R/epicurve.R
In DanielGardiner/EpiFunc: Epidemiology Functions
Defines functions
epicurve
Documented in
epicurve
#' Create epicurve
#'
#' @import ggplot2
#' @import ISOweek
#' @import scales
#' @author Daniel Gardiner (daniel.gardiner@@phe.gov.uk)
#'
#' @param x a data.frame
#' @param date.col a character specifying the column containing dates
#' @param time.period a character of the desired time period for the epicurve, this can either be day, year, month, year.month, iso.year, iso.week, iso.year.week, use.date.col.as.is NOTE: if time.period = use.date.col.as.is the date.col will be treated as a factor and will be used as the x-axis
#' @param fill.by a character specifying the column to stratify by using colour
#' @param split.by a character specifying the column to facet by
#' @param shade.by a character specifying the column to stratify by using shading
#' @param start.at a character in the format "yyyy-mm-dd" to specify the start date for the epicurve
#' @param stop.at a character in the format "yyyy-mm-dd" to specify the stop date for the epicurve
#' @param xlab a character specifying the x-axis label for the epicurve
#' @param ylab a character specifying the y-axis label for the epicurve
#' @param fill.by.legend.title a character specifying the fill legend title
#' @param shade.by.legend.title a character specifying the shade legend title
#' @param angle a numeric to specify the x-axis label angel for the epicurve
#' @param col.pal a numeric specifying the colour palette (range 1-8 inclusive) OR a character stating 'phe' to use the phe colour palette
#' @param label.breaks a numeric specifying the interval for x-axis label breaks
#' @param epi.squares a logical specifying if episquares should be used on the epicurve
#' @param blank.background a logical specifying if the figure background should be blank
#' @param na.rm a logical specifying if missing dates should be removed from the epicurve
#'
#' @return an epicurve
#'
#' @examples
#' # set dummy data
#'
#' set.seed(2)
#'
#' data = data.frame(dates = sample(seq(as.Date('2014-01-01'), as.Date('2016-04-01'), by="day"), 200, replace = TRUE),
#' sex = c("Male", "Female"),
#' conf = sample(c("Confirmed", "Probable", "possible"), 200, replace = TRUE),
#' status = sample(c("Student", "Staff"), 200, replace = TRUE))
#'
#'
#' # use function
#'
#' epicurve(data,
#' date.col = "dates")
#'
#' epicurve(data,
#' date.col = "dates",
#' start.at = "2015-01-01",
#' stop.at = "2016-05-15")
#'
#' epicurve(data,
#' date.col = "dates",
#' start.at = "2015-01-01",
#' stop.at = "2016-05-15",
#' time.period = "iso.year.week",
#' label.breaks = 2)
#'
#' epicurve(data,
#' date.col = "dates",
#' time.period = "month",
#' xlab = "Month",
#' angle = 0)
#'
#' epicurve(data,
#' date.col = "dates",
#' time.period = "month",
#' shade.by = "sex",
#' xlab = "Month",
#' angle = 0)
#'
#' epicurve(data,
#' date.col = "dates",
#' time.period = "month",
#' fill.by = "sex",
#' xlab = "month",
#' angle = 0)
#'
#' epicurve(data,
#' date.col = "dates",
#' fill.by = "conf",
#' split.by = "sex")
#'
#' epicurve(data,
#' date.col = "dates",
#' time.period = "month",
#' start.at = "2014-01-01",
#' stop.at = "2016-04-20",
#' fill.by = "sex",
#' split.by = NULL,
#' shade.by = "conf",
#' xlab=NULL,
#' ylab="Count",
#' fill.by.legend.title = "Sex",
#' shade.by.legend.title = NULL,
#' angle = 0 ,
#' col.pal = 6,
#' label.breaks = 0,
#' epi.squares = FALSE,
#' na.rm = TRUE)
#'
#' data$dates.year.month = factor(format(data$dates, "%Y_%m"),
#' levels = unique(format(seq(min(data$dates),
#' max(data$dates), 1), "%Y_%m")))
#'
#' epicurve(x = data,
#' date.col = "dates.year.month",
#' time.period = "use.date.col.as.is",
#' start.at = "2015-02-01",
#' stop.at = "2015-06-22",
#' fill.by ="status",
#' split.by = NULL,
