R/conditional_edge_prediction_correlation_plot.R

Defines functions conditional_edge_prediction_correlation_plot

Documented in conditional_edge_prediction_correlation_plot

#' @title A Function generate a scatter plot of observed vs predicted edge values.
#' @description Scatter plot of observed vs. predicted edge values generated by the
#' `conditional_edge_prediction()` function. Also calculated correlation coefficient.
#'
#' @param edge_prediction_results A list object returned by the
#' `conditional_edge_prediction()` function.
#' @param xlim Defaults to NULL, but can be set by the user if desired to a
#' numeric vector of the form c(lower,upper) for observed edge values.
#' @param ylim Defaults to NULL, but can be set by the user if desired to a
#' numeric vector of the form c(lower,upper) for predicted edge values.
#' @param plot_max_entropy_predictions Defaults to FALSE, can be set to TRUE to
#' show maximum entropy edge predictions as red X's.
#' @return Saves a PDF plot to the current working directory
#' @export
conditional_edge_prediction_correlation_plot <- function(
  edge_prediction_results,
  xlim = NULL,
  ylim = NULL,
  plot_max_entropy_predictions = FALSE) {

  # make diagnoal NA's
  diag(edge_prediction_results$predicted_edge_values) <- NA
  diag(edge_prediction_results$observed_network) <- NA

  # turn into a vector
  predicted_vals <- c(edge_prediction_results$predicted_edge_values)
  observed_vals <- c(edge_prediction_results$observed_network)

  # calculate correlation coefficient
  corcoef <- cor(predicted_vals, observed_vals, use = "complete.obs")

  # now calculate the average correlation coefficient across all simulated
  # networks
  num_sim <- length(edge_prediction_results$edge_predictions[,,1])
  predicted_corcoef <- rep(0, num_sim)
  for (i in 1:num_sim) {
    cur <- edge_prediction_results$edge_predictions[,,i]
    diag(cur) <- NA
    cur_predicted_vals <- c(cur)
    predicted_corcoef[i] <- cor(cur_predicted_vals,
                                observed_vals,
                                use = "complete.obs")
  }
  #summary(predicted_corcoef)

  if (plot_max_entropy_predictions) {
    diag(edge_prediction_results$max_ent_predicted_edge_values) <- NA
    max_ent_predicted_vals <- c(edge_prediction_results$max_ent_predicted_edge_values)
    corcoef2 <- cor(max_ent_predicted_vals, observed_vals, use = "complete.obs")

    num_sim <- length(edge_prediction_results$max_ent_edge_predictions[,,1])
    predicted_corcoef2 <- rep(0, num_sim)
    for (i in 1:num_sim) {
      cur <- edge_prediction_results$max_ent_edge_predictions[,,i]
      diag(cur) <- NA
      cur_predicted_vals <- c(cur)
      predicted_corcoef2[i] <- cor(cur_predicted_vals,
                                  observed_vals,
                                  use = "complete.obs")
    }
    summary(predicted_corcoef2)

  }

  # deal with NULL x and y limits
  if (is.null(xlim)) {
    xlim <- c(min(observed_vals, na.rm = TRUE),
              max(observed_vals, na.rm = TRUE))
  }
  if (is.null(ylim)) {
    ylim <- c(min(predicted_vals, na.rm = TRUE),
              max(predicted_vals, na.rm = TRUE))
    if (plot_max_entropy_predictions) {
      ylim <- c(min(c(predicted_vals,max_ent_predicted_vals), na.rm = TRUE),
                max(c(predicted_vals,max_ent_predicted_vals), na.rm = TRUE))
    }
  }

  UMASS_BLUE <- rgb(51,51,153,155,maxColorValue = 255)
  UMASS_RED <- rgb(153,0,51,150,maxColorValue = 255)

  # reset pars
  par(mfrow = c(1,1))

  if (plot_max_entropy_predictions) {
    plot(y = predicted_vals,
         x = observed_vals,
         pch = 19,
         col = UMASS_BLUE,
         xlab = "Observed Edge Value",
         ylab = "Predicted Edge Value",
         xlim = xlim, ylim = ylim,
         main = paste("Correlation Coefficient -- predicted values:",
                      round(corcoef,4),
                      " -- average of simulations:", round(mean(predicted_corcoef),4),
                      "\nMax Entropy Corr. Coef. -- predicted values:",
                      round(corcoef2,4),
                      " -- average of simulations:", round(mean(predicted_corcoef2),4)))
    points(x = observed_vals,
           y = max_ent_predicted_vals,
           pch = 4,
           col = UMASS_RED)
    abline(a = 0, b = 1, lwd = 2)
  } else {
    plot(y = predicted_vals,
         x = observed_vals,
         pch = 19,
         col = UMASS_BLUE,
         xlab = "Observed Edge Value",
         ylab = "Predicted Edge Value",
         xlim = xlim, ylim = ylim,
         main = paste("Correlation Coefficient:",round(corcoef,4)))
    abline(a = 0, b = 1, lwd = 2)
  }
}
matthewjdenny/GERGM documentation built on May 15, 2018, 4:22 p.m.