0.602846751 # Probability of transition that Low-ranking Breeders become Breeders
bSH <- 0.037954669 # Probability of transition that High-ranking Subadults become Breeders
bBH <- 0.487935995 # Probability of transition that High-ranking Breeders become Breeders
bNBH <- 0.680345616 # Probability of transition that High-ranking Breeders become Breeders