ssm

{ "data": [ { "name": "all_CDC_inc", "require": { "path": "data/data.csv", "fields": ["date", "all_CDC_inc"] } }, { "name": "paris_CDC_prev", "require": { "path": "data/data.csv", "fields": ["date", "paris_CDC_prev"] } }, { "name": "all_google_inc", "require": { "path": "data/data.csv", "fields": ["date", "all_google_inc"] } }, { "name": "nyc_CDC_inc", "require": { "path": "data/data.csv", "fields": ["date", "nyc_CDC_inc"] } } ], "inputs": [ { "name": "N_nyc", "require": { "path": "data/N.csv", "fields": ["date", "nyc"] } }, { "name": "N_paris", "require": { "path": "data/N.csv", "fields": ["date", "paris"] } }, { "name": "mu_b_paris", "require": { "path": "data/mu_b.csv", "fields": ["date", "paris"] } }, { "name": "mu_b_nyc", "require": { "path": "data/mu_b.csv", "fields": ["date", "nyc"] } }, { "name": "mu_d_paris", "require": { "path": "data/mu_d.csv", "fields": ["date", "paris"] } }, { "name": "mu_d_nyc", "require": { "path": "data/mu_d.csv", "fields": ["date", "nyc"] } }, { "name": "prop_all_CDC_inc", "require": { "path": "data/prop.csv", "fields": ["date", "all_CDC_inc"] } }, { "name": "prop_paris_CDC_prev", "require": { "path": "data/prop.csv", "fields": ["date", "paris_CDC_prev"] } }, { "name": "prop_all_google_inc", "require": { "path": "data/prop.csv", "fields": ["date", "all_google_inc"] } }, { "name": "prop_nyc_CDC_inc", "require": { "path": "data/prop.csv", "fields": ["date","nyc_CDC_inc"] } }, { "name": "S_paris", "description": "Number of susceptible", "require": {"name": "pr_S_paris", "path": "data/pr_S_paris.json"}, "transformation": "pr_S_paris*N_paris", "to_resource": "S_paris/N_paris" }, { "name": "S_nyc", "description": "Number of susceptible", "transformation": "pr_S_paris*N_nyc" }, { "name": "I_paris", "description": "Number of infectious", "keywords": ["infectious"], "require": {"name": "pr_I_paris", "path": "data/pr_I_paris.json" }, "transformation": "pr_I_paris*N_paris", "to_resource": "I_paris/N_paris" }, { "name": "I_nyc", "description": "Number of infectious", "keywords": ["infectious"], "require": {"name": "pr_I_nyc", "path": "data/pr_I_nyc.json"}, "transformation": "pow(10, -pr_I_nyc) * N_nyc", "to_resource": "-log(I_nyc)/(log(10)*N_nyc)" }, { "name": "r0_paris", "description": "basic reproduction number", "require": {"name": "r0_paris", "path": "data/r0_paris.json"} }, { "name": "r0_nyc", "description": "basic reproduction number", "require": {"name": "r0_nyc", "path": "data/r0_nyc.json"} }, { "name": "vol", "description": "volatility of the diffusion", "require": {"name": "vol", "path": "data/vol.json"} }, { "name": "v", "description": "recovery rate", "require": {"name": "pr_v", "path": "data/pr_v.json"}, "transformation": "1/pr_v", "to_resource": "1/v" }, { "name": "sto", "description": "noise intensity", "require": {"name": "sto", "path": "data/sto.json"} }, { "name": "rep_all_CDC_inc", "description": "reporting rate", "require": {"name": "rep_all_CDC_inc", "path": "data/rep_all_CDC_inc.json"} }, { "name": "rep_paris_CDC_prev", "description": "reporting rate", "require": {"name": "rep_paris_CDC_prev", "path": "data/rep_paris_CDC_prev.json"} }, { "name": "rep_all_google_inc", "description": "reporting