R/graph.rbf.R

In amsantac/geospt: Geostatistical Analysis and Design of Optimal Spatial Sampling Networks

assign("graph.rbf",
       function (formula, data, eta.opt, rho.opt, n.neigh, func, np, 
                 x0 = c(0.5, 0.5), eta.dmax, rho.dmax, P.T = NULL, iter, ...) 
       {
         if (!is.logical(P.T) & !is.null(P.T)) 
           stop(paste("P.T must be logical or null"))
         if (!is.logical(eta.opt)) 
           stop(paste("eta.opt must be logical"))
         if (!is.logical(rho.opt)) 
           stop(paste("rho.opt must be logical"))
         if (eta.opt == TRUE & rho.opt == FALSE) {
           Opt <- optimize(rbf.cv, c(1e-25, eta.dmax), formula = formula, 
                           data = data, rho = 0, n.neigh = n.neigh, func = func, 
                           ...)
           Datos <- as.data.frame(matrix(NA, nrow = length(seq(1e-25, 
                                                               eta.dmax, length.out = np)), ncol = 2))
           eta <- seq(1e-25, eta.dmax, length.out = np)
           colnames(Datos) <- c("P", "RMSPE")
           pb <- txtProgressBar(min = 0, max = np, char = "=", style = 3)
           for (i in 1:np) {
             Datos[i, 1] <- eta[i]
             Datos[i, 2] <- rbf.cv(formula, data, eta[i], rho = 0, 
                                   n.neigh, func)
             setTxtProgressBar(pb, i)
           }
           close(pb)
           Table0 <- rbind(Datos, c(Opt$minimum, Opt$objective))
           orden <- order(Table0$P)
           Table <- Table0[orden, ]
           plot(Table, lty = 3, ylab = "RMSPE", col = 3, xlab = "ETA", 
                type = "l")
           Optim <- Table[which.min(Table[, 2]), ]
           ifelse(P.T == TRUE, list(print(Table), cat("Optimal eta RBF: ", 
                                                      func, "\n", "ETA  = ", Optim$P, "\n", "RMSPE   = ", 
                                                      Optim$RMSPE, "\n")), list(cat("Optimal eta RBF: ", 
                                                                                    func, "\n", "ETA  = ", Optim$P, "\n", "RMSPE   = ", 
                                                                                    Optim$RMSPE, "\n")))
         }
         if (rho.opt == TRUE & eta.opt == FALSE) {
           Opt <- optimize(rbf.cv, c(1e-25, rho.dmax), formula = formula, 
                           data = data, eta = 1e-25, n.neigh = n.neigh, func = func, 
                           ...)
           Datos <- as.data.frame(matrix(NA, nrow = length(seq(1e-25, 
                                                               rho.dmax, length.out = np)), ncol = 2))
           rho <- seq(1e-25, rho.dmax, length.out = np)
           colnames(Datos) <- c("P", "RMSPE")
           pb <- txtProgressBar(min = 0, max = np, char = "=", style = 3)
           for (i in 1:np) {
             Datos[i, 1] <- rho[i]
             Datos[i, 2] <- rbf.cv(formula, data, eta = 0, rho[i], 
                                   n.neigh, func)
             setTxtProgressBar(pb, i)
           }
           close(pb)
           Table0 <- rbind(Datos, c(Opt$minimum, Opt$objective))
           orden <- order(Table0$P)
           Table <- Table0[orden, ]
           plot(Table, lty = 3, ylab = "RMSPE", col = 3, xlab = "RHO", 
                type = "l")
           Optim <- Table[which.min(Table[, 2]), ]
           ifelse(P.T == TRUE, list(print(Table), cat("Optimal eta RBF: ", 
                                                      func, "\n", "RHO  = ", Optim$P, "\n", "RMSPE   = ", 
                                                      Optim$RMSPE, "\n")), list(cat("Optimal eta RBF: ", 
                                                                                    func, "\n", "RHO  = ", Optim$P, "\n", "RMSPE   = ", 
                                                                                    Optim$RMSPE, "\n")))
         }
         if (eta.opt == FALSE & rho.opt == FALSE) {
           eta <- seq(1e-25, eta.dmax, length.out = np)
           rho <- seq(1e-25, rho.dmax, length.out = np)
           grid.opt <- expand.grid(eta = eta, rho = rho)
           grid.rmspe <- as.data.frame(matrix(NA, nrow = nrow(grid.opt), 
                                              ncol = 3))
           colnames(grid.rmspe) <- c("eta", "rho", "rmspe")
           pb <- txtProgressBar(min = 0, max = nrow(grid.opt), char = "=", 
                                style = 3)
           for (i in 1:nrow(grid.opt)) {
             grid.rmspe[i, 3] <- rbf.cv(formula, data, eta = grid.opt[i, 
                                                                      1], rho = grid.opt[i, 2], n.neigh, func)
             grid.rmspe[, 1:2] <- grid.opt
             grid.rmspe
             setTxtProgressBar(pb, i)
           }
           close(pb)
           coordinates(grid.rmspe) = c("eta", "rho")
           opt.table <- data.frame(coordinates(grid.rmspe), grid.rmspe@data)[which.min(data.frame(coordinates(grid.rmspe), 
                                                                                                  grid.rmspe@data)[, 3]), ]
           gridded(grid.rmspe) <- TRUE
           p <- spplot(grid.rmspe, "rmspe", col.regions = heat.colors(100), 
                       cuts = 60, cex.main = 0.2, scales = list(draw = TRUE), 
                       xlab = expression(eta), ylab = expression(rho), key.space = list(space = "right", 
                                                                                        cex = 0.6))
           list(opt.table = opt.table, spplot = p)
         }
         else if (eta.opt == TRUE & rho.opt == TRUE) {
           Opt <- bobyqa(x0, rbf.cv1, lower = c(1e-25, 0), upper = c(eta.dmax, 
                                                                     rho.dmax), formula = formula, data = data, n.neigh = n.neigh, 
                         func = func, control = list(maxfun = iter), ...)
           cat("Optimal eta RBF: ", func, "\n", "ETA  = ", Opt$par[1], 
               "RHO  = ", Opt$par[2], "\n", "RMSPE   = ", Opt$fval, 
               "\n")
           list(Opt = Opt)
         }
       }
)