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commit.R
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commit.R
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library(ggplot2)
library(data.table)
library(cowplot)
library(stringr)
# previous_data = existing
# new_data = rlang::duplicate(existing)
# new_data[between(date, "2020-07-01", "2020-07-06"), value := value + 5]
# new_data[between(date, "2020-07-01", "2020-07-06")]
# new_data = rbind(new_data, new_data[date == "2020-07-01", .(date = ymd("2020-07-15"), location, indicator, value, description)])
# new_data = new_data[date > "2020-03-15"]
#
# previous_data = rbind(previous_data, data.table(date = ymd("2020-05-05"), location = "Wales", indicator = "some_old_thing", value = 42, description = "Who cares?"))
# new_data = rbind(new_data, data.table(date = ymd("2020-05-05"), location = "East of England", indicator = "some_new_thing", value = 42, description = "Who knows?"))
# TODO
# 4. add age groups as well!?
commit = function(previous_data, new_data)
{
# Make previous and new data into data.tables
setDT(previous_data)
setDT(new_data)
# TODO check all columns expected and check no value is NA
# Enumerate all indicators in previous and new data
indicators = union(previous_data[, unique(indicator)], new_data[, unique(indicator)]);
# Create final data interactively, one indicator at a time
final_data = NULL;
for (ind in indicators) {
# Extract previous data for this indicator
previous_indicator = previous_data[indicator == ind];
setnames(previous_indicator, "value", "previous_value");
# Extract new data for this indicator
new_indicator = new_data[indicator == ind];
setnames(new_indicator, "value", "new_value");
# Merge data and mark type of change
merged_indicator = merge(previous_indicator, new_indicator, by = c("date", "location", "indicator", "description"), all = T);
merged_indicator[is.na(previous_value) & !is.na(new_value), change := "added"];
merged_indicator[!is.na(previous_value) & is.na(new_value), change := "removed"];
merged_indicator[!is.na(previous_value) & !is.na(new_value) & previous_value == new_value, change := "unchanged"];
merged_indicator[!is.na(previous_value) & !is.na(new_value) & previous_value != new_value, change := "updated"];
# Build plot for showing changes
plot = ggplot();
manual_colours = character(0);
if (merged_indicator[change == "added", .N] > 0) {
plot = plot +
geom_point(data = merged_indicator[change == "added"], aes(x = date, y = new_value, colour = "added", shape = "added"));
manual_colours = c(manual_colours, "#009900");
}
if (merged_indicator[change == "removed", .N] > 0) {
plot = plot +
geom_point(data = merged_indicator[change == "removed"], aes(x = date, y = previous_value, colour = "removed", shape = "removed"));
manual_colours = c(manual_colours, "#cc0000");
}
if (merged_indicator[change == "unchanged", .N] > 0) {
plot = plot +
geom_line (data = merged_indicator[change == "unchanged"], aes(x = date, y = new_value, colour = "unchanged")) +
geom_point(data = merged_indicator[change == "unchanged"], aes(x = date, y = new_value, colour = "unchanged", shape = "unchanged"), size = 0);
manual_colours = c(manual_colours, "#bbbbbb");
}
if (merged_indicator[change == "updated", .N] > 0) {
plot = plot +
geom_point(data = merged_indicator[change == "updated"], aes(x = date, y = previous_value, colour = "updated (old)", shape = "updated (old)"), size = 1) +
geom_point(data = merged_indicator[change == "updated"], aes(x = date, y = new_value, colour = "updated (new)", shape = "updated (new)"), size = 0.5);
manual_colours = c(manual_colours, "#6666ff", "#6666ff");
}
plot = plot +
facet_wrap(~location, scales = "free_x") +
scale_x_date(limits = merged_indicator[, c(min(date), max(date))], date_labels = "%b", date_breaks = "1 month") +
labs(x = "date", y = ind, title = ind, subtitle = str_wrap(merged_indicator[, description[1]])) +
theme_cowplot(font_size = 8) +
theme(legend.position = c(0.7, 0.15), strip.background = element_blank()) +
scale_colour_manual(values = c(added = "#009900", removed = "#cc0000", unchanged = "#bbbbbb", "updated (old)" = "#6666ff", "updated (new)" = "#6666ff"), guide = "none") +
scale_shape_manual(values = c(added = 3, removed = 4, unchanged = 15, "updated (old)" = 1, "updated (new)" = 16),
