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global.R
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global.R
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library(dplyr)
library(ggplot2)
library(purrr)
library(magrittr)
library(tidyr)
library(stringr)
library(forcats)
library(DT)
library(waiter)
library(qs)
library(bslib) # is also loaded in ui.R ?!
library(shinycssloaders)
library(markdown)
library(ggiraph)
library(mapproj)
library(patchwork) # smaller objects
library(shiny.i18n)
# activate these for the creation of maps
#library(gfonts)
#library(raster)
#options("sp_evolution_status"=2)
#library(sp)
#library(sf)
#library(cowplot) # creates too large objects! used for ggdraw
#library(jpeg)
#library(magick) # for LSA maps
#library(scales)
# on Ubuntu/engelmann, install packages with:
# sudo su - -c "R -e \"install.packages('party', repos='http://cran.rstudio.com/')\""
enableBookmarking(store = "url")
## Some settings
# 1. load paths externally
paths <- rio::import("paths/paths.csv")
SERVER_local <- filter(paths, name == "SERVER_local") %>%
dplyr::select(path) %>%
as.character()
SERVER <- filter(paths, name == "SERVER") %>%
dplyr::select(path) %>%
as.character()
## Font stuff
#get_all_fonts()
# setup_font(
# id = "open-sans",
# output_dir = "fonts",
# variants = c("regular", "italic", "700", "700italic"),
# prefer_local_source = FALSE)
#
# use_font("open-sans", "fonts/css/open-sans.css", selector = ".dummy-selector")
# setup_font(
# id = "roboto",
# output_dir = "fonts",
# variants = c("regular", "italic", "700", "700italic"),
# prefer_local_source = FALSE)
# setup_font(
# id = "domine",
# output_dir = "./Variatiounsatlas/fonts",
# variants = c("regular", "italic", "700", "700italic"),
# prefer_local_source = FALSE)
#use_font("domine", "fonts/css/domine.css")
#use_font("roboto", "fonts/css/roboto.css")
#validated_fonts(list(sans = "roboto", serif = "roboto"))
preloader <- list(html = tagList(spin_1(), "De Variatiounsatlas gëtt gelueden ..."), color = "#343a40")
## Prepare stuff
# Polygoner fir Kanonten a Gemengen
# Create new polygones for Gemengen
#library(rgdal) # R wrapper around GDAL/OGR
#library(ggplot2) # for general plotting
#library(ggmaps) # for fortifying shapefiles
# First read in the shapefile, using the path to the shapefile and the shapefile name minus the
# extension as arguments
#shapefile <- readOGR("/Users/peter.gilles/Downloads/gadm36_LUX_shp/gadm36_LUX_3.shp")
# Then modify polygons in QGIS, save
# Next the shapefile has to be converted to a dataframe for use in ggplot2
#shapefile_df <- fortify(shapefile, region = "NAME_3")
# Save as RDS
#saveRDS(shapefile_df, "communes_df.RDS")
# load prepared polygon data for cantons and communes
cantons_df <- readRDS("seed/cantons_df.RDS")
communes_df <- readRDS("seed/communes_df.RDS")
Gemengen_Statistiken <- qread("seed/Gemengen_Statistiken.qs")
# Weider Elementer fir d'Kaartéierung
# rivers <- readRDS("river.RDS")
# rivers <- rivers[["osm_lines"]] %>%
# filter(name %in% c("Alzette", "Sûre", "Sauer", "Sauer - Sûre", "Mosel", "Moselle"))
#bbox_lux_2500.sf <-readRDS("bbox_lux_2500.sf.rds")
#elevation_raster <- readRDS("elevation_raster.rds")
# OSM base map
#osm_map <- qread("osm_map.qs")
color_palette <- c('#56cc9d','#beaed4','#fdc086','#ffff99','#386cb0','#f0027f','#bf5b17','#666666')
# Internationalisation
i18n <- Translator$new(translation_json_path='translations/translation.json')
i18n$set_translation_language('lb')
# update Kaartesettings from Google Docs
# library(googlesheets4)
# gs4_deauth()
# variables <- range_read(ss = "1IDtvxHgccWg2JMu-dqJyqsCpwsurpYLOgm6rfE0mMGU", sheet = "kaartesettings", col_names=T, col_types = "c") %>%
# filter(active == "yes") %>%
# arrange(map_category, input_choice) %>%
# write_csv(file = "./Variatiounsatlas/kaartesettings.csv")
# load Kaartesettings from local csv
variables <- read.csv("seed/kaartesettings.csv") %>%
