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CDIpool.psc
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CDIpool.psc
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###################################################
# Dynamic Transmission Model of C. difficile #
# Fecal Microbiota Transplant Based Interventions #
# 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
iota*H
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 > $pool
theta_p*Up
R12:
$pool > Up
nu_up*(theta_p*(Up+Cp+Ut+Ct)+theta_a*(Ua+Ca)+zeta*D+gamma*D)
# Reactions Involving Uncontaminated, High Risk Patients (Ua) #
R13:
Ua > Ca
rho_a*psi_a*Ua*(H/(Us + H + Cp + Ca + Up + Ua + Ct + Ca + D))
R14:
Ua > Ca
mu_p*sigma_p*Ua*(Cp/(Us + H + Cp + Ca + Up + Ua + Ct + Ca + D))
R15:
Ua > Ca
mu_a*sigma_a*Ua*(Ca/(Us + H + Cp + Ca + Up + Ua + Ct + Ca + D))
R16:
Ua > Ca
mu_p*sigma_p*Ua*(Ct/(Us + H + Cp + Ca + Up + Ua + Ct + Ca + D))
R17:
Ua > $pool
theta_a*Ua
R18:
$pool > Ua
nu_ua*(theta_p*(Up+Cp+Ut+Ct)+theta_a*(Ua+Ca)+zeta*D+gamma*D)
R19:
Ua > Ut + Treated
chi*phi_u*Ua
# Reactions Involving Contaminated, Low Risk Patients (Cp) #
R20:
Cp > Ca
alpha*Cp
R21:
Cp > D + Incident
kappa*colonization*incubation*Cp
R22:
Cp > $pool
theta_p*Cp
R23:
$pool > Cp
nu_cp*(theta_p*(Up+Cp+Ut+Ct)+theta_a*(Ua+Ca)+zeta*D+gamma*D)
# Reactions Involving Contaminated, High Risk Patients (Ca) #
R24:
Ca > D + Incident
kappa*colonization*incubation*tau*Ca
R25:
Ca > $pool
theta_a*Ca
R26:
$pool > Ca
nu_ca*(theta_p*(Up+Cp+Ut+Ct)+theta_a*(Ua+Ca)+zeta*D+gamma*D)
R27:
Ca > Ct + Treated
chi*phi_c*Ca
# Reactions Involving Patients Under Treatment (Xt) *
R28:
Ut > $pool
theta_p*Ut
R29:
Ct > $pool
theta_p*Ct
R30:
Ct > Ca
alpha_t*Ct
R31:
Ut > Ua
alpha_t*Ut
R32:
Ct > D + Incident
kappa*colonization*incubation*Ct
R33:
Ut > Ct
rho_a*psi_a*Ut*(H/(Us + H + Cp + Ca + Up + Ua + Ct + Ca + D))
R34:
Ut > Ct
mu_p*sigma_p*Ut*(Cp/(Us + H + Cp + Ca + Up + Ua + Ct + Ca + D))
R35:
Ut > Ct
mu_a*sigma_a*Ut*(Ca/(Us + H + Cp + Ca + Up + Ua + Ct + Ca + D))
R36:
Ut > Ct
mu_p*sigma_p*Ut*(Ct/(Us + H + Cp + Ca + Up + Ua + Ct + Ca + D))
# Reactions Involving Active CDI Cases #
R37:
D > FT + Treated
gamma*chi_postCDI*D
R38:
D > NFT
gamma*(1-chi_postCDI)*D
R39:
D > $pool
zeta*D
R40:
$pool > D
nu_d*(theta_p*(Up+Cp+Ut+Ct)+theta_a*(Ua+Ca)+zeta*D+gamma*D)
# Reactions Involving the Fate of Discharged Patients #
R41:
FT > $pool
eta*(1-omega)*FT
R42:
FT > Recur
(1-eta)*omega*FT
R43:
NFT > $pool
(1-omega)*NFT
R44:
NFT > Recur
omega*NFT
### 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
FT = 0
NFT = 0
Recur = 0
Incident = 0
Treated = 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