Some variable name and plot size adjustments
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@ -97,6 +97,7 @@ mycols <- c("#434F4F", "#78004B", "#FF6900", "#3CB4DC", "#91C86E", "Black")
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cluster <- cutree(hc, k = k)
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pdf("results/figures/dendrogram_items.pdf", width = 6.5, height = 5.5, pointsize = 10)
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# TODO: Move code for plots to /thesis/
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factoextra::fviz_dend(hc, k = k,
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cex = 0.5,
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@ -182,10 +183,10 @@ coor_2d <- cmdscale(dist_mat, k = 2)
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items <- sprintf("%03d", as.numeric(rownames(datitem)))
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#pdf("results/figures/clustering_artworks.pdf", height = 8, width = 8, pointsize = 10)
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png("results/figures/clustering_artworks.png", units = "in", height = 8, width = 8, pointsize = 10, res = 300)
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pdf("results/figures/clustering_artworks.pdf", height = 8, width = 8, pointsize = 16)
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#png("results/figures/clustering_artworks.png", units = "in", height = 8, width = 8, pointsize = 16, res = 300)
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par(mai = c(.4,.4,.1,.1), mgp = c(2.4, 1, 0))
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par(mai = c(.6,.6,.1,.1), mgp = c(2.4, 1, 0))
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plot(coor_2d, type = "n", ylim = c(-3.7, 2.6), xlim = c(-5, 10.5),
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xlab = "", ylab = "")
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@ -208,7 +209,7 @@ for (item in items) {
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points(x, y,
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col = mycols[cluster[items == item]],
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cex = 9,
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cex = 6,
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pch = 15)
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rasterImage(img,
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@ -25,10 +25,10 @@ dat <- dat[as.Date(dat$date.start) > "2017-12-31" &
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#--------------- (2) Extract characteristics for cases ---------------
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datcase <- aggregate(cbind(distance, scaleSize, rotationDegree) ~
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datcase18 <- aggregate(cbind(distance, scaleSize, rotationDegree) ~
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case, dat, function(x) mean(x, na.rm = TRUE), na.action = NULL)
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datcase$length <- aggregate(item ~ case, dat, length)$item
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datcase18$length <- aggregate(item ~ case, dat, length)$item
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eventtab <- aggregate(event ~ case, dat, table)["case"]
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eventtab$nmove <- aggregate(event ~ case, dat, table)$event[, "move"]
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@ -36,44 +36,44 @@ eventtab$nflipCard <- aggregate(event ~ case, dat, table)$event[, "flipCard"]
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eventtab$nopenTopic <- aggregate(event ~ case, dat, table)$event[, "openTopic"]
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eventtab$nopenPopup <- aggregate(event ~ case, dat, table)$event[, "openPopup"]
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datcase <- datcase |>
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datcase18 <- datcase18 |>
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merge(eventtab, by = "case", all = TRUE)
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rm(eventtab)
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datcase$nitems <- aggregate(item ~ case, dat, function(x)
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datcase18$nitems <- aggregate(item ~ case, dat, function(x)
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length(unique(x)), na.action = NULL)$item
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datcase$npaths <- aggregate(path ~ case, dat, function(x)
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datcase18$npaths <- aggregate(path ~ case, dat, function(x)
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length(unique(x)), na.action = NULL)$path
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dat_split <- split(dat, ~ case)
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dat_list <- pbapply::pblapply(dat_split, time_minmax_ms)
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dat_minmax <- dplyr::bind_rows(dat_list)
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datcase$min_time <- aggregate(min_time ~ case, dat_minmax, unique)$min_time
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datcase$max_time <- aggregate(max_time ~ case, dat_minmax, unique)$max_time
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datcase18$min_time <- aggregate(min_time ~ case, dat_minmax, unique)$min_time
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datcase18$max_time <- aggregate(max_time ~ case, dat_minmax, unique)$max_time
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datcase$duration <- datcase$max_time - datcase$min_time
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datcase$min_time <- NULL
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datcase$max_time <- NULL
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datcase18$duration <- datcase18$max_time - datcase18$min_time
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datcase18$min_time <- NULL
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datcase18$max_time <- NULL
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artworks <- unique(dat$item)[!unique(dat$item) %in% c("501", "502", "503")]
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datcase$infocardOnly <- pbapply::pbsapply(dat_split, check_infocards, artworks = artworks)
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datcase18$infocardOnly <- pbapply::pbsapply(dat_split, check_infocards, artworks = artworks)
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# Clean up NAs
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datcase$distance <- ifelse(is.na(datcase$distance), 0, datcase$distance)
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datcase$scaleSize <- ifelse(is.na(datcase$scaleSize), 1, datcase$scaleSize)
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datcase$rotationDegree <- ifelse(is.na(datcase$rotationDegree), 0, datcase$rotationDegree)
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datcase18$distance <- ifelse(is.na(datcase18$distance), 0, datcase18$distance)
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datcase18$scaleSize <- ifelse(is.na(datcase18$scaleSize), 1, datcase18$scaleSize)
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datcase18$rotationDegree <- ifelse(is.na(datcase18$rotationDegree), 0, datcase18$rotationDegree)
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#--------------- (3) Select features for navigation behavior ---------------
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dattree18 <- data.frame(case = datcase$case,
