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November 19, 2018 09:07
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BCE // Vállalati Pénzügyi Információs Rendszerek // 2018
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## ############################################################################# | |
## PCA demo on image processing | |
## ############################################################################# | |
download.file('http://bit.ly/nasa-image-pca', 'image.jpg') # mode = »bw« | |
library(jpeg) | |
img <- readJPEG('image.jpg') | |
str(img) | |
dim(img) | |
h <- dim(img)[1] | |
w <- dim(img)[2] | |
img1d <- matrix(img, h * w) | |
pca <- prcomp(img1d) | |
pca | |
summary(pca) | |
image(matrix(pca$x[, 1], h)) | |
image(matrix(pca$x[, 2], h)) | |
image(matrix(pca$x[, 2], h), col = gray.colors(100)) | |
image(matrix(pca$x[, 3], h)) | |
## ############################################################################# | |
## MDS | |
## ############################################################################# | |
download.file('http://bit.ly/hun-cities-distance', 'cities.xls') # mode = »bw« | |
library(readxl) | |
cities <- read_excel('cities .xls') | |
## get rid of 1st column and last row (metadata) | |
cities <- cities[, -1] | |
cities <- cities[-nrow(cities), ] | |
mds <- cmdscale(as.dist(cities)) | |
plot(mds) | |
text(mds[, 1], mds[, 2], tail(names(cities), -1)) | |
mds <- -mds | |
plot(mds) | |
text(mds[, 1], mds[, 2], tail(names(cities), -1)) | |
mds <- cmdscale(dist(mtcars)) | |
plot(mds) | |
text(mds[, 1], mds[, 2], rownames(mtcars)) | |
mds <- as.data.frame(mds) | |
library(ggplot2) # start with geom_point | |
ggplot(mds, aes(V1, -V2, label = rownames(mtcars))) + geom_text() | |
library(ggrepel) | |
ggplot(mds, aes(V1, -V2, label = rownames(mtcars))) + geom_text_repel() | |
## ############################################################################# | |
## feature selection | |
## ############################################################################# | |
str(iris) | |
plot(iris$Sepal.Length, iris$Sepal.Width) | |
fit <- lm(Sepal.Width ~ Sepal.Length, data = iris) | |
fit | |
summary(fit) | |
plot(iris$Sepal.Length, iris$Sepal.Width) | |
abline(fit, col = 'red', lwd = 5) | |
## now try | |
plot(iris$Sepal.Length, iris$Sepal.Width, col = iris$Species) | |
summary(lm(Sepal.Width ~ Sepal.Length + Species, data = iris)) | |
ggplot(iris, aes(Sepal.Length, Sepal.Width, col = Species)) + | |
geom_point() + geom_smooth(method = 'lm') | |
ggplot(iris, aes(Sepal.Length, Sepal.Width)) + | |
geom_point(aes(col = Species)) + | |
geom_smooth(aes(col = Species), method = 'lm') + | |
geom_smooth(method = 'lm', col = 'black') + theme_bw() | |
## ############################################################################# | |
## PCA demo to show the steps in hierarchical clustering | |
## ############################################################################# | |
prcomp(iris[, 1:4]) | |
PC <- prcomp(iris[, 1:4])$x | |
dm <- dist(iris[, 1:4]) | |
hc <- hclust(dm) | |
plot(hc) | |
for (i in 2:8) { | |
plot(hc) | |
rect.hclust(hc, k = i, border = 'red') | |
Sys.sleep(1) | |
} | |
library(animation) | |
ani.options(interval = 1) | |
saveGIF({ | |
for (i in 2:8) { | |
plot(hc) | |
rect.hclust(hc, k = i, border = 'red') | |
} | |
}) | |
library(animation) | |
ani.options(interval = 1) | |
saveGIF({ | |
for (i in 1:8) { | |
plot(-PC[, 1:2], col = cutree(hc, i), pch = as.numeric(factor(iris$Species)) + 5) | |
} | |
}) | |
## ############################################################################# | |
## basic decision tress | |
## ############################################################################# | |
rm(iris) | |
set.seed(100) | |
mysample <- sample(1:150, 100) | |
str(mysample) | |
train <- iris[mysample, ] | |
test <- iris[setdiff(1:150, mysample), ] | |
library(rpart) | |
ct <- rpart(Species ~ ., data = train) | |
summary(ct) | |
