From eee4229dce5d0e6e59dd278b9a776f6260e6725e Mon Sep 17 00:00:00 2001
From: xuefliang <xuefliang@gmail.com>
Date: Sun, 3 May 2026 21:59:04 +0800
Subject: [PATCH] feat:Compute local collinearity diagnostics including VIF,
 CN, and VDP

---
 R/gwr_collin_diag.R | 324 ++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 324 insertions(+)
 create mode 100755 R/gwr_collin_diag.R

diff --git a/R/gwr_collin_diag.R b/R/gwr_collin_diag.R
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+#' GWR Collinearity Diagnostics
+#'
+#' Compute local collinearity diagnostics including VIF, CN, and VDP
+#' for geographically weighted regression. This implementation follows
+#' the methodology of GWmodel::gwr.collin.diagno().
+#'
+#' @param formula Regression model formula.
+#' @param data A `sf` object.
+#' @param bw Bandwidth value.
+#' @param adaptive Whether the bandwidth is adaptive (number of neighbors).
+#' @param kernel Kernel function: "gaussian", "exp", "bisquare", "tricube", "boxcar".
+#' @param longlat Whether coordinates are longitude/latitude.
+#' @param p Power of Minkowski distance (2 = Euclidean).
+#' @param theta Angle to rotate coordinates (radians).
+#' @param dMat Optional pre-computed distance matrix.
+#'
+#' @return A list containing:
+#' \describe{
+#'   \item{SDF}{sf object with VIF, local_CN, VDP, and correlations}
+#'   \item{local_CN}{Local condition numbers}
+#'   \item{VIF}{Matrix of local VIF values (locations x variables, excluding intercept)}
+#'   \item{VDP}{Matrix of variance decomposition proportions for smallest singular value}
+#'   \item{corr.mat}{Local correlation coefficients between variable pairs}
+#' }
+#'
+#' @details
+#' Collinearity diagnostics interpretation:
+#' \itemize{
+#'   \item VIF > 10: indicates problematic collinearity
+#'   \item CN > 30: indicates severe collinearity
+#'   \item VDP: values > 0.5 for two or more variables with high CN indicate collinearity
+#' }
+#'
+#' @references
+#' Belsley, D.A., Kuh, E., and Welsch, R.E. (1980). Regression Diagnostics.
+#' New York: John Wiley & Sons.
+#'
+#' Wheeler, D. and Tiefelsdorf, M. (2005). Multicollinearity and correlation
+#' among local regression coefficients in geographically weighted regression.
+#' Journal of Geographical Systems, 7(2), 161-187.
+#'
+#' @examples
+#' data(LondonHP)
+#' diag <- gwr_collin_diag(
+#'   PURCHASE ~ FLOORSZ + UNEMPLOY + PROF,
+#'   data = LondonHP,
+#'   bw = 64,
+#'   adaptive = TRUE
+#' )
+#' print(diag)
+#'
+#' @importFrom stats model.frame model.extract model.matrix terms cov.wt
+#' @export
+gwr_collin_diag <- function(
+    formula,
+    data,
+    bw,
+    adaptive = FALSE,
+    kernel = c("bisquare", "gaussian", "exp", "tricube", "boxcar"),
+    longlat = FALSE,
+    p = 2.0,
+    theta = 0.0,
+    dMat = NULL
+) {
+    kernel <- match.arg(kernel)
+
+    ### Extract coords
+    coords <- as.matrix(sf::st_coordinates(sf::st_centroid(data)))
+    n <- nrow(coords)
+
+    ### Extract variables
+    mf <- model.frame(formula = formula(formula), data = sf::st_drop_geometry(data))
+    mt <- attr(mf, "terms")
+    y <- model.extract(mf, "response")
+    x <- model.matrix(mt, mf)
+
+    has_intercept <- attr(terms(mf), "intercept") == 1
+    indep_vars <- colnames(x)
+    indep_vars[which(indep_vars == "(Intercept)")] <- "Intercept"
+    colnames(x) <- indep_vars
+
+    var_n <- ncol(x)  # number of variables including intercept
+
+    if (var_n <= 1) {
+        stop("The number of independent variables must be larger than one")
+    }
+
+    # x1: design matrix without intercept (for VIF calculation)
+    if (has_intercept) {
+        x1 <- x[, -1, drop = FALSE]
+    } else {
+        x1 <- x
+    }
+
+    ### Compute distance matrix if not provided
+    if (is.null(dMat)) {
+        if (longlat) {
+            # Haversine formula for great circle distance
+            lon_rad <- coords[, 1] * pi / 180
+            lat_rad <- coords[, 2] * pi / 180
