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Cleaned up item clustering; works well now

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This commit is contained in:
Nora Wickelmaier 2024-03-08 18:05:40 +01:00
parent 66fab4fa18
commit 26ba7265f5
1 changed files with 70 additions and 74 deletions
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114
code/07_item-clustering.R
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@ -10,13 +10,14 @@
# input: results/haum/eventlogs_pre-corona_cleaned.RData # input: results/haum/eventlogs_pre-corona_cleaned.RData
# results/haum/pn_infos_items.csv # results/haum/pn_infos_items.csv
# output: results/haum/eventlogs_pre-corona_item-clusters.csv # output: results/haum/eventlogs_pre-corona_item-clusters.csv
# results/figures/clustering_artworks.pdf
# results/figures/clustering_artworks.png
# #
# last mod: 2024-03-06 # last mod: 2024-03-08
# setwd("C:/Users/nwickelmaier/Nextcloud/Documents/MDS/2023ss/60100_master_thesis/analysis/code") # setwd("C:/Users/nwickelmaier/Nextcloud/Documents/MDS/2023ss/60100_master_thesis/analysis/code")
library(bupaverse) source("R_helpers.R")
library(factoextra)
#--------------- (1) Read data --------------- #--------------- (1) Read data ---------------
@ -31,17 +32,6 @@ datitem <- read.table("results/haum/pn_infos_items.csv", header = TRUE,
#--------------- (1.3) Extract additional infos for clustering --------------- #--------------- (1.3) Extract additional infos for clustering ---------------
time_minmax_ms <- function(subdata) {
subdata$min_time <- min(subdata$timeMs.start)
if (all(is.na(subdata$timeMs.stop))) {
subdata$max_time <- NA
} else {
subdata$max_time <- max(subdata$timeMs.stop, na.rm = TRUE)
}
subdata
}
# TODO: Move to helper file
# Get average duration per path # Get average duration per path
dat_split <- split(dat, ~ path) dat_split <- split(dat, ~ path)
dat_list <- pbapply::pblapply(dat_split, time_minmax_ms) dat_list <- pbapply::pblapply(dat_split, time_minmax_ms)
@ -63,11 +53,14 @@ datitem$nflipCard <- aggregate(event ~ item, dat, table)$event[,"flipCard"]
datitem$nopenTopic <- aggregate(event ~ item, dat, table)$event[,"openTopic"] datitem$nopenTopic <- aggregate(event ~ item, dat, table)$event[,"openTopic"]
datitem$nopenPopup <- aggregate(event ~ item, dat, table)$event[,"openPopup"] datitem$nopenPopup <- aggregate(event ~ item, dat, table)$event[,"openPopup"]
rm(datpath)
#--------------- (2) Clustering --------------- #--------------- (2) Clustering ---------------
df <- datitem[, c("precision", "generalizability", "nvariants", "duration", df <- datitem[, c("precision", "generalizability", "nvariants", "duration",
"distance", "scaleSize", "rotationDegree", "npaths", "distance", "scaleSize", "rotationDegree", "npaths",
"ncases", "nmoves", "nopenTopic", "nopenPopup")] |> "ncases", "nmoves", "nflipCard", "nopenTopic",
"nopenPopup")] |>
scale() scale()
dist_mat <- dist(df) dist_mat <- dist(df)
@ -87,52 +80,54 @@ for (hc in hcs) plot(hc, main = "")
hc <- hcs$ward hc <- hcs$ward
k <- 4 # number of clusters factoextra::fviz_nbclust(df, FUNcluster = factoextra::hcut, method = "wss")
factoextra::fviz_nbclust(df, FUNcluster = factoextra::hcut, method = "silhouette")
mycols <- c("#78004B", "#FF6900", "#3CB4DC", "#91C86E") gap_stat <- cluster::clusGap(df, FUNcluster = factoextra::hcut,
hc_func = "agnes", hc_method = "ward",
K.max = 10)
factoextra::fviz_gap_stat(gap_stat)
grp <- cutree(hc, k = k) k <- 6 # number of clusters
datitem$grp <- grp
fviz_dend(hc, k = k, mycols <- c("#434F4F", "#78004B", "#FF6900", "#3CB4DC", "#91C86E", "Black")
cluster <- cutree(hc, k = k)
factoextra::fviz_dend(hc, k = k,
cex = 0.5, cex = 0.5,
k_colors = mycols, k_colors = mycols,
#type = "phylogenic", #type = "phylogenic",
rect = TRUE rect = TRUE
) )
p <- fviz_cluster(list(data = df, cluster = grp), factoextra::fviz_cluster(list(data = df, cluster = cluster),
palette = mycols, palette = mycols,
ellipse.type = "convex", ellipse.type = "convex",
repel = TRUE, repel = TRUE,
show.clust.cent = FALSE, ggtheme = theme_bw()) show.clust.cent = FALSE,
p ggtheme = ggplot2::theme_bw())
aggregate(cbind(duration, distance, scaleSize , rotationDegree, npaths, aggregate(cbind(duration, distance, scaleSize , rotationDegree, npaths,
ncases, nmoves, nflipCard, nopenTopic, nopenPopup) ~ grp, ncases, nmoves, nflipCard, nopenTopic, nopenPopup) ~ cluster,
datitem, mean) datitem, mean)
aggregate(cbind(duration, distance, scaleSize , rotationDegree, npaths, aggregate(cbind(duration, distance, scaleSize , rotationDegree, npaths,
