chi2CorrAge {Interatrix}

Searches for parasite interactions taking the cumulative effect of age and other risk factors into account.

Description

This function implements a method to correct for the cumulative effect of age and for other potentially confounding risk factors in the search for interactions. It provides the observed chi-square value, a measure of the association between two parasites, and simulates bootstrapped data taking risk factors into account.

Usage

chi2CorrAge(formula, data.obs, namepara1, namepara2, nameage, w1, w2, mort, a, 
nsimu, nbcore = 3)

Arguments

formula

a string of characters indicating a symbolic description of the model of shared risk factors (including age) to be fitted without any response variable

data.obs

the name of the data set to be used

namepara1

the name of the column giving the status to the first parasite

namepara2

the name of the column giving the status to the second parasite

nameage

the column name of the age classes

w1

a real number between 0 and 1 indicating the antibodies' disappearance rate of the first studied parasite

w2

a real number between 0 and 1 indicating the antibodies' disappearance rate of the second studied parasite

mort

a vector of real numbers between 0 and 1 giving the mortality rates of all age classes

a

a vector of integers giving the bounds of the age classes

nsimu

an integer indicating the number of repetitions for the bootstrap simulation

nbcore

an integer indicating the number of cores available on the computer to set up a parallel calculation

Value

The value returned is a list containing:

formula

the model fitted without any response variable

time

duration in seconds of the simulations

nbcore

the number of cores used for parallel simulations

chi2.corr.obs

the Pearson's chi2 statistic calculated on data.obs

pval

p-value of the corrected chi-square test under the null hypothesis of independence of the two parasites. pval was given by the proportion of bootstrapped corrected chi-squares smaller than the observed value (chi2.corr.obs).

tab.th

expected frequencies, ie. the contingency table calculated on the theoretical (bootstrapped) data

tab.obs

observed frequencies, ie. the contingency table calculated on data.obs

chi2.corr.sim

a vector containing the nsimu Pearson's chi2 statistics calculated on simulated data.

The distribution of the bootstrapped corrected chi-squares (an histogram) is also provided.

References

Unknown age in health disorders: a method to account for its cumulative effect and an application to feline viruses interactions. Hellard E., Pontier D., Siberchicot A., Sauvage F. and Fouchet D. (2015). Epidemics 11: 48-55. doi:10.1016/j.epidem.2015.02.004.

Examples

## Not run: 
  library(Interatrix)
  data(dataInteratrix)
  res2 <- chi2CorrAge("F1+F2+AGE", dataInteratrix, "Parasite1", "Parasite2", "AGE", w1 = 0, 
    w2 = 0, mort = c(0.2, 0.2, 0.2), a = c(0, 1, 2, 10), nsimu = 500, nbcore = 2)

## End(Not run)