plot(ct); text(ct) | |
library(partykit) | |
plot(as.party(ct)) | |
predict(ct, newdata = test) | |
predict(ct, newdata = test, type = 'class') | |
## confusion matrix | |
table(test$Species, | |
predict(ct, newdata = test, | |
type = 'class')) | |
ct <- rpart(Species ~ ., data = train, | |
minsplit = 1, cp = 0.001) | |
## ?rpart.control | |
plot(ct); text(ct) | |
plot(as.party(ct)) | |
table(test$Species, | |
predict(ct, newdata = test, | |
type = 'class')) | |
## back to slides on high level overview on bagging, random forest, gbm etc | |
## ############################################################################# | |
## H2O | |
## ############################################################################# | |
## start and connect to H2O | |
library(h2o) | |
h2o.init() | |
## in a browser check http://localhost:54321 | |
rpart() | |
h2o.randomForest() | |
## demo data | |
library(hflights) | |
rm(hflights) | |
str(hflights) | |
## copy to H2O | |
hflights.hex <- as.h2o(hflights, 'hflights') | |
str(hflights.hex) | |
str(head(hflights.hex)) | |
head(hflights.hex, 3) | |
summary(hflights.hex) | |
## check flight number: numeric? | |
## check on H2O web interface as well (enum vs factor) | |
## convert numeric to factor/enum | |
hflights.hex[, 'FlightNum'] <- as.factor(hflights.hex[, 'FlightNum']) | |
summary(hflights.hex) | |
## boring | |
for (v in c('Month', 'DayofMonth', 'DayOfWeek', 'DepTime', 'ArrTime', 'Cancelled')) { | |
hflights.hex[, v] <- as.factor(hflights.hex[, v]) | |
} | |
summary(hflights.hex) | |
## feature engineering: departure time? is it OK? hour of the day? | |
## redo everything... just use the R script | |
library(data.table) | |
hflights <- data.table(hflights) | |
hflights[, hour := substr(DepTime, 1, 2)] | |
hflights[, .N, by = hour] | |
hflights[, hour := substr(DepTime, 1, nchar(DepTime) - 2)] | |
hflights[, .N, by = hour][order(hour)] | |
hflights[hour == ''] | |
hflights[, hour := cut(as.numeric(hour), seq(0, 24, 4))] | |
hflights[, .N, by = hour] | |
hflights[is.na(hour)] | |
hflights[, .N, by = .(is.na(hour), Cancelled == 1)] | |
## drop columns | |
hflights <- hflights[, .(Month, DayofMonth, DayOfWeek, Dest, Origin, | |
UniqueCarrier, FlightNum, TailNum, Distance, | |
Cancelled = factor(Cancelled))] | |
## re-upload to H2O | |
h2o.ls() | |
hflights.hex <- as.h2o(as.data.frame(hflights), 'hflights') | |
## split the data | |
h2o.splitFrame(data = hflights.hex , ratios = 0.75, | |
destination_frames = paste0('hflights', 0:1)) | |
h2o.ls() | |
## build the first model | |
hflights.rf <- h2o.randomForest( | |
model_id = 'hflights_rf', | |
x = setdiff(names(hflights), 'Cancelled'), | |
y = 'Cancelled', | |
training_frame = 'hflights0', | |
validation_frame = 'hflights1') | |
hflights.rf | |
## more trees | |
hflights.rf <- h2o.randomForest( | |
model_id = 'hflights_rf500', | |
x = setdiff(names(hflights), 'Cancelled'), | |
y = 'Cancelled', | |
training_frame = 'hflights0', | |
validation_frame = 'hflights1', ntrees = 500) | |
## change to UI and check ROC curve & AUC | |
## GBM | |
hflights.gbm <- h2o.gbm( | |
x = setdiff(names(hflights), 'Cancelled'), | |
y = 'Cancelled', | |
training_frame = 'hflights0', | |
validation_frame = 'hflights1', | |
model_id = 'hflights_gbm') | |
## more trees should help, again !!! | |
hflights.gbm <- h2o.gbm( | |
x = setdiff(names(hflights), 'Cancelled'), | |
y = 'Cancelled', | |
training_frame = 'hflights0', | |
validation_frame = 'hflights1', | |
model_id = 'hflights_gbm2', ntrees = 550) | |
## but no: although higher training AUC, lower validation AUC => overfit | |
## more trees should help, again !!! | |
hflights.gbm <- h2o.gbm( | |
x = setdiff(names(hflights), 'Cancelled'), | |
y = 'Cancelled', | |
training_frame = 'hflights_part0', | |
validation_frame = 'hflights_part1', | |
model_id = 'hflights_gbm2', ntrees = 250, learn_rate = 0.01) | |
## bye | |
h2o.shutdown() |
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