filter(active == "yes") %>%
arrange(map_category, input_choice, .locale = "de")
# Functions
make_choices <- function(category) {
choices <- variables %>%
#dplyr::filter(map_category == {{category}}) %>%
dplyr::select(variable, input_choice) %>%
arrange(tolower(input_choice))
choices <- set_names(choices$variable, choices$input_choice)
#choices
# selectInput(inputId = category, label = h3(category),
# choices = choices,
# selectize = FALSE,
# size = 25)
}
# make_choices <- function(category) {
# choices <- variables %>%
# dplyr::filter(map_category == {{category}}) %>%
# dplyr::select(variable, input_choice) %>%
# arrange(input_choice)
# choices <- set_names(choices$variable, choices$input_choice)
# #choices
# # selectInput(inputId = category, label = h3(category),
# # choices = choices,
# # selectize = FALSE,
# # size = 25)
# }
# Function frequencies of variants
plot_freq_variants <- function(data, variable, selection, caption = "") {
color <- color_palette[1:length(selection)]
bar_df <- data %>%
dplyr::select(variable = {{variable}}) %>% # Filter the desired variable
filter(variable %in% selection) %>% # Only include variants from the selection
drop_na() %>%
mutate(Varianten = "Varianten", # Dummy variable for stacking
variable = factor(variable, levels = selection))
# Simple bar chart
bar <- ggplot(data = bar_df %>%
count(Varianten, variable) %>%
mutate(total = sum(n),
label = paste0(round(n/total, 2)*100, "%\n", n)),
aes(x = Varianten, y = n, fill = variable, label = label)) +
geom_bar(stat = "identity") +
scale_fill_manual(values = color, breaks = selection) +
geom_text(position = position_stack(vjust = .5), size = 5, alpha = 0.9, color = "antiquewhite") +
coord_flip() +
theme(axis.title.x = element_blank(),
axis.text.y = element_blank(),
axis.title.y = element_blank(),
legend.position = "bottom",
legend.title = element_blank(),
legend.text = element_text(size = 13),
legend.box = "horizontal",
text = element_text(size = 13),
plot.background = element_blank(),
panel.grid.major = element_blank(),
panel.grid.minor = element_blank(),
panel.border = element_blank(),
panel.background = element_blank(),
axis.ticks = element_blank(),
axis.text.x = element_blank())
return(bar)
}
#############################
# Function Iwwerbléckskaart #
make_summary_plot <- function(dataset, lsa_map_number, selection, color_num, map_title, item_number ="", item_text = "", geo_type) {
print(geo_type)
color <- color_palette[1:color_num]
# get count of all observations
variant_count <- dataset %>% distinct(id, total)
variant_count <- sum(variant_count$total)
dataset <- dataset %>%
group_by(id) %>%
mutate(prozent = n/total) %>%
filter(n == max(n)) %>%
mutate(max_variant = variants)
p <- ggplot() +
# variant data
geom_polygon_interactive(data = dataset, aes(x = long, y = lat, fill=max_variant, group = id,
tooltip = paste0(i18n$t("Lokalitéit: "), id,
i18n$t("\nHeefegst Variant: "), max_variant,
i18n$t("\nRelativ Heefegkeet: "), round(freq, 2)*100,
i18n$t(" %\nParticipanten: "), n)),
# alpha per polygon steered by percentage, if not useful, set alpha back to 0.8
linewidth=0, alpha = dataset$prozent) +
# add Rivers
#geom_sf(data = rivers, color = "#46b4e7") +
# borders of cantons
geom_polygon(data = cantons_df, aes(x = long, y = lat, group = id),
linewidth= .1, colour = "#a9a9a9", fill = NA) +
coord_map() +
# coord_sf(xlim = c(5.715637, 6.54680),
# ylim = c(49.393100, 50.192726),
# expand = FALSE) +
scale_colour_identity() +
scale_fill_manual(values = color[1:color_num],
breaks = selection) +
labs(title = paste(i18n$t("Variabel: "), word(map_title, 2, sep="_")),
fill = paste0(i18n$t("Haaptvariant\npro "), word(geo_type, 1, sep = "_")),
x = "", y = "",
