/
CDIqueue.psc
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CDIqueue.psc
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###################################################
# Dynamic Transmission Model of C. difficile #
# Fecal Microbiota Transplant Based Interventions #
# Queue-based Steady State Population #
# Author: Eric Lofgren (Eric.Lofgren@gmail.com) #
###################################################
# Descriptive Information for PML File
Modelname: FecalTransplant
Description: PML Implementation of C. difficile transmission model with FMT intervention
# Set model to run with numbers of individuals
Species_In_Conc: False
Output_In_Conc: False
### Model Reactions ###
# Reactions Governing Movement of Healthcare Workers #
R1:
H > Us
H*iota
R2:
Us > H
rho_p*sigma_p*Cp*(Us/(Us + H + Cp + Ca + Up + Ua + Ct + Ca + D))
R3:
Us > H
rho_d*sigma_d*D*(Us/(Us + H + Cp + Ca + Up + Ua + Ct + Ca + D))
R4:
Us > H
rho_a*sigma_a*Ca*(Us/(Us + H + Cp + Ca + Up + Ua + Ct + Ca + D))
R5:
Us > H
rho_p*sigma_p*Ct*(Us/(Us + H + Cp + Ca + Up + Ua + Ct + Ca + D))
# Reactions Involving Uncontaminated, Low Risk Patients (Up) #
R6:
Up > Ua
alpha*Up
R7:
Up > Cp
rho_p*psi_p*Up*(H/(Us + H + Cp + Ca + Up + Ua + Ct + Ca + D))
R8:
Up > Cp
mu_p*sigma_p*Up*(Cp/(Us + H + Cp + Ca + Up + Ua + Ct + Ca + D))
R9:
Up > Cp
mu_a*sigma_a*Up*(Ca/(Us + H + Cp + Ca + Up + Ua + Ct + Ca + D))
R10:
Up > Cp
mu_p*sigma_p*Up*(Ct/(Us + H + Cp + Ca + Up + Ua + Ct + Ca + D))
R11:
Up > Up
theta_p*Up*nu_up
R12:
Up > Ua
theta_p*Up*nu_ua
R13:
Up > Cp
theta_p*Up*nu_cp
R14:
Up > Ca
theta_p*Up*nu_ca
R15:
Up > D
theta_p*Up*nu_d
# Reactions Involving Uncontaminated, High Risk Patients (Ua) #
R16:
Ua > Ca
rho_a*psi_a*Ua*(H/(Us + H + Cp + Ca + Up + Ua + Ct + Ca + D))
R17:
Ua > Ca
mu_p*sigma_p*Ua*(Cp/(Us + H + Cp + Ca + Up + Ua + Ct + Ca + D))
R18:
Ua > Ca
mu_a*sigma_a*Ua*(Ca/(Us + H + Cp + Ca + Up + Ua + Ct + Ca + D))
R19:
Ua > Ca
mu_p*sigma_p*Ua*(Ct/(Us + H + Cp + Ca + Up + Ua + Ct + Ca + D))
R20:
Ua > Ua
theta_a*Ua*nu_ua
R21:
Ua > Up
theta_a*Ua*nu_up
R22:
Ua > Ca
theta_a*Ua*nu_ca
R23:
Ua > Cp
theta_a*Ua*nu_cp
R24:
Ua > D
theta_a*Ua*nu_d
R25:
Ua > Ut + Treated
chi*phi_u*Ua
# Reactions Involving Contaminated, Low Risk Patients (Cp) #
R26:
Cp > Ca
alpha*Cp
R27:
Cp > D + Incident
kappa*colonization*incubation*Cp
R28:
Cp > Cp
theta_p*Cp*nu_cp
R29:
Cp > Ca
theta_p*Cp*nu_ca
R30:
Cp > Up
theta_p*Cp*nu_up
R31:
Cp > Ua
theta_p*Cp*nu_ua
R32:
Cp > D
theta_p*Cp*nu_d
# Reactions Involving Contaminated, High Risk Patients (Ca) #
R33:
Ca > D + Incident
kappa*colonization*incubation*tau*Ca
R34:
Ca > Ca
theta_a*Ca*nu_ca
R35:
Ca > Cp
theta_a*Ca*nu_cp
R36:
Ca > Ua
theta_a*Ca*nu_ua
R37:
Ca > Up
theta_a*Ca*nu_up
R38:
Ca > D
theta_a*Ca*nu_d
R39:
Ca > Ct + Treated
chi*phi_c*Ca
# Reactions Involving Patients Under Treatment (Xt) *
R40:
Ut > Ua
theta_p*Ut*nu_ua
R41:
Ut > Up
theta_p*Ut*nu_up
R42:
Ut > Ca
theta_p*Ut*nu_ca
R43:
Ut > Cp
theta_p*Ut*nu_cp
R44:
Ut > D
theta_p*Ut*nu_d
R45:
Ct > Ua
theta_p*Ct*nu_ua
R46:
Ct > Up
theta_p*Ct*nu_up
R47:
Ct > Ca
theta_p*Ct*nu_ca
R48:
Ct > Cp