#' shade.by = NULL,
#' xlab = "Year_week",
#' ylab="Count",
#' fill.by.legend.title = "",
#' shade.by.legend.title = NULL,
#' angle = 90,
#' col.pal = 1,
#' label.breaks = 0,
#' epi.squares = TRUE,
#' na.rm = TRUE)
#'
#' @export
epicurve <- function(x,
date.col,
time.period = NULL,
start.at = NULL,
stop.at = NULL,
fill.by = NULL,
split.by = NULL,
shade.by = NULL,
xlab = NULL,
ylab = "Number of cases",
fill.by.legend.title = NULL,
shade.by.legend.title = NULL,
angle = 90,
col.pal = "phe",
label.breaks = 0,
epi.squares = TRUE,
blank.background = TRUE,
na.rm = TRUE) {
# make sure x is a data.frame
x = as.data.frame(x)
# check values supplied to col.pal argument
if(!(col.pal == "phe" | (col.pal >= 0 & col.pal <= 8))) {
col.pal = "phe"
warning("col.pal must either be an integer from 1 to 8 or 'phe',
setting col.pal='phe'")
}
# check values supplied to time.period argument
if(is.null(time.period)){
NULL
} else if(!(time.period %in% c("day", "year", "month", "quarter", "year.month",
"year.quarter", "iso.year", "iso.week",
"iso.year.week", "use.date.col.as.is"))){
stop("time.period must be either: day, year, quarter, month, year.quarter, year.month, iso.year, iso.week, iso.year.week, use.date.col.as.is, NULL")
} else {
NULL
}
##############################################################################
# Define factor column (date.col.temp) to be used along the x-axis
# if time.period argument is use.date.col.as.is then use date.col along the x-axis
time.period = ifelse(is.null(time.period), "NULL", time.period)
if (time.period == "use.date.col.as.is") {
x$date.col.temp = x[, date.col]
# otherwise convert the date provided in date.col to the time period specified
# in the time.period argument
} else {
# load get.dates function
get.dates = function(x){
if(class(x) == "Date"){
NULL
} else {
stop("x is not a date")
}
df = data.frame(day = as.character(x),
year = format(x, "%Y"),
month = format(x, "%m"))
df$year.month = paste0(df$year, df$month)
df$iso.year = sapply(strsplit(ISOweek(x), "-W"), function(x) x[1])
df$iso.week = sapply(strsplit(ISOweek(x), "-W"), function(x) x[2])
df$iso.year.week = gsub("-W", "", ISOweek(x))
df$quarter = NA
df$quarter[!is.na(df$day)] = sprintf("%02d", ceiling(as.numeric(as.character(df$month[!is.na(df$day)]))/3))
df$year.quarter = paste0(df$year, df$quarter)
df[is.na(df$day), ] = NA
df
}
# append the get.dates data.frame to the data.frame provided
x = data.frame(x, get.dates(x[, date.col]))
# create a new factor column for the x-axis (levels of the factor contain
# dates ranging from start.at to stop.at)
# if start.at and stop.at are not defined by user (i.e. are NULL) then
# auto generate start.at/stop.at
if(is.null(start.at)){
start.at = min(x[, date.col]) - 5
} else {
start.at = as.Date(start.at)
}
if(is.null(stop.at)){
stop.at = max(x[, date.col]) + 5
} else {
stop.at = as.Date(stop.at)
}
# if time.period are not defined by user (i.e. is NULL) then auto generate
# time.period
if(time.period == "NULL"){
n.days = length(seq(start.at, stop.at, 1))
if(n.days < 31*2){
time.period = "day"
if(is.null(xlab)) xlab = "Day"
} else if (n.days < 365) {
time.period = "iso.year.week"
if(is.null(xlab)) xlab = "ISO Year Week"
} else {
time.period = "year.month"
if(is.null(xlab)) xlab = "Year - Month"
}
} else {
NULL
}
all.dates = get.dates(seq(start.at, stop.at, 1))
all.dates = unique(all.dates[, time.period])
x$date.col.temp = factor(x[, time.period],
levels = all.dates)
# recode dates that fall outside of start.at/stop.at to NA
x[!(as.character(x[, date.col]) %in%
as.character(get.dates(seq(start.at, stop.at, 1))$day)), "date.col.temp"] = NA
## REMOVE MISSING DATES ##
message(paste(sum(is.na(x$date.col.temp)), "rows have missing dates OR dates outside of the start/stop period"))