caption = paste0(variant_count, i18n$t(" Participanten | Klengst Polygoner: "), word(geo_type, 1, sep = "_"), i18n$t("\n© Uni Lëtzebuerg | generéiert "), date())
) +
#theme_void(base_family = "sans") +
theme_void() +
theme(plot.title = element_text(size=38, hjust = 0.5, face="bold"),
plot.caption = element_text(size=26),
legend.position = c(0.8, 0.9),
legend.text = element_text(size=34),
legend.title = element_text(size=35, face = "bold"))
# plot with or without LSA
# with LSA
if(lsa_map_number != "NO") {
# prepare LSA map into grid
# für Docker
#lsa <- readJPEG(source = paste0("atlas/Kaarten-LSA_small/", lsa_map_number, "_lux.jpg"))
lsa <- readJPEG(source = paste0("./Kaarten-LSA_small/", lsa_map_number, "_lux.jpg"))
lsa <- ggdraw() + draw_image(lsa) +
labs(caption =paste0(i18n$t("Vergläichskaart aus dem 'Luxemburgischer Sprachatlas', LSA (1963), Kaart "), lsa_map_number)) +
theme_void() +
theme(plot.caption = element_text(size=26))
plot_row <- wrap_plots(lsa, p, nrow = 1, ncol = 2)
plot_row <- girafe(code = print(plot_row),
width_svg = 27, height_svg = 18,
#fonts = list(sans = "roboto"),
options = list(
opts_hover(css = "fill:#FF3333;stroke:black;cursor:pointer;", reactive = TRUE),
opts_selection(
type = "multiple", css = "fill:#FF3333;stroke:black;")))
} else {
#without LSA map
plot_row <- girafe(code = print(p),
width_svg = 20, height_svg = 24,
#fonts = list(sans = "Sans"),
options = list(
opts_hover(css = "fill:#FF3333;stroke:black;cursor:pointer;", reactive = TRUE),
opts_selection(
type = "multiple", css = "fill:#FF3333;stroke:black;")))
}
# to save map as pdf and png
#ggsave(plot = plot_row, filename = paste0(map_title, ".png"), units = "cm", width = 22)
#ggsave(plot = p, filename = paste0(map_title, ".pdf"), units = "cm", width = 22)
#ggsave(plot = plot_row, filename = paste0(map_title, "_mat_LSA.pdf"), device="pdf", dpi=400, units = "cm", width = 28)
qsave(plot_row, file = paste0("./overview_maps/Iwwerbleckskaart_", map_title, ".qs"))
return(plot_row)
}
########################################
# Function Iwwerbléckskaarte per Alter #
make_summary_plot_age <- function(dataset, lsa_map_number, selection, color_num, map_title, item_number ="", item_text = "", geo_type) {
color <- color_palette[1:color_num]
# TODO remove '_' from selection
#selection <- str_replace(selection, "_", "")
# get count of all observations
variant_count1 <- dataset %>% distinct(id, Alter, total)
variant_count <- sum(variant_count1$total)
freq_alter <- variant_count1 %>%
group_by(Alter) %>%
summarise(freq_alter = sum(total))
# define a function to create the labels
my_labeller <- function(value) {
freq_alter2 <- unique(freq_alter$freq_alter[freq_alter$Alter == value])
label <- paste0(value, "\n(N = ", freq_alter2, ")")
return(label)
}
dataset <- dataset %>%
group_by(id, Alter) %>%
mutate(prozent = n/total) %>%
filter(n == max(n)) %>%
mutate(max_variant = variants)
# create maps
p <- ggplot() +
# variant data
geom_polygon(data = dataset, aes(x = long, y = lat, fill=max_variant, group = id),
# alpha per polygon steered by percentage, if not useful, set alpha back to 0.8
linewidth=0, alpha = dataset$prozent) +
# borders of cantons
geom_polygon(data = cantons_df, aes(x = long, y = lat, group = id),
linewidth= .1, colour = "#a9a9a9", fill = NA) +
coord_map() +
scale_colour_identity() +
scale_fill_manual(values = color[1:color_num],
breaks = selection) +
labs(title = paste("Variabel '", word(map_title, 2, sep="_"), "' no Alter"),
fill = paste0("Haaptvariant\npro ", word(geo_type, 1, sep = "_")),
x = "", y = "",
caption = paste0(variant_count, " Participanten | Klengst Polygoner: Kanton\n© Uni Lëtzebuerg | generéiert ", date())
) +
theme_void(base_family = "Roboto") +
# potential error in connection with randomForest for 'margin', hence ggplot2::margin
# see: https://github.com/tidyverse/ggplot2/issues/2150
theme(plot.title = element_text(size=18, hjust = 0.5, face="bold", margin = ggplot2::margin(0, 0, 20, 0)),
