contact-fitter: Fitting Contact Data onto Serological Data

In TeaKov/serostat: Modeling Infectious Disease Parameters Based on Serological and Social Contact Data R Package

Description

This function can be used to fit contact data to serological data. The resulting fit contains deviance, aic, bic, and R0, enabling us to compare the fitted profiles for various types of contacts.

Usage

contact.fitter(a, y, rij, muy, N, D, Lmax, A, plots, startpar)

Arguments

a	Numeric vector of age categories.
y	The response variable (binary, 1=past infection, 0=otherwise).
rij	The smoothed contact matrix.
muy	Mortality function.
N	Population size.
D	Mean infectious period.
Lmax	Maximum age.
A	Age of loss of maternal immunity (0<A<1).
plots	Generate plots during fitting process.
startpar	Starting values for the “nlm” method used in this function.

See Also

pwcrate, waifw.6parms

Examples

ND <- c(489,47,29,21,12,12,16,15,15,6,6,14,17,19,17,23,34,33,62,71,68,68,78,71,71,96,86,83,79,
  80,83,93,126,120,121,132,135,176,161,193,196,218,257,277,331,376,356,435,460,453,535,545,
  576,668,692,759,722,819,939,1015,1051,973,1113,996,940,1074,1252,1367,1468,1541,1661,1838,
  2012,2236,2517,2793,2938,2994,3311,3516,3727,3857,4088,4161,4261,4274,4061,2509,2049,2159,
  2205,2550,2330,1992,1569,1242,1000,726,533,996)
PS <- c(118366,117271,114562,113894,116275,118030,116761,117742,119583,119887,118963,119958,
  124637,129143,131030,129724,127187,126433,124377,124883,122201,124482,126459,130129,133897,
  135009,134516,133495,132705,132040,130602,135638,140537,146151,150467,152113,151656,151412,
  153371,158268,162456,167652,164871,161671,162060,159735,160672,157030,153820,151114,148978,
  145929,142374,141215,135525,135968,134692,135991,134291,134131,113024,112198,105880,92772,
  84462,93787,100820,101866,97208,94145,92451,93027,91640,93593,91933,89900,81718,77891,73104,
  70082,67057,62178,57642,51786,47466,42065,28004,17186,14492,13838,13957,13358,10442,8063,5604,
  4289,2843,2068,1368,2146)
AGE<-c(0:(length(ND)-1))

estimL <- estimateLifeExpectancy(ND, PS, AGE)

# Using Belgian B19 data
data("VZV_B19_BE_0103")
VZV_B19_BE_0103 <- VZV_B19_BE_0103[!is.na(VZV_B19_BE_0103$parvores)&!is.na(VZV_B19_BE_0103$age)&
  VZV_B19_BE_0103$age<70&VZV_B19_BE_0103$age>=1,]
VZV_B19_BE_0103 <- VZV_B19_BE_0103[order(VZV_B19_BE_0103$age),]

y <- VZV_B19_BE_0103$parvores
a <- VZV_B19_BE_0103$age

# Mean duration of infectiousness
D <- 6/365

# Maximum life (if type mortality this is the life expectancy)
Lmax<-100

# Age of loss of maternal immunity (0<A<1)
A <- 0.5

# Mortality function
My <- estimL$My[1:Lmax]
muy <- estimL$muy[1:Lmax]

# Population size
N <- sum(PS)

data("scd_all_contacts")
contact.result<-contact.fitter(a=a,y=y,rij=scd_all_contacts,muy=muy,N=N,D=D,
  Lmax=85,A=A,plots="TRUE",startpar=5e-2)
c(contact.result$q,contact.result$R0,contact.result$aic)

data("scd_close_m15")
contact.result<-contact.fitter(a=a,y=y,rij=scd_close_m15,muy=muy,N=N,D=D,
  Lmax=85,A=A,plots="TRUE",startpar=5e-2)
c(contact.result$q,contact.result$R0,contact.result$aic)

data("scd_close_nonclose_p1h")
contact.result<-contact.fitter(a=a,y=y,rij=scd_close_nonclose_p1h,muy=muy,N=N,
  D=D,Lmax=85,A=A,plots="TRUE",startpar=5e-2)
c(contact.result$q,contact.result$R0,contact.result$aic)

data("scd_close_p15_nonclose_p1h")
contact.result<-contact.fitter(a=a,y=y,rij=scd_close_p15_nonclose_p1h,muy=muy,
  N=N,D=D,Lmax=85,A=A,plots="TRUE",startpar=5e-2)
c(contact.result$q,contact.result$R0,contact.result$aic)

data("scd_close_p15")
contact.result<-contact.fitter(a=a,y=y,rij=scd_close_p15,muy=muy,N=N,D=D,
  Lmax=85,A=A,plots="TRUE",startpar=5e-1)
c(contact.result$q,contact.result$R0,contact.result$aic)

data("scd_close_p1h")
contact.result<-contact.fitter(a=a,y=y,rij=scd_close_p1h,muy=muy,N=N,D=D,
  Lmax=85,A=A,plots="TRUE",startpar=5e-1)
c(contact.result$q,contact.result$R0,contact.result$aic)

data("scd_close_p4h")
contact.result<-contact.fitter(a=a,y=y,rij=scd_close_p4h,muy=muy,N=N,D=D,
  Lmax=85,A=A,plots="TRUE",startpar=5e-2)
c(contact.result$q,contact.result$R0,contact.result$aic)

data("scd_close")
contact.result<-contact.fitter(a=a,y=y,rij=scd_close,muy=muy,N=N,D=D,Lmax=85,
  A=A,plots="TRUE",startpar=5e-2)
c(contact.result$q,contact.result$R0,contact.result$aic)

data("scd_nonclose_p1h")
contact.result<-contact.fitter(a=a,y=y,rij=scd_nonclose_p1h,muy=muy,N=N,D=D,
  Lmax=85,A=A,plots="TRUE",startpar=5e-2)
c(contact.result$q,contact.result$R0,contact.result$aic)

data("scd_nonclose")
contact.result<-contact.fitter(a=a,y=y,rij=scd_nonclose,muy=muy,N=N,D=D,
  Lmax=85,plots="TRUE",A=A,startpar=5e-2)
c(contact.result$q,contact.result$R0,contact.result$aic)

TeaKov/serostat documentation built on May 21, 2019, 1:21 p.m.