R/analysis-data-function.R

In kyarlagadda/499-project: Network Analysis in R

Analysis <- function(x_list, permutations = 5000, intercept = TRUE, directed = "undirected", 
                     diagonal = FALSE, test.statistic = "beta", tol = 1e-07, randomisations = 5000){
  if(length(x_list) == 2){ #For the 2 object list, run the mantel test and MRQAP
    mantel_test_results <- mantel(x_list[[1]], x_list[[2]], permutations=permutations)
    MRQAP_results <- mrqap.dsp(x_list[[2]]~x_list[[1]], intercept=intercept, directed=directed, 
                               diagonal=diagonal, test.statistic=test.statistic, tol=tol, 
                               randomisations=randomisations)
    #Store results in a new list
    results <- list(mantel_test_results, MRQAP_results)
    return(results)
  }
  if(length(x_list) == 3){ #For the 3 object list, run the mantel test 3 times, with each matrix pair
    mantel_test_results_1 <- mantel(x_list[[1]], x_list[[2]], permutations=permutations)
    mantel_test_results_2 <- mantel(x_list[[3]], x_list[[2]], permutations=permutations)
    mantel_test_results_3 <- mantel(x_list[[1]], x_list[[3]], permutations=permutations)
    #Then MRQAP, treating the second matrix as dependent when possible, or third matrix for the last test
    MRQAP_results_1 <- mrqap.dsp(x_list[[2]]~x_list[[1]], intercept=intercept, directed=directed, 
                                 diagonal=diagonal, test.statistic=test.statistic, tol=tol, 
                                 randomisations=randomisations)
    MRQAP_results_2 <- mrqap.dsp(x_list[[2]]~x_list[[3]], intercept=intercept, directed=directed, 
                                 diagonal=diagonal, test.statistic=test.statistic, tol=tol, 
                                 randomisations=randomisations)
    MRQAP_results_3 <- mrqap.dsp(x_list[[3]]~x_list[[1]], intercept=intercept, directed=directed, 
                                 diagonal=diagonal, test.statistic=test.statistic, tol=tol, 
                                 randomisations=randomisations)
    mantel_ptest_results <- mantel.partial(x_list[[2]], x_list[[3]], x_list[[1]], permutations=permutations)
    #Store results in a new list
    results <- list(mantel_test_results_1, mantel_test_results_2, mantel_test_results_3, 
                    MRQAP_results_1, MRQAP_results_2, MRQAP_results_3, mantel_ptest_results)
    return(results)
  }else{
    #Exception for lists of incorrect length
    stop("Data input not valid for this analysis")
  }
}