guide = guide_legend(title = NULL, override.aes = list(colour = manual_colours, size = 1)))
# Show plot and prompt user
print(plot);
cat(paste0("\n", "Indicator: ", ind, "\n", merged_indicator[, description[1]], "\n"));
print(merged_indicator[, table(changes = change)]);
a = readline(prompt = "Commit changes for this indicator? (y/n/u/a) ");
if (a %in% c("Y", "y")) {
setnames(new_indicator, "new_value", "value");
final_data = rbind(final_data, new_indicator);
} else if (a %in% c("U", "u")) {
merged_indicator[, value := ifelse(is.na(new_value), previous_value, new_value)];
final_data = rbind(final_data, merged_indicator[, .(date, location, indicator, value, description)]);
} else if (a %in% c("A", "a")) {
merged_indicator[, value := ifelse(is.na(previous_value), new_value, previous_value)];
final_data = rbind(final_data, merged_indicator[, .(date, location, indicator, value, description)]);
} else {
setnames(previous_indicator, "previous_value", "value");
final_data = rbind(final_data, previous_indicator);
}
}
return (final_data)
}
most_recent = function(path, tag, format_converter)
{
files = list.files(path, tag);
files = files[!files %like% "^~\\$"]; # Exclude "owner lock" files created by MS Office
dates = format_converter(str_extract(str_replace_all(files, "[ -]", ""), "[0-9]{6,12}"));
return (file.path(path, files[which.max(dates)]))
}
read_normal = function(path, sheet)
{
if (str_sub(path, -4) %like% "xls") {
return (data.table(read_excel(path, sheet)));
} else {
return (fread(path))
}
}
read_2_row_header = function(path, sheet)
{
# Read header, abbreviating names
header = data.table(read_excel(path, sheet, n_max = 1));
empty = which(names(header) %like% "\\.\\.\\.[0-9]+");
names(header)[empty] = names(header)[empty - 1];
append = unname(unlist(header[1]));
names(header) = paste0(names(header), ifelse(is.na(append), "", paste0(" ", append)));
names(header) = make.unique(abbreviate(str_replace_all(names(header), "[^.0-9A-Za-z]", "")));
# Read data
data = data.table(read_excel(path, sheet, skip = 2, col_names = FALSE));
names(data) = names(header);
return (data)
}
read_horiz_date = function(path, sheet, range, variable.name, value.name)
{
# Read and tame data
data = t(data.table(read_excel(path, sheet, range, col_names = FALSE)));
data = matrix(str_trim(c(data)), nrow = nrow(data), ncol = ncol(data));
# Cut out summary/note rows at right side of data
rows_keep = tail(data[, 1], -1) == as.numeric(head(data[, 1], -1)) + 1;
rows_keep = sum(rows_keep, na.rm = TRUE) + 1;
data = data[1:(rows_keep + 1), ];
# Reread data as data.table and fix date column
data[1, 1] = "date";
data_string = paste(apply(data, 1, function(v) paste(v, collapse = "\t")), collapse = "\n");
dt = fread(data_string);
dt[, date := ymd("1900-01-01") + date - 2];
dt = melt(dt, id.vars = "date");
dt[, value := as.numeric(value)];
setnames(dt, c("variable", "value"), c(variable.name, value.name));
return (dt)
}
read_wales_bulk_export = function(path)
{
files = list.files(path, "BulkExport|bulk_export");
exports = list();
for (f in seq_along(files)) {
exports[[f]] = fread(file.path(path, files[f]));
}
exports = rbindlist(exports);
exports = exports[!duplicated(exports, by = 1:7)];
exports = exports[order(UpdateDateTime, HealthBoard, Hospital, Dataset, Section, Question, Measure)];
exports[, date := as.Date(ymd_hms(UpdateDateTime))];
return (exports)
}
melt_annotate = function(data)
{
melted = melt(data, id.vars = c("date", "location"), variable.name = "indicator", value.name = "value");
melted[indicator == "death_inc_line", description := "All deaths (by date of death)"];
melted[indicator == "hospital_inc", description := "New and newly confirmed patients in hospital"];
melted[indicator == "hospital_prev", description := "Total beds occupied"];
melted[indicator == "icu_prev", description := "ICU beds occupied"];
return (melted)
}
blank_fill = function(data, date_col, fill_value)
{
date_min = data[, min(get(date_col), na.rm = T)];
date_max = data[, max(get(date_col), na.rm = T)];
new_data = data.table(date000 = seq(date_min, date_max, by = "1 day"));
setnames(new_data, "date000", date_col);
new_data = merge(new_data, data, by = date_col, all = T)
new_data[is.na(new_data)] = fill_value;
return (new_data)
}