plot.caption = element_text(size=12),
legend.position = "bottom",
legend.text = element_text(size=12),
legend.title = element_text(size=12, face = "bold"),
strip.text = element_text(size = 13, face = "bold"), # set strip.text to bold and size 12
) +
facet_wrap(. ~ Alter, labeller = as_labeller(my_labeller), scales = "fixed"
)
# Save maps
#qsave(p, file = paste0("./overview_maps/Iwwerbleckskaarten_Alter_", map_title, ".qs"))
# return maps
return(p)
}
### Function Variantekaarten #
make_plot <- function(dataset, variable, color) {
# Get count of all observations
variant_count <- dataset %>%
distinct(id, n) %>%
summarize(sum(n))
# Create ggplot
plot <- ggplot() +
geom_polygon(data = dataset, aes(x = long, y = lat, fill = freq,
group = id), linewidth = 0, alpha = 1, colour = "lightgrey") +
geom_polygon(data = cantons_df, aes(x = long, y = lat, group = id),
linewidth = .1, colour = "#a9a9a9", fill = NA) +
coord_map() +
scale_fill_gradient(guide = guide_legend(), low = "white", high = color,
name = paste(variant_count, "Participanten"), na.value = "white", limits = 0:1, labels = scales::percent(0.25 * 0:4)) +
labs(title = stringr::str_replace({{variable}}, "_", " "), x = "", y = "") +
theme_void() +
theme(plot.title = element_text(size = 16, face = "bold", hjust = 0.5),
legend.position = "bottom",
legend.text = element_text(size = 11),
legend.title = element_text(size = 12),
plot.margin = unit(c(0.2, 0, 0.2, 0), "cm")) +
guides(fill = guide_colourbar(barwidth = 7, barheight = .7, ticks = FALSE, title.position = "bottom", title.hjust = 0.5))
return(plot)
}
# Function to plot Sozialdaten #
plot_social_categories <- function(data, social_category, variable, selection, caption = "") {
color <- color_palette[1:length(selection)]
bar_df <- data %>%
# Einschränkung auf gewünschte Kategorie und Variable
dplyr::select({{social_category}}, variable = {{variable}}) %>%
# Nur Varianten aus der Selection
filter(variable %in% selection) %>%
drop_na() %>%
# Prozente berechnen
group_by({{social_category}}, variable) %>%
count() %>%
group_by({{social_category}}) %>%
mutate(total = sum(n)) %>%
mutate(Prozent = n/total) %>%
dplyr::rename(count_variant = n) %>%
group_by({{social_category}}) %>%
mutate(total_alter = sum(count_variant)) %>%
mutate(Prozent = count_variant/total_alter) %>%
ungroup() %>%
mutate(total_variable = sum(count_variant)) %>%
mutate(Prozent_variable = count_variant/total_variable) %>%
dplyr::select(-total_alter, -total_variable) %>%
group_by({{social_category}}) %>%
mutate(Prozent_social_category = sum(Prozent_variable))
#bar_df$w <- cumsum(bar_df$total)
#bar_df$wm <- bar_df$w - bar_df$total
#bar_df$wt <- with(bar_df, wm + (w - wm)/2)
# # Groups: Alter [6]
# Alter variable count_variant total Prozent
# <chr> <chr> <int> <int> <dbl>
# 1 ≤ 24 lo[g]ie 40 224 0.179
# 2 ≤ 24 lo[ʒ]ie 184 224 0.821
# 3 25 bis 34 lo[g]ie 45 305 0.148
# 4 25 bis 34 lo[ʒ]ie 260 305 0.852
# 5 35 bis 44 lo[g]ie 11 179 0.0615
# 6 35 bis 44 lo[ʒ]ie 168 179 0.939
# 7 45 bis 54 lo[g]ie 20 183 0.109
# 8 45 bis 54 lo[ʒ]ie 163 183 0.891
# 9 55 bis 64 lo[g]ie 8 123 0.0650
# 10 55 bis 64 lo[ʒ]ie 115 123 0.935
# 11 65+ lo[g]ie 2 40 0.05
# 12 65+ lo[ʒ]ie 38 40 0.95
# # A tibble: 4 x 5
# # Groups: Geschlecht [2]
# Geschlecht variable count_variant total Prozent
# <chr> <chr> <int> <int> <dbl>
# 1 Männlech lo[g]ie 31 328 0.0945
# 2 Männlech lo[ʒ]ie 297 328 0.905
# 3 Weiblech lo[g]ie 95 726 0.131
# 4 Weiblech lo[ʒ]ie 631 726 0.869
xlabel <- as.character(ensym(social_category))
#print(xlabel)
# Stacked barplot with multiple groups
bar <- ggplot(data=bar_df, aes(x= {{social_category}}, y = Prozent, fill = variable, label = count_variant), alpha = 0.9) +
geom_col(position = position_stack()) +