+
+            dMat <- matrix(0, n, n)
+            for (i in 1:(n - 1)) {
+                for (j in (i + 1):n) {
+                    dlat <- lat_rad[j] - lat_rad[i]
+                    dlon <- lon_rad[j] - lon_rad[i]
+                    a <- sin(dlat / 2)^2 + cos(lat_rad[i]) * cos(lat_rad[j]) * sin(dlon / 2)^2
+                    dMat[i, j] <- 2 * 6371 * asin(sqrt(a))  # Earth radius 6371 km
+                    dMat[j, i] <- dMat[i, j]
+                }
+            }
+        } else {
+            # Euclidean or Minkowski distance
+            if (p == 2.0 && theta == 0.0) {
+                dMat <- as.matrix(stats::dist(coords))
+            } else {
+                # Minkowski with rotation
+                coords_rot <- coords
+                if (theta != 0) {
+                    cos_t <- cos(theta)
+                    sin_t <- sin(theta)
+                    coords_rot[, 1] <- coords[, 1] * cos_t - coords[, 2] * sin_t
+                    coords_rot[, 2] <- coords[, 1] * sin_t + coords[, 2] * cos_t
+                }
+                dMat <- as.matrix(stats::dist(coords_rot, method = "minkowski", p = p))
+            }
+        }
+    }
+
+    ### Kernel weight function
+    gw_weight <- function(dist, bw, kernel, adaptive) {
+        if (adaptive) {
+            # Adaptive: bw is number of neighbors
+            bw_dist <- sort(dist)[min(bw, length(dist))]
+        } else {
+            bw_dist <- bw
+        }
+
+        w <- switch(kernel,
+            "gaussian" = exp(-0.5 * (dist / bw_dist)^2),
+            "exp" = exp(-dist / bw_dist),
+            "bisquare" = ifelse(dist <= bw_dist, (1 - (dist / bw_dist)^2)^2, 0),
+            "tricube" = ifelse(dist <= bw_dist, (1 - (dist / bw_dist)^3)^3, 0),
+            "boxcar" = ifelse(dist <= bw_dist, 1, 0)
+        )
+        return(w)
+    }
+
+    ### Initialize output matrices
+    # Correlation matrix: (var_n-1)*var_n/2 pairs
+    n_corr_pairs <- (var_n - 1) * var_n / 2
+    corr_mat <- matrix(0, nrow = n, ncol = n_corr_pairs)
+
+    # VIF matrix: var_n-1 variables (excluding intercept)
+    vifs_mat <- matrix(0, nrow = n, ncol = var_n - 1)
+
+    # Condition index: var_n values per location
+    vdp_idx <- matrix(0, nrow = n, ncol = var_n)
+
+    # VDP array: n x var_n x var_n
+    vdp_pi <- array(0, dim = c(n, var_n, var_n))
+
+    ### Compute diagnostics for each location
+    for (i in 1:n) {
+        # Get distances to location i
+        dist_vi <- dMat[, i]
+
+        # Compute weights
+        W_i <- gw_weight(dist_vi, bw, kernel, adaptive)
+
+        # Normalize weights (sum to 1) - as in GWmodel
+        sum_w <- sum(W_i)
+        Wi <- W_i / sum_w
+
+        ### Local correlations between all variable pairs
+        tag <- 0
+        for (j in 1:(var_n - 1)) {
+            for (k in (j + 1):var_n) {
+                tag <- tag + 1
+                corr_mat[i, tag] <- cov.wt(cbind(x[, j], x[, k]),
+                                           wt = Wi, cor = TRUE)$cor[1, 2]
+            }
+        }
+
+        ### VIF calculation using weighted correlation matrix (without intercept)
+        # This is the standard approach: VIF = diag(solve(R))
+        # where R is the correlation matrix
+        tryCatch({
+            corr_mati <- cov.wt(x1, wt = Wi, cor = TRUE)$cor
+            vifs_mat[i, ] <- diag(solve(corr_mati))
+        }, error = function(e) {
+            vifs_mat[i, ] <- NA
+        })
+
+        ### Variance-decomposition proportions (VDP)
+        # Following Belsley, Kuh, and Welsch (1980)
+        # 1. Weight the design matrix: X * W (element-wise by row)
+        xw <- sweep(x, 1, Wi, "*")
+
+        # 2. Column-scale to unit length: divide each column by its L2 norm
+        col_norms <- sqrt(colSums(xw^2))
+        col_norms[col_norms == 0] <- 1  # avoid division by zero
+        xw_scaled <- sweep(xw, 2, col_norms, "/")
+
