Future unit tests for SFCB
SFCB method
load("PATHTO/sensiClim/data/simulated_1.rda")
out1 <- sfcb(x, Y, group.method = "adjclust", summary.method = "pls")
out2 <- sfcb(x, Y, group.method = "cclustofvar", summary.method = "cclustofvar")
out3 <- sfcb(x, Y, group.method = "cclustofvar", summary.method = "basics")
out4 <- sfcb(x, Y, group.method = "adjclust", summary.method = "pls", range.at = c(5, 7))
out5 <- sfcb(x, Y, group.method = "cclustofvar", summary.method = "cclustofvar", range.at = c(5, 7))
out6 <- sfcb(x, Y, group.method = "adjclust", summary.method = "basics", range.at = c(5, 7))
out7 <- sfcb(x, Y, group.method = "adjclust", summary.method = "pls", selection.method = "relief")
out8 <- sfcb(x, Y, group.method = "adjclust", summary.method = "pls", selection.method = "relief", range.at = c(5, 7))
out9 <- sfcb(x, Y, group.method = "adjclust", summary.method = "basics", selection.method = "relief")
out10 <- sfcb(x, Y, group.method = "adjclust", summary.method = "pls", selection.method = "boruta", seed = 3)
out11 <- sfcb(x, Y, group.method = "adjclust", summary.method = "basics", selection.method = "relief", range.at = c(5, 7))
out12 <- sfcb(x, Y, group.method = "adjclust", summary.method = "pls", selection.method = "relief", range.at = c(5, 12))
Plot SFCB results
Importance
plot(out1, plot.type = "importance")
plot(out1, plot.type = "importance", shape.imp = "histogram")
plot(out8, plot.type = "importance")
plot(out8, plot.type = "importance", shape.imp = "histogram")
plot(out3, plot.type = "importance")
plot(out3, plot.type = "importance", shape.imp = "histogram")
plot(out6, plot.type = "importance")
plot(out6, plot.type = "importance", shape.imp = "histogram")
plot(out11, plot.type = "importance")
plot(out11, plot.type = "importance", shape.imp = "histogram")
Selection
(also test check of options)
plot(out1, plot.type = "selection")
plot(out7, plot.type = "selection")
plot(out8, plot.type = "selection")
plot(out3, plot.type = "selection")
plot(out6, plot.type = "selection")
plot(out7, plot.type = "selection", sel.type = "selection")
plot(out9, plot.type = "selection", sel.type = "selection")
plot(out8, plot.type = "selection", sel.type = "selection")
plot(out11, plot.type = "selection", sel.type = "selection")
plot(out1, plot.type = "selection", sel.type = "selection", threshold = 0.00011)
plot(out4, plot.type = "selection", sel.type = "selection", threshold = 0.02)
plot(out3, plot.type = "selection", sel.type = "selection", threshold = 0.0015)
plot(out6, plot.type = "selection", sel.type = "selection", threshold = 0.005)
Dendrograms
plot(out1)
plot(out2)
plot(out3)
plot(out4)
plot(out5)
plot(out6)
plot(out7)
plot(out8)
plot(out9)
plot(out10)
plot(out11)
plot(out12)
Extract SFCB results
extract_at(out4, c(5, 7))
extract_at(out5, 6)
extract_at(out6, 5:6)
out13 <- extract_at(out8, 6)
plot(out13, plot.type = "importance")
plot(extract_at(out11, 5:6), plot.type = "selection")
out14 <- extract_at(out12, c(9, 11:12))
plot(out14)
Qualities
out1b <- quality(out1, beta, threshold = 0.001)
quality(out3, beta, threshold = 0.001)
out4b <- quality(out4, beta, threshold = 0.001)
quality(out6, beta, threshold = 0.01)
quality(out7, beta)
quality(out8, beta)
quality(out9, beta)
quality(out11, beta)
quality(out12, beta)
quality(out14, beta)
out14b <- quality(out14, beta, threshold = 0.01)
Quality plots
plot(out1b, plot.type = "quality", quality.crit = "mse")
plot(out1b, plot.type = "quality", quality.crit = "time")
plot(out1b, plot.type = "quality", quality.crit = c("mse", "time"))
plot(out1b, plot.type = "quality", quality.crit = "ARI")
plot(out1b, plot.type = "quality", quality.crit = "NMI")
plot(out1b, plot.type = "quality", quality.crit = c("mse", "NMI"))
plot(out1b, plot.type = "quality", quality.crit = c("Precision", "Recall"))
plot(out4b, plot.type = "quality", quality.crit = "mse")
plot(out4b, plot.type = "quality", quality.crit = "time")
plot(out4b, plot.type = "quality", quality.crit = "NMI")
plot(out4b, plot.type = "quality", quality.crit = c("mse", "ARI"))
plot(out4b, plot.type = "quality", quality.crit = c("Precision", "Recall"))
plot(out14b, plot.type = "quality", quality.crit = "mse")
plot(out14b, plot.type = "quality", quality.crit = "time")
plot(out14b, plot.type = "quality", quality.crit = "ARI")
plot(out14b, plot.type = "quality", quality.crit = c("mse", "NMI"))
plot(out14b, plot.type = "quality", quality.crit = c("Precision", "Recall"))