diff options
| -rw-r--r-- | tests.R | 137 |
1 files changed, 99 insertions, 38 deletions
@@ -4,14 +4,34 @@ require(mp) source("measures.R") -automated.m <- function(D, labels) { - D.m <- D +#automated.m <- function(D, labels) { +# D.m <- D +# for (label in unique(labels)) { +# same.label <- labels == label +# D.m[same.label, same.label] <- D[same.label, same.label] * 0.1 +# } +# +# D.m +#} +automated.m <- function(Xs, labels) { + n <- nrow(Xs) + p <- ncol(Xs) + Xs <- cbind(Xs, matrix(data=0, nrow=n, ncol=p)) for (label in unique(labels)) { - same.label <- labels == label - D.m[same.label, same.label] <- D[same.label, same.label] * 0.1 + for (j in 1:p) { + Xs[labels == label, j + p] <- mean(Xs[labels == label, j]) + } } - D.m + dist(Xs) +} + +color_scale.blue_orange <- function(name) { + scale_colour_gradient(name = name, high = "#376092", low = "#e46c0a", space = "Lab") +} + +color_scale.gradient2 <- function(name) { + scale_colour_gradient2(name = name, mid = "#dddddd", space = "Lab") } test <- function(file, suffix, output.dir) { @@ -62,6 +82,12 @@ test <- function(file, suffix, output.dir) { precision <- klDivergence(Q, P) recall <- klDivergence(P, Q) + measures <- rbind(data.frame(mean=mean(np), median=median(np), sd=sd(np)), + data.frame(mean=mean(silh), median=median(silh), sd=sd(silh)), + data.frame(mean=mean(precision), median=median(precision), sd=sd(precision)), + data.frame(mean=mean(recall), median=median(recall), sd=sd(recall))) + write.table(measures, paste(output.dir, suffix, "-measures.csv", sep=""), row.names=F) + if (!(all(is.finite(np)) && all(is.finite(silh)) && all(is.finite(precision)) && @@ -71,48 +97,59 @@ test <- function(file, suffix, output.dir) { # Plot results message("\tPlotting results") - color_scale <- scale_colour_gradient(high = "#376092", low = "#e46c0a", space = "Lab") - shape_scale <- scale_shape_manual(values = 1:nlevels(classes)) + shape_scale <- scale_shape_manual(name = "Classe", values = 1:nlevels(classes)) Ys <- cbind(as.data.frame(Ys), classes.s) Y <- cbind(as.data.frame(Y), classes, np, silh, precision, recall) p.s <- ggplot(Ys) + theme_bw() + labs(x = "", y = "") + geom_point(aes(x = V1, y = V2, shape = classes.s, colour = classes.s)) + - shape_scale + shape_scale + scale_color_manual(name = "Classe", values = 1:nlevels(classes)) + ggsave(paste(output.dir, "subsample-", suffix, ".pdf", sep=""), p.s, width=5, height=5) + p <- ggplot(Y) + theme_bw() + labs(x = "", y = "") + geom_point(aes(x = V1, y = V2, shape = classes, colour = classes)) + - shape_scale + shape_scale + scale_color_manual(name = "Classe", values = 1:nlevels(classes)) + ggsave(paste(output.dir, suffix, ".pdf", sep=""), p, width=5, height=5) + p.np <- ggplot(Y) + theme_bw() + - labs(x = "", y = "", title = "NP (9)") + + labs(x = "", y = "") + geom_point(aes(x = V1, y = V2, shape = classes, colour = np)) + - shape_scale + color_scale + shape_scale + color_scale.blue_orange("NP") + ggsave(paste(output.dir, "np-", suffix, ".pdf", sep=""), p.np, width=5, height=5) + p.silh <- ggplot(Y) + theme_bw() + - labs(x = "", y = "", title = "Silhouette") + + labs(x = "", y = "") + geom_point(aes(x = V1, y = V2, shape = classes, colour = silh)) + - shape_scale + color_scale + shape_scale + color_scale.blue_orange("Silhueta") + ggsave(paste(output.dir, "silh-", suffix, ".pdf", sep=""), p.silh, width=5, height=5) + p.precision <- ggplot(Y) + theme_bw() + - labs(x = "", y = "", title = "Precision") + + labs(x = "", y = "") + geom_point(aes(x = V1, y = V2, shape = classes, colour = precision)) + - shape_scale + color_scale + shape_scale + color_scale.blue_orange("Precisão") + ggsave(paste(output.dir, "precision-", suffix, ".pdf", sep=""), p.precision, width=5, height=5) + p.recall <- ggplot(Y) + theme_bw() + - labs(x = "", y = "", title = "Recall") + + labs(x = "", y = "") + geom_point(aes(x = V1, y = V2, shape = classes, colour = recall)) + - shape_scale + color_scale + shape_scale + color_scale.blue_orange("Revocação") + ggsave(paste(output.dir, "recall-", suffix, ".pdf", sep=""), p.recall, width=5, height=5) + - pdf(paste(output.dir, "original-", suffix, ".pdf", sep=""), width = 12, height = 16) + pdf(paste(output.dir, "all-", 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]) + Dx.m <- automated.m(X[sample.indices, ], labels[sample.indices]) Ys.m <- forceScheme(Dx.m, Ys[, 1:2]) # LAMP @@ -135,6 +172,12 @@ test <- function(file, suffix, output.dir) { precision <- klDivergence(Q, P) - precision recall <- klDivergence(P, Q) - recall + measures <- rbind(data.frame(mean=mean(np), median=median(np), sd=sd(np)), + data.frame(mean=mean(silh), median=median(silh), sd=sd(silh)), + data.frame(mean=mean(precision), median=median(precision), sd=sd(precision)), + data.frame(mean=mean(recall), median=median(recall), sd=sd(recall))) + write.table(measures, paste(output.dir, suffix, "-manip-measures.csv", sep=""), row.names=F) + if (!(all(is.finite(np)) && all(is.finite(silh)) && all(is.finite(precision)) && @@ -144,46 +187,64 @@ test <- function(file, suffix, output.dir) { # 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, silh, precision, recall) - p.s <- ggplot(Ys.m) + + pm.s <- ggplot(Ys.m) + theme_bw() + labs(x = "", y = "") + geom_point(aes(x = V1, y = V2, shape = classes.s, colour = classes.s)) + - shape_scale - p <- ggplot(Y.m) + + shape_scale + scale_color_manual(name = "Classe", values = 1:nlevels(classes)) + ggsave(paste(output.dir, "manip-subsample-", suffix, ".pdf", sep=""), pm.s, width=5, height=5) + + pm <- ggplot(Y.m) + theme_bw() + labs(x = "", y = "") + geom_point(aes(x = V1, y = V2, shape = classes, colour = classes)) + - shape_scale + shape_scale + scale_color_manual(name = "Classe", values = 1:nlevels(classes)) + ggsave(paste(output.dir, "manip-", suffix, ".pdf", sep=""), pm, width=5, height=5) + p.np <- ggplot(Y.m) + theme_bw() + - labs(x = "", y = "", title = "NP (9)") + + labs(x = "", y = "") + geom_point(aes(x = V1, y = V2, shape = classes, colour = np)) + - shape_scale + color_scale + shape_scale + color_scale.gradient2("NP") + ggsave(paste(output.dir, "manip-np-", suffix, ".pdf", sep=""), p.np, width=5, height=5) + p.silh <- ggplot(Y.m) + theme_bw() + - labs(x = "", y = "", title = "Silhouette") + + labs(x = "", y = "") + geom_point(aes(x = V1, y = V2, shape = classes, colour = silh)) + - shape_scale + color_scale + shape_scale + color_scale.gradient2("Silhueta") + ggsave(paste(output.dir, "manip-silh-", suffix, ".pdf", sep=""), p.silh, width=5, height=5) + p.precision <- ggplot(Y.m) + theme_bw() + - labs(x = "", y = "", title = "Precision") + + labs(x = "", y = "") + geom_point(aes(x = V1, y = V2, shape = classes, colour = precision)) + - shape_scale + color_scale + shape_scale + color_scale.gradient2("Precisão") + ggsave(paste(output.dir, "manip-precision-", suffix, ".pdf", sep=""), p.precision, width=5, height=5) + p.recall <- ggplot(Y.m) + theme_bw() + - labs(x = "", y = "", title = "Recall") + + labs(x = "", y = "") + geom_point(aes(x = V1, y = V2, shape = classes, colour = recall)) + - shape_scale + color_scale + shape_scale + color_scale.gradient2("Revocação") + ggsave(paste(output.dir, "manip-recall-", suffix, ".pdf", sep=""), p.recall, width=5, height=5) + + pdf(paste(output.dir, "original-manip-", suffix, ".pdf", sep=""), width = 10, height = 8) + grid.arrange(p.s, p, pm.s, pm, ncol = 2) + dev.off() + + pdf(paste(output.dir, "manip-measures-", suffix, ".pdf", sep=""), width = 10, height = 8) + grid.arrange(p.np, p.silh, p.precision, p.recall, ncol = 2) + dev.off() - 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) + pdf(paste(output.dir, "manip-all-", suffix, ".pdf", sep=""), width = 12, height = 16) + grid.arrange(pm.s, pm, p.np, p.silh, p.precision, p.recall, ncol = 2) dev.off() } -test(file = "datasets/iris-std.tbl", suffix = "iris", "plots/") -test(file = "datasets/wdbc.tbl", suffix = "wdbc", "plots/") -test(file = "datasets/segmentation.tbl", suffix = "segmentation", "plots/") -test(file = "datasets/images.tbl", suffix = "images", "plots/") +#test(file = "datasets/iris.tbl", suffix = "iris", "tests/") +test(file = "datasets/wdbc.tbl", suffix = "wdbc", "tests/") +test(file = "datasets/segmentation.tbl", suffix = "segmentation", "tests/") +test(file = "datasets/glass.tbl", suffix = "glass", "tests/") |