# with proportional bar widths
# geom_col(position = position_stack(), aes(width = Prozent_social_category * 2)) +
#geom_rect(position = position_stack(), aes(xmin = wm, xmax = w,
# ymax = Prozent, fill = variable)) +
geom_text(position = position_stack(vjust = .5), size = 5, alpha = 0.9, color = "antiquewhite") +
labs(fill = word(variable, 2, sep="_"),
caption = caption) +
# to displace labels, when too crowded
#scale_x_discrete(guide = guide_axis(n.dodge = 2)) +
scale_y_continuous(labels = scales::percent_format()) +
scale_fill_manual(values = color[1:length(selection)], breaks = selection) +
theme_minimal() +
labs(x = i18n$t(xlabel)) +
theme(legend.text = element_text(size=14),
legend.position="bottom",
legend.title = element_blank(),
plot.caption = element_text(size = 11),
axis.title = element_text(size=15),
axis.text = element_text(size=14))
return(bar)
}
# Function for decision tree
plot_decision_tree <- function(data, variable, selection) {
cond_df <- data %>%
dplyr::filter(Mammesprooch != "Neen") %>%
dplyr::select(variable = {{variable}}, Alter, Geschlecht, Dialektgebiet, Däitsch = `Kompetenz am Däitschen`, Franséisch = `Kompetenz am Franséischen`, Ausbildung) %>%
dplyr::filter((variable) %in% selection) %>%
na.omit() %>%
# filter variants above a certain frequency level
group_by(variable) %>%
dplyr::filter(n()/nrow(data) >= 0.04) %>%
ungroup()
cond_df[sapply(cond_df, is.character)] <- lapply(cond_df[sapply(cond_df, is.character)], as.factor)
# age as ordered factor
ageorder <- c("≤ 24", "25 bis 34", "35 bis 44", "45 bis 54", "55 bis 64", "65+")
cond_df$Alter <- factor(cond_df$Alter,
ordered = is.ordered(ageorder))
set.seed(1234)
cond_tree <- party::ctree(formula = variable ~ Alter + Geschlecht + Dialektgebiet + Däitsch + Franséisch + Ausbildung,
data = cond_df,
control = party::ctree_control(testtype = "Univariate", minbucket = 20))
# plot tree
plot(cond_tree)
}
# Function for RF variable importance
plot_VariableImportance <- function(data, variable, selection) {
forest_df <- data %>%
filter(Mammesprooch != "Neen") %>%
dplyr::select(variable = {{variable}}, Alter, Geschlecht, Dialektgebiet, Däitsch = `Kompetenz am Däitschen`, Franséisch = `Kompetenz am Franséischen`, Ausbildung) %>%
dplyr::filter((variable) %in% selection) %>%
na.omit() %>%
# filter variants above a certain frequency level
group_by(variable) %>%
filter(n()/nrow(data) >= 0.04) %>%
ungroup()
forest_df[sapply(forest_df, is.character)] <- lapply(forest_df[sapply(forest_df, is.character)], as.factor)
# age as ordered factor
ageorder <- c("≤ 24", "25 bis 34", "35 bis 44", "45 bis 54", "55 bis 64", "65+")
forest_df$Alter <- factor(forest_df$Alter,
ordered = is.ordered(ageorder))
# # mutate Index in forest_df as ordered factor
# indexorder <- c("<= 0.4", "0.6", "0.8", "1")
# forest_df$Index <- factor(forest_df$Index,
# ordered = is.ordered(indexorder))
# Random forest model
rf <- randomForest::randomForest(variable ~ Alter + Geschlecht + Dialektgebiet + Däitsch + Franséisch + Ausbildung,
data=forest_df, importance=TRUE, ntree=2000, keep.forest=FALSE)
# plot Variable Importance
randomForest::varImpPlot(rf, main = "Variable Importance", type = 1) # type = 1: mean decrease in accuracy
# save
#qsave(plot, file = paste0(variable, "_VariableImportance.qs"))
return(plot)
}
# Function for data table
plot_datatable <- function(data, variable) {
datatable(data %>%
dplyr::select(Gemeng, Variant = as.name({{variable}}), recordingURL, Kanton, Dialektgebitt = Dialektgebiet) %>%
dplyr::filter(Variant != "FALSE") %>%
mutate(Lauschtert = paste0("<audio controls preload=\"none\" type=\"audio/wav\" src=\"", recordingURL, "\"> </audio>")) %>%
dplyr::select(-recordingURL) %>%
dplyr::select(Variant, Lauschtert, Dialektgebitt, Gemeng, Kanton),
escape = FALSE,
#height = 600,
extensions = 'Scroller',
filter = 'top', options = list(
deferRender = TRUE,
scrollY = 600,
scroller = TRUE,
autoWidth = TRUE
))
}