Cperiodogram: Contingency periodogram

In adespatial: Multivariate Multiscale Spatial Analysis

Contingency periodogram

Description

Function to compute a contingency periodogram for a univariate series of qualitative data

Usage

Cperiodogram(x, T1 = 2, T2 = NULL, nperm = NULL, alpha = 0.05, graph = TRUE)

Arguments

x	a qualitative variable (factor)
T1	first period included in the calculations (default: T1 = 2)
T2	last period included in the calculations (default: T2 = n/2)
nperm	Number of permutations for the chi-square test. For chi-square tests using the chi- square distribution, use the default nperm=NULL
alpha	significance level for computation of the confidence limits
graph	a logical indicating if a graph is requested, by default TRUE.

Details

The contingency periodogram of Legendre et al. (1981) identifies periodic components in qualitative data vectors. The vector may contain classes of a qualitative variable or the classes obtained by hierarchical clustering or partitioning of a multivariate data table. The method is also described in Legendre & Legendre (2012). The optional graph produced by the function shows the following information:

• In red: the B statistics (information in common).

• In blue: Confidence limits for B without correction.

• In green: Bonferroni-corrected limits of the confidence intervals.

• In black: Confidence limits with progressive Bonferroni correction.

Value

A table with the statistics for the selected periods:

• Wilks' chi-square statistic (Wilks.chisq)

• information in common (B),

• degrees of freedom (df),

• p-value (prob)

Confidence interval limits:

• critical value of B without correction (B.crit),

• critical value of B with Bonferroni correction based on the number of periods studied in the periodogram (B.crit.Bonf),

• critical value of B with progressive Bonferroni correction (B.prog.Bonf).

Author(s)

Pierre Legendre [e-mail]

References

Legendre, L., M. Fréchette & P. Legendre. 1981. The contingency periodogram: a method of identifying rhythms in series on nonmetric ecological data. Journal of Ecology 69: 965-979.

Legendre, P. and Legendre, L. 2012. Numerical Ecology. 3rd English ed. Elsevier, Amsterdam

Examples

# Data from the numerical example of Subsection 12.4.2 of Legendre and Legendre (2012).
test.vec <- c(1,1,2,3,3,2,1,2,3,2,1,1,2,3,3,1)
# Periodogram with tests using the chi-square distribution
res <- Cperiodogram(test.vec)
# Periodogram with permutation tests
res <- Cperiodogram(test.vec, nperm=2000, graph=FALSE)

adespatial documentation built on Sept. 11, 2024, 7:04 p.m.