diff options
Diffstat (limited to 'tests.R')
| -rw-r--r-- | tests.R | 76 |
1 files changed, 51 insertions, 25 deletions
@@ -15,7 +15,7 @@ automated.m <- function(D, labels) { } test <- function(file, suffix, output.dir) { - message("Testing dataset ", file) + message("Testing dataset: ", file) dataset <- read.table(file) # Extract labels @@ -51,23 +51,30 @@ test <- function(file, suffix, output.dir) { Dy <- as.matrix(Dy) message("\tCalculating P and Q") - sigmas <- vector("numeric", n) - sigmas[] <- 1 - P <- d2p(Dx, sigmas) - Q <- d2p(Dy, sigmas) + prob <- d2p(Dx^2) + P <- prob$P + Q <- d2p.beta(Dy^2, prob$beta) # Calculate measures message("\tCalculating measures") np <- NP(Dx, Dy) + silh <- silhouette(Dy, classes) precision <- klDivergence(Q, P) recall <- klDivergence(P, Q) + if (!(all(is.finite(np)) && + all(is.finite(silh)) && + all(is.finite(precision)) && + all(is.finite(recall)))) { + stop("Non-finite measures found") + } + # Plot results - #color_scale <- scale_colour_gradientn(colours = c("#e46c0a", "#dddddd", "#376092")) - color_scale <- scale_colour_gradient2(mid = "#dddddd", space = "Lab") - shape_scale <- scale_shape(solid = FALSE) + message("\tPlotting results") + color_scale <- scale_colour_gradient(high = "#376092", low = "#e46c0a", space = "Lab") + shape_scale <- scale_shape_manual(values = 1:nlevels(classes)) Ys <- cbind(as.data.frame(Ys), classes.s) - Y <- cbind(as.data.frame(Y), classes, np, precision, recall) + Y <- cbind(as.data.frame(Y), classes, np, silh, precision, recall) p.s <- ggplot(Ys) + theme_bw() + labs(x = "", y = "") + @@ -83,6 +90,11 @@ test <- function(file, suffix, output.dir) { labs(x = "", y = "", title = "NP (9)") + geom_point(aes(x = V1, y = V2, shape = classes, colour = np)) + shape_scale + color_scale + p.silh <- ggplot(Y) + + theme_bw() + + labs(x = "", y = "", title = "Silhouette") + + geom_point(aes(x = V1, y = V2, shape = classes, colour = silh)) + + shape_scale + color_scale p.precision <- ggplot(Y) + theme_bw() + labs(x = "", y = "", title = "Precision") + @@ -94,14 +106,14 @@ test <- function(file, suffix, output.dir) { geom_point(aes(x = V1, y = V2, shape = classes, colour = recall)) + shape_scale + color_scale - pdf(paste(output.dir, "original-", suffix, ".pdf", sep=""), width = 16, height = 8) - grid.arrange(p.s, p, p.np, p.precision, p.recall, ncol=3) + pdf(paste(output.dir, "original-", suffix, ".pdf", sep=""), width = 12, height = 16) + grid.arrange(p.s, p, p.np, p.silh, p.precision, p.recall, ncol = 2) dev.off() # Perform manipulation message("\tCalculating Ys.m") Dx.m <- automated.m(Dx.s, labels[sample.indices]) - Ys.m <- forceScheme(Dx.m) + Ys.m <- forceScheme(Dx.m, Ys[, 1:2]) # LAMP message("\tCalculating Y.m") @@ -114,46 +126,60 @@ test <- function(file, suffix, output.dir) { Dy <- as.matrix(Dy) message("\tCalculating Q") - Q <- d2p(Dy, sigmas) + Q <- d2p.beta(Dy^2, prob$beta) # Calculate measures message("\tCalculating measures") - np <- np - NP(Dx, Dy) - precision <- precision - klDivergence(Q, P) - recall <- recall - klDivergence(P, Q) + np <- NP(Dx, Dy) - np + silh <- silhouette(Dy, classes) - silh + precision <- klDivergence(Q, P) - precision + recall <- klDivergence(P, Q) - recall + + if (!(all(is.finite(np)) && + all(is.finite(silh)) && + all(is.finite(precision)) && + all(is.finite(recall)))) { + stop("Non-finite measures found") + } # Plot results + message("\tPlotting results") + color_scale <- scale_colour_gradient2(mid = "#dddddd", space = "Lab") Ys.m <- cbind(as.data.frame(Ys.m), classes.s) - Y.m <- cbind(as.data.frame(Y.m), classes, np, precision, recall) - p.s <- ggplot(cbind(Ys.m, classes.s)) + + Y.m <- cbind(as.data.frame(Y.m), classes, np, silh, precision, recall) + p.s <- ggplot(Ys.m) + theme_bw() + labs(x = "", y = "") + geom_point(aes(x = V1, y = V2, shape = classes.s, colour = classes.s)) + - scale_shape_identity() + shape_scale - p <- ggplot(cbind(Y.m, classes)) + + p <- ggplot(Y.m) + theme_bw() + labs(x = "", y = "") + geom_point(aes(x = V1, y = V2, shape = classes, colour = classes)) + shape_scale - p.np <- ggplot(cbind(Y.m, np)) + + p.np <- ggplot(Y.m) + theme_bw() + labs(x = "", y = "", title = "NP (9)") + geom_point(aes(x = V1, y = V2, shape = classes, colour = np)) + shape_scale + color_scale - p.precision <- ggplot(cbind(Y.m, precision)) + + p.silh <- ggplot(Y.m) + + theme_bw() + + labs(x = "", y = "", title = "Silhouette") + + geom_point(aes(x = V1, y = V2, shape = classes, colour = silh)) + + shape_scale + color_scale + p.precision <- ggplot(Y.m) + theme_bw() + labs(x = "", y = "", title = "Precision") + geom_point(aes(x = V1, y = V2, shape = classes, colour = precision)) + shape_scale + color_scale - p.recall <- ggplot(cbind(Y.m, recall)) + + p.recall <- ggplot(Y.m) + theme_bw() + labs(x = "", y = "", title = "Recall") + geom_point(aes(x = V1, y = V2, shape = classes, colour = recall)) + shape_scale + color_scale - pdf(paste(output.dir, "manip-", suffix, ".pdf", sep=""), width = 16, height = 8) - grid.arrange(p.s, p, p.np, p.precision, p.recall, ncol=3) + pdf(paste(output.dir, "manip-", suffix, ".pdf", sep=""), width = 12, height = 16) + grid.arrange(p.s, p, p.np, p.silh, p.precision, p.recall, ncol = 2) dev.off() } |