theta_p*Ct*nu_cp
R49:
Ct > D
theta_p*Ct*nu_d
R50:
Ct > Ca
alpha_t*Ct
R51:
Ut > Ua
alpha_t*Ut
R52:
Ct > D + Incident
kappa*colonization*incubation*Ct
R53:
Ut > Ct
rho_a*psi_a*Ut*(H/(Us + H + Cp + Ca + Up + Ua + Ct + Ca + D))
R54:
Ut > Ct
mu_p*sigma_p*Ut*(Cp/(Us + H + Cp + Ca + Up + Ua + Ct + Ca + D))
R55:
Ut > Ct
mu_a*sigma_a*Ut*(Ca/(Us + H + Cp + Ca + Up + Ua + Ct + Ca + D))
R56:
Ut > Ct
mu_p*sigma_p*Ut*(Ct/(Us + H + Cp + Ca + Up + Ua + Ct + Ca + D))
# Reactions Involving Active CDI Cases *
R57:
D > Up
gamma*(1-chi_postCDI)*D*(1-omega)*nu_up
R58:
D > Ua
gamma*(1-chi_postCDI)*D*(1-omega)*nu_ua
R59:
D > Cp
gamma*(1-chi_postCDI)*D*(1-omega)*nu_cp
R60:
D > Ca
gamma*(1-chi_postCDI)*D*(1-omega)*nu_ca
R61:
D > D
gamma*(1-chi_postCDI)*D*(1-omega)*nu_d
R62:
D > Up + Treated
gamma*chi_postCDI*D*nu_up*eta*(1-omega)
R63:
D > Ua + Treated
gamma*chi_postCDI*D*nu_ua*eta*(1-omega)
R64:
D > Cp + Treated
gamma*chi_postCDI*D*nu_cp*eta*(1-omega)
R65:
D > Ca + Treated
gamma*chi_postCDI*D*nu_ca*eta*(1-omega)
R66:
D > D + Treated
gamma*chi_postCDI*D*nu_d*eta*(1-omega)
R67:
D > Up + Recur
gamma*(1-chi_postCDI)*D*nu_up*omega
R68:
D > Ua + Recur
gamma*(1-chi_postCDI)*D*nu_ua*omega
R69:
D > Cp + Recur
gamma*(1-chi_postCDI)*D*nu_cp*omega
R70:
D > Ca + Recur
gamma*(1-chi_postCDI)*D*nu_ca*omega
R71:
D > D + Recur
gamma*(1-chi_postCDI)*D*nu_d*omega
R72:
D > Up + Recur + Treated
D*gamma*chi_postCDI*(1-eta)*omega*nu_up
R73:
D > Ua + Recur + Treated
D*gamma*chi_postCDI*(1-eta)*omega*nu_ua
R74:
D > Cp + Recur + Treated
D*gamma*chi_postCDI*(1-eta)*omega*nu_cp
R75:
D > Ca + Recur + Treated
D*gamma*chi_postCDI*(1-eta)*omega*nu_ca
R76:
D > D + Recur + Treated
D*gamma*chi_postCDI*(1-eta)*omega*nu_d
R77:
D > Up + Death
zeta*D*nu_up
R78:
D > Ua + Death
zeta*D*nu_ua
R79:
D > Cp + Death
zeta*D*nu_cp
R80:
D > Ca + Death
zeta*D*nu_ca
R81:
D > D + Death
zeta*D*nu_d
### Parameter Values ###
## Time Values are in HOURS ##
# Compartments #
Us = 4
H = 1
Up = 3
Cp = 3
Ua = 3
Ca = 3
Ut = 0
Ct = 0
D = 0
Recur = 0
Incident = 0
Treated = 0
Death = 0
# Contact Rates and Contamination Probabilities
rho_p = 4.244 # direct care tasks per patient per hour
rho_d = 4.244
rho_a = 4.244
sigma_p = 0.35
sigma_d = 0.50
sigma_a = 0.35
psi_p = 0.90
psi_a = 0.90
# High-risk treatment rates
# Currently disabled
# Risk determined at admission
alpha = 0
# Patient to Patient transmission rates
# Currently disabled
mu_p = 0
mu_a = 0
# Exit (death/discharge) rates
theta_p = 0.01255717
theta_a = 0.003470383
zeta = 0.0006252176
gamma = 0.001880387
# Admission Proportions
# 77.65% are high risk
# Cx =0.02, Ux = 0.936
nu_cp = 0.00447
nu_ca = 0.01553
nu_up = 0.209196
nu_ua = 0.726804
nu_d = 0.044
# Disease Natural History Parameters
incubation = 0.01389
kappa = 0.0002077
colonization = 1.00 # Colonization/disease are a single process
tau = 3.37 # RR for high-risk patients
# Handwashing Rate
iota = 9.365 #10.187 direct care tasks per hour with 94% compliance and 97.8% efficacy
# Fecal Transplant Intervention Parameters
eta = 0.938
omega = 0.30
chi = 0
chi_postCDI = 0
phi_c = 0
phi_u = 0
alpha_t = 0