chi2CorrAge: Searches for parasite interactions taking the cumulative...
In Interatrix: Compute Chi-Square Measures with Corrections

Description Usage Arguments Value References Examples

View source: R/chi2CorrAge.R

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.

1 2	chi2CorrAge(formula, data.obs, namepara1, namepara2, nameage, w1, w2, mort, a, nsimu, nbcore = 3)

`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

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.

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.

## 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)