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PropItems = datcase$nitems / length(unique(dat$item)),
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SearchInfo = (datcase$nopenTopic +
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datcase$nopenPopup) / datcase$length,
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PropMoves = datcase$nmove / datcase$length,
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PathLinearity = datcase$nitems / datcase$npaths,
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Singularity = datcase$npaths / datcase$length
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dattree18 <- data.frame(case = datcase18$case,
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PropItems = datcase18$nitems / length(unique(dat$item)),
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SearchInfo = (datcase18$nopenTopic +
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datcase18$nopenPopup) / datcase18$length,
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PropMoves = datcase18$nmove / datcase18$length,
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PathLinearity = datcase18$nitems / datcase18$npaths,
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Singularity = datcase18$npaths / datcase18$length
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)
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# centrality <- pbapply::pbsapply(dattree18$case, get_centrality, data = dat)
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@ -97,10 +97,10 @@ dattree18$AvDurItem <- aggregate(duration ~ case, tmp, mean)$duration
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rm(tmp)
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# Indicator variable if table was used as info terminal only
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dattree18$InfocardOnly <- factor(datcase$infocardOnly, levels = 0:1,
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dattree18$InfocardOnly <- factor(datcase18$infocardOnly, levels = 0:1,
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labels = c("no", "yes"))
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# Add pattern to datcase; loosely based on Bousbia et al. (2009)
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# Add pattern
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dattree18$Pattern <- "Dispersion"
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dattree18$Pattern <- ifelse(dattree18$PathLinearity > 0.8, "Scholar",
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dattree18$Pattern)
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@ -118,13 +118,13 @@ df <- dattree18[, c("PropItems", "SearchInfo", "PropMoves", "AvDurItemNorm",
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dist_mat18 <- cluster::daisy(df, metric = "gower")
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coor_3d <- smacof::mds(dist_mat, ndim = 3, type = "ordinal")$conf
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coor_2d <- coor_3d[, 1:2]
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coor_3d_18 <- smacof::mds(dist_mat18, ndim = 3, type = "ordinal")$conf
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coor_2d_18 <- coor_3d_18[, 1:2]
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plot(coor_2d)
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rgl::plot3d(coor_3d)
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plot(coor_2d_18)
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rgl::plot3d(coor_3d_18)
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hc18 <- cluster::agnes(dist_mat, method = "ward")
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hc18 <- cluster::agnes(dist_mat18, method = "ward")
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k <- 5
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@ -134,27 +134,27 @@ cluster18 <- cutree(as.hclust(hc18), k = k)
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table(cluster18)
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plot(coor_2d, col = mycols[cluster18], pch = 16)
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plot(coor_2d_18, col = mycols[cluster18], pch = 16)
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legend("topleft", c("Searching", "Exploring", "Scanning", "Flitting", "Info"),
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col = mycols, bty = "n", pch = 16)
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rgl::plot3d(coor_3d, col = mycols[cluster18])
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rgl::plot3d(coor_3d_18, col = mycols[cluster18])
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print(ftable(xtabs( ~ InfocardOnly + Pattern + cluster18, dattree18)), zero = "-")
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aggregate(. ~ cluster18, df, mean)
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aggregate(. ~ cluster18, dattree18[, -1], mean)
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save(coor_2d, coor_3d, cluster18, dattree18, dist_mat18, hc18,
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save(coor_2d_18, coor_3d_18, cluster18, dattree18, dist_mat18, hc18,
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file = "../../thesis/figures/data/clustering_cases_2018.RData")
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#--------------- (5) Fit tree ---------------
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c1 <- rpart::rpart(as.factor(cluster18) ~ ., data = dattree18[, c("PropMoves",
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"PropItems",
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"SearchInfo",
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"AvDurItem",
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"Pattern",
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"InfocardOnly")],
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"PropItems",
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"SearchInfo",
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"AvDurItem",
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"Pattern",
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"InfocardOnly")],
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method = "class")
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plot(partykit::as.party(c1), tp_args = list(fill = mycols, col = mycols))
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@ -164,11 +164,11 @@ plot(partykit::as.party(c1), tp_args = list(fill = mycols, col = mycols))
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load("../../thesis/figures/data/clustering_cases.RData")
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c19 <- rpart::rpart(as.factor(cluster) ~ ., data = dattree[, c("PropMoves",
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"PropItems",
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"SearchInfo",
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"AvDurItem",
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"Pattern",
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"InfocardOnly")],
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"PropItems",
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"SearchInfo",
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"AvDurItem",
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"Pattern",
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"InfocardOnly")],
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method = "class")
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cl18 <- rpart:::predict.rpart(c1, type = "class", newdata = dattree18)
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