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

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

if (FALSE) { # \dontrun{
  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)
} # }