rate", "require": {"name": "rep_all_google_inc", "path": "data/rep_all_google_inc.json"} }, { "name": "rep_nyc_CDC_inc", "description": "reporting rate", "require": {"name": "rep_nyc_CDC_inc", "path": "data/rep_nyc_CDC_inc.json"} }, { "name": "phi", "description": "over-dispertion", "require": {"name": "phi", "path": "data/phi.json"} } ], "populations": [ {"name": "paris", "composition": ["S_paris", "I_paris", "R_paris"], "remainder": {"name": "R_paris", "pop_size": "N_paris"}}, {"name": "nyc", "composition": ["S_nyc", "I_nyc", "R_nyc"], "remainder": {"name": "R_nyc", "pop_size": "N_nyc"}} ], "reactions": [ {"from": "U", "to": "S_nyc", "rate": "mu_b_nyc*N_nyc", "description":"birth"}, {"from": "U", "to": "S_paris", "rate": "mu_b_paris*N_paris", "description":"birth"}, {"from": "S_nyc", "to": "I_nyc", "rate": "r0_nyc/N_nyc*v*I_nyc", "description":"infection", "keywords": ["transmission"], "accumulators": ["Inc_in_nyc"], "white_noise": {"name": "noise_SI", "sd": "sto"}}, {"from": "S_paris", "to": "I_paris", "rate": "r0_paris/N_paris*v*I_paris", "description":"infection", "keywords": ["transmission"]}, {"from": "I_nyc", "to": "R_nyc", "rate": "correct_rate(v)", "description":"recovery", "accumulators": ["Inc_out"]}, {"from": "I_paris", "to": "R_paris", "rate": "correct_rate(v)", "description":"recovery", "accumulators": ["Inc_out"]}, {"from": "S_nyc", "to": "U", "rate": "mu_d_nyc", "description":"death"}, {"from": "S_paris", "to": "U", "rate": "mu_d_paris", "description":"death"}, {"from": "I_nyc", "to": "U", "rate": "mu_d_nyc", "description":"death", "accumulators": ["Inc_out"]}, {"from": "I_paris", "to": "U", "rate": "mu_d_paris", "description":"death", "accumulators": ["Inc_out"]} ], "sde": { "drift": [ {"name": "r0_paris", "f": 0.0, "transformation": "log(r0_paris)"}, {"name": "r0_nyc", "f": 0.0, "transformation": "log(r0_nyc)"} ], "dispersion":[ ["vol", 0], [0, "vol"] ] }, "observations": [ { "name": "all_CDC_inc", "start": "2012-07-26", "distribution": "discretized_normal", "mean": "rep_all_CDC_inc * prop_all_CDC_inc * Inc_out", "sd": "sqrt(rep_all_CDC_inc * ( 1.0 - rep_all_CDC_inc ) * prop_all_CDC_inc * Inc_out + pow(rep_all_CDC_inc * phi * prop_all_CDC_inc * Inc_out, 2) )" }, { "name": "paris_CDC_prev", "start": "2012-07-26", "distribution": "discretized_normal", "mean": "rep_paris_CDC_prev * prop_paris_CDC_prev * I_paris", "sd": "sqrt(rep_paris_CDC_prev * ( 1.0 - rep_paris_CDC_prev ) * prop_paris_CDC_prev * I_paris + pow(rep_paris_CDC_prev * phi * prop_paris_CDC_prev * I_paris, 2) )" }, { "name": "all_google_inc", "start": "2012-07-26", "distribution": "discretized_normal", "mean": "rep_all_google_inc * prop_all_google_inc * Inc_out", "sd": "sqrt(rep_all_google_inc * ( 1.0 - rep_all_google_inc ) * prop_all_google_inc * Inc_out + pow(rep_all_google_inc * phi * prop_all_google_inc * Inc_out, 2) )" }, { "name": "nyc_CDC_inc", "start": "2012-07-26", "distribution": "discretized_normal", "mean": "rep_nyc_CDC_inc * prop_nyc_CDC_inc * Inc_in_nyc", "sd": "sqrt(rep_nyc_CDC_inc * ( 1.0 - rep_nyc_CDC_inc ) * prop_nyc_CDC_inc * Inc_in_nyc + pow(rep_nyc_CDC_inc * phi * prop_nyc_CDC_inc * Inc_in_nyc, 2) )" } ] }