ncases, nmoves, nflipCard, nopenTopic, nopenPopup) ~ grp, ncases, nmoves, nflipCard, nopenTopic, nopenPopup) ~ cluster,
datitem, max) datitem, max)
item <- sprintf("%03d", as.numeric(gsub("item_([0-9]{3})", "\\1",
row.names(datitem))))
# Something like a scree plot (??) res <- merge(dat, data.frame(item, cluster), by = "item", all.x = TRUE)
plot(rev(hc$height), type = "b", pch = 16, cex = .5)
datitem$item <- sprintf("%03d",
as.numeric(gsub("item_([0-9]{3})", "\\1", row.names(datitem))))
res <- merge(dat, datitem[, c("item", "grp")], by = "item", all.x = TRUE)
res <- res[order(res$fileId.start, res$date.start, res$timeMs.start), ] res <- res[order(res$fileId.start, res$date.start, res$timeMs.start), ]
# Look at clusters # Look at clusters
par(mfrow = c(2,2)) par(mfrow = c(2,2))
vioplot::vioplot(duration ~ grp, res) vioplot::vioplot(duration ~ cluster, res)
vioplot::vioplot(distance ~ grp, res) vioplot::vioplot(distance ~ cluster, res)
vioplot::vioplot(scaleSize ~ grp, res) vioplot::vioplot(scaleSize ~ cluster, res)
vioplot::vioplot(rotationDegree ~ grp, res) vioplot::vioplot(rotationDegree ~ cluster, res)
write.table(res, write.table(res,
file = "results/haum/eventlogs_pre-corona_item-clusters.csv", file = "results/haum/eventlogs_pre-corona_item-clusters.csv",
@ -144,59 +139,60 @@ write.table(res,
res$start <- res$date.start res$start <- res$date.start
res$complete <- res$date.stop res$complete <- res$date.stop
for (cluster in sort(unique(res$grp))) { for (clst in sort(unique(res$cluster))) {
alog <- activitylog(res[res$grp == cluster, ], alog <- bupaR::activitylog(res[res$cluster == clst, ],
case_id = "path", case_id = "path",
activity_id = "event", activity_id = "event",
resource_id = "item", resource_id = "item",
timestamps = c("start", "complete")) timestamps = c("start", "complete"))
dfg <- process_map(alog, dfg <- processmapR::process_map(alog,
type_nodes = frequency("relative", color_scale = "Greys"), type_nodes = processmapR::frequency("relative", color_scale = "Greys"),
sec_nodes = frequency("absolute"), sec_nodes = processmapR::frequency("absolute"),
type_edges = frequency("relative", color_edges = "#FF6900"), type_edges = processmapR::frequency("relative", color_edges = "#FF6900"),
sec_edges = frequency("absolute"), sec_edges = processmapR::frequency("absolute"),
rankdir = "LR", rankdir = "LR",
render = FALSE) render = FALSE)
export_map(dfg,
file_name = paste0("results/processmaps/dfg_cluster", cluster, "_R.pdf"), processmapR::export_map(dfg,
file_name = paste0("results/processmaps/dfg_cluster", clst, "_R.pdf"),
file_type = "pdf", file_type = "pdf",
title = paste("DFG Cluster", cluster)) title = paste("DFG Cluster", clst))
} }
#--------------- (3) Visualization with pictures --------------- #--------------- (3) Visualization with pictures ---------------
library(png) coor_2d <- cmdscale(dist_mat, k = 2)
library(jpeg)
library(grid)
pdf("results/figures/clustering_artworks.pdf", height = 8, width = 8, pointsize = 10) items <- sprintf("%03d", as.numeric(rownames(datitem)))
#png("results/figures/clustering_artworks.png", units = "in", height = 8, width = 8, pointsize = 10, res = 300)
#pdf("results/figures/clustering_artworks.pdf", height = 8, width = 8, pointsize = 10)
png("results/figures/clustering_artworks.png", units = "in", height = 8, width = 8, pointsize = 10, res = 300)
par(mai = c(.4,.4,.1,.1), mgp = c(2.4, 1, 0)) par(mai = c(.4,.4,.1,.1), mgp = c(2.4, 1, 0))
plot(y ~ x, p$data, type = "n", ylim = c(-3.5, 2.8), xlim = c(-5, 10), plot(coor_2d, type = "n", ylim = c(-3.7, 2.6), xlim = c(-5, 10.5),
xlab = "", ylab = "") xlab = "", ylab = "")
for (item in sprintf("%03d", as.numeric(rownames(p$data)))) { for (item in items) {
if (item == "125") { if (item == "125") {
pic <- readJPEG(paste0("../data/haum/ContentEyevisit/eyevisit_cards_light/", pic <- jpeg::readJPEG(paste0("../data/haum/ContentEyevisit/eyevisit_cards_light/",
item, "/", item, ".jpg")) item, "/", item, ".jpg"))
} else { } else {
pic <- readPNG(paste0("../data/haum/ContentEyevisit/eyevisit_cards_light/", pic <- png::readPNG(paste0("../data/haum/ContentEyevisit/eyevisit_cards_light/",
item, "/", item, ".png")) item, "/", item, ".png"))
} }
img <- as.raster(pic[,,1:3]) img <- as.raster(pic[,,1:3])
x <- p$data$x[sprintf("%03d", as.numeric(rownames(p$data))) == item] x <- coor_2d[items == item, 1]
y <- p$data$y[sprintf("%03d", as.numeric(rownames(p$data))) == item] y <- coor_2d[items == item, 2]
points(x, y, points(x, y,
col = mycols[p$data$cluster[sprintf("%03d", as.numeric(rownames(p$data))) == item]], col = mycols[cluster[items == item]],
cex = 9, cex = 9,
pch = 15) pch = 15)