+        # 3. SVD of scaled weighted design matrix
+        svd_x <- svd(xw_scaled)
+
+        # 4. Condition indices: max(d) / d[k]
+        vdp_idx[i, ] <- svd_x$d[1] / pmax(svd_x$d, 1e-10)
+
+        # 5. VDP calculation
+        # Phi = V * diag(1/d), then square and transpose
+        Phi <- svd_x$v %*% diag(1 / pmax(svd_x$d, 1e-10))
+        Phi <- t(Phi^2)
+
+        # 6. Normalize by column (prop.table by column)
+        col_sums <- colSums(Phi)
+        col_sums[col_sums == 0] <- 1
+        pi_ij <- sweep(Phi, 2, col_sums, "/")
+
+        vdp_pi[i, , ] <- pi_ij
+    }
+
+    ### Create column names for correlations
+    corr_nms <- c()
+    for (i in 1:(var_n - 1)) {
+        for (j in (i + 1):var_n) {
+            corr_nms <- c(corr_nms, paste("Corr", paste(indep_vars[i], indep_vars[j], sep = "."), sep = "_"))
+        }
+    }
+
+    ### Extract final outputs (following GWmodel convention)
+    # local_CN: the largest condition index (last column)
+    local_CN <- vdp_idx[, var_n]
+
+    # VDP: proportions for the smallest singular value (last column of each pi_ij)
+    VDP <- vdp_pi[, var_n, ]
+
+    ### Create result data frame
+    # VIF column names (without intercept)
+    vif_nms <- paste(indep_vars[-1], "VIF", sep = "_")
+
+    # VDP column names (all variables)
+    vdp_nms <- paste(indep_vars, "VDP", sep = "_")
+
+    res_df <- data.frame(
+        vifs_mat,
+        local_CN = local_CN,
+        VDP,
+        corr_mat
+    )
+    colnames(res_df) <- c(vif_nms, "local_CN", vdp_nms, corr_nms)
+
+    ### Create sf object
+    res_df$geometry <- sf::st_geometry(data)
+    SDF <- sf::st_sf(res_df)
+
+    ### Return results
+    result <- list(
+        SDF = SDF,
+        corr.mat = corr_mat,
+        VIF = vifs_mat,
+        local_CN = local_CN,
+        VDP = VDP,
+        indep_vars = indep_vars,
+        call = match.call()
+    )
+    class(result) <- "gwcollindiag"
+    result
+}
+
+#' Print GWR Collinearity Diagnostics
+#' @param x A gwcollindiag object
+#' @param ... Additional arguments
+#' @method print gwcollindiag
+#' @export
+print.gwcollindiag <- function(x, ...) {
+    cat("GWR Collinearity Diagnostics\n")
+    cat("============================\n")
+    cat("Formula:", deparse(x$call$formula), "\n")
+    cat("Variables:", paste(x$indep_vars, collapse = ", "), "\n\n")
+
+    cat("Local Condition Number (CN) Summary:\n")
+    print(summary(x$local_CN))
+    cat("\n")
+
+    cat("Local VIF Summary (excluding intercept):\n")
+    vif_summary <- apply(x$VIF, 2, summary)
+    colnames(vif_summary) <- x$indep_vars[-1]
+    print(vif_summary)
+    cat("\n")
+
+    n_high_cn <- sum(x$local_CN > 30, na.rm = TRUE)
+    n_high_vif <- sum(apply(x$VIF, 1, function(v) any(v > 10, na.rm = TRUE)), na.rm = TRUE)
+
+    cat("Diagnostic Summary:\n")
+    cat(sprintf("  Locations with CN > 30: %d (%.1f%%)\n",
+                n_high_cn, 100 * n_high_cn / length(x$local_CN)))
+    cat(sprintf("  Locations with any VIF > 10: %d (%.1f%%)\n",
+                n_high_vif, 100 * n_high_vif / length(x$local_CN)))
+
+    cat("\nLocal VDP Summary (for smallest singular value):\n")
+    vdp_summary <- apply(x$VDP, 2, summary)
+    colnames(vdp_summary) <- x$indep_vars
+    print(vdp_summary)
+}
+
+#' Plot GWR Collinearity Diagnostics
+#' @param x A gwcollindiag object
+#' @param which Which plot: "CN" for condition number, "VIF" for VIF maps, "VDP" for VDP maps
+#' @param ... Additional arguments passed to sf::plot
+#' @method plot gwcollindiag
+#' @export
+plot.gwcollindiag <- function(x, which = "CN", ...) {
+    if (which == "CN") {
+        plot(x$SDF["local_CN"], main = "Local Condition Number", ...)
+    } else if (which == "VIF") {
+        vif_cols <- grep("_VIF$", names(x$SDF), value = TRUE)
+        plot(x$SDF[vif_cols], ...)
+    } else if (which == "VDP") {
+        vdp_cols <- grep("_VDP$", names(x$SDF), value = TRUE)
+        plot(x$SDF[vdp_cols], ...)
+    }
+}