# chiperm

##### R function for permutation-based chi-square test of independence

The function performs the chi-square test of independence on the basis of permuted tables, whose number is selected by user.

- Keywords
- chiperm

##### Usage

```
chiperm(data, B = 999, resid = FALSE, filter = FALSE,
thresh = 1.96, cramer = FALSE)
```

##### Arguments

- data
Dataframe containing the input contingency table.

- B
Desired number of permuted tables (999 by default).

- resid
TRUE or FALSE (default) if the user does or doesn't want to plot the table of Pearson's standardized residuals.

- filter
Takes TRUE or FALSE (default) if the user does or does't want to filter the Pearson's standardized residuals according to the threshold provided by the thresh parameter; by default, the threshold is set at 1.96, which corresponds to an alpha level of 0.05.

- thresh
Value of the standardized residuals below which the residuals will be not displayed (by default, the threshold is set at 1.96, which corresponds to an alpha level of 0.05).

- cramer
Takes TRUE or FALSE (default) if the user does or doesn't want to calculate and plot the bootstrap confidence interval for Cramer's V.

##### Details

For the rationale of this approach, see for instance the description provided by: Beh E.J., Lombardo R. 2014, Correspondence Analysis: Theory, Practice and New Strategies, Chichester, Wiley, pages 62-64.

##### Value

The function produces: (1) a chart that displays the permuted distribution of the chi-square statistic based on B permuted tables. The selected number of permuted tables, the observed chi-square, the 95th percentile of the permuted distribution, and the associated p value are reported at the bottom of the chart;

(2) a chart that displays the bootstrap distribution of Cramer's V coefficient, based on a number of bootstrap replicates which is equal to the value of the function's parameter B;

(3) a chart that the Pearson's Standardized Residuals: a colour scale allows to easily understand which residual is smaller (BLUE) or larger (RED) than expected under the hypothesis of independence. Should the user want to only display residuals larger than a given threshold, it suffices to set the filter parameter to TRUE, and to specify the desired threshold by means of the thresh parameter, which is set at 1.96 by default.

##### Examples

```
# NOT RUN {
data(assemblage)
chiperm(data=assemblage, B=199, resid=TRUE, cramer=TRUE)
# }
```

*Documentation reproduced from package GmAMisc, version 1.0.0, License: GPL (>= 2)*