/
run.R
34 lines (32 loc) · 1.72 KB
/
run.R
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system("gcc -Wextra -Wall C/*.c -o SEIRS -lm -lgsl -lgslcblas")
n_sim = "200" # simulation times
t_simulate = "360" # time for simulation in days
input_folder = "INPUT_CN" # input folder for parameters
t_epistart = "457" # start date of epidemic, "457" indicates "2022-03-01"
n_initialinfectors = "5" # initial infectors introduced
R0 = "7.2" # reproduction number
booster_target = "18p" # target booster age-group
booster_regimen = "Inactivated" # booster vaccination type Inactivated/mRNA
booster_supply = "5000000" # booster supply since epidemic
booster_acceptance = "0.9" # rate for people accept to have booster shot
drug_uptake = "0" # proportion of drug uptake
drug_effect = "0.75" # effectiveness for drug
cm = "baseline" # contact matrix setting
sus_type = "hetero" # susceptibility setting
kappa = "1" # infectivity for asymptomatic cases
GT = "L" # rate for transmission setting, include generation time
RNG_seed = "1" # seed for random number generator, must be an int
VE_setting = "OPT_ONE" # VE setting, see table above for "INPUT_CN"
limits4elderly = "YES" # limits for vaccination for elderly
prob_folder = "SA" # folder name for probability parameter
save_prefix = "OUTPUT/OPT=A_baseline" # save path prefix
asymp_scale = "0.15" # adjusted ratio for asymptomatic cases
delta_infection = "0" # proportion for prior delta_infection
paste("./SEIRS", n_sim, t_simulate, input_folder, t_epistart,
n_initialinfectors, R0, booster_target, booster_regimen,
booster_supply, booster_acceptance, drug_uptake,
drug_effect, cm, sus_type, kappa, GT, RNG_seed,
VE_setting, limits4elderly, prob_folder, save_prefix,
asymp_scale, delta_infection, sep = " ") -> tmp_command
print(tmp_command)
system(tmp_command, intern = T)