if(na.rm) x = x[!is.na(x$date.col.temp), ]
# order the levels of the date.col.temp column
x$date.col.temp = factor(x$date.col.temp,
levels = sort(levels(x$date.col.temp)))
}
# we have now defined the factor column (date.col.temp) to be used along the x-axis
##############################################################################
# order data for plotting
if(!is.null(fill.by) & !is.null(shade.by)){
x = x[order(x[, fill.by], x[, shade.by]), ]
} else if(!is.null(fill.by)){
x = x[order(x[, fill.by]), ]
} else if(!is.null(shade.by)){
x = x[order(x[, shade.by]), ]
} else{
NULL
}
# add dummy fill.by column if fill.by = NULL
if(is.null(fill.by)){
fill.by = ".dummy"
x$.dummy = "dummy"
} else {
NULL
}
# create blocks column (this is to allow for epi squares to be added)
x$blocks = 1:nrow(x)
##############################################################################
# generate plot
# generate main body of plot
p = ggplot(x)
# add geom_bar layer with either epi-squares or no epi-squares
if(epi.squares){
p = p + geom_bar(aes_string(x = "date.col.temp", fill = fill.by, alpha = shade.by, group = "blocks"),
colour = "black")
} else {
p = p + geom_bar(aes_string(x = "date.col.temp", fill = fill.by, alpha = shade.by),
colour = "black")
}
# add labs
p = p + labs(x = xlab, y = ylab)
# add x-axis label breaks
p = p + scale_x_discrete(breaks = levels(x$date.col.temp)[c(T, rep(F, label.breaks))],
drop = FALSE)
# format y-axis breaks
p = p + scale_y_continuous(breaks = function(x) unique(floor(pretty(seq(0, (max(x) + 1)*1.1)))),
expand = c(0,0))
# add a solid line running across the bottom of the figure
p = p + geom_hline(aes(yintercept = 0))
# add theme aesthetics
p = p + theme(title = element_text(size = 11, colour = "black", face = "bold"),
axis.title.x = element_text(size = 13, face = "bold", margin = margin(t = 20, r = 0, b = 0, l = 0)),
axis.title.y = element_text(size = 13, face = "bold", margin = margin(t = 0, r = 20, b = 0, l = 0)),
axis.text.x = element_text(angle = angle, hjust = 0.5, vjust = 0, size = 11, face = "plain", colour = "black"),
axis.text.y = element_text(hjust = 0, vjust = 0.5, size = 11, face = "plain", colour = "black"),
legend.title = element_text(size = 11, face = "bold", colour = "black"),
legend.text= element_text(hjust = 1, size = 11, face = "plain", colour = "black"),
legend.position = "right",
legend.justification = c(0.018,0.975),
legend.text.align = 0,
strip.text.y = element_text(hjust = 1, size = 13, colour = "black", face = "bold"),
plot.margin = (unit(c(0.5, 0.5, 0.5, 0.5), "cm")))
# remove background if specified in blank.background argument
if (blank.background) {
p = p + theme(panel.background = element_blank())
} else {
NULL
}
# add labels for the fill.by and shade.by legends
p = p + labs(fill = fill.by.legend.title,
alpha = shade.by.legend.title)
# specify a range for the shady.by level
p = p + scale_alpha_discrete(range = c(0.35, 1))
# facet using split.by
if (!is.null(split.by)) p = p + facet_grid(paste(split.by, ".", sep = "~"),
drop = FALSE)
# add the phe colour palette or a generic colour palette
if (col.pal == "phe") {
phe.cols = c("#822433", "#00B092", "#002776", "#EAAB00", "#8CB8C6",
"#E9994A", "#00A551", "#A4AEB5", "#00549F", "#DAD7CB")
p = p + scale_fill_manual(values = phe.cols, drop = FALSE)
} else if (!is.null(col.pal)) {
p = p + scale_fill_brewer(type = "qual",
palette = col.pal, drop = FALSE)
} else {
NULL
}
# remove dummy legend if fill.by = NULL
if(fill.by == ".dummy"){
p = p + theme(legend.position = "none")
} else {
NULL
}
# return the final output
p
}
DanielGardiner/EpiFunc documentation built on July 25, 2019, 10:53 p.m.
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Defines functions epicurve
Documented in epicurve
#' Create epicurve
#'
#' @import ggplot2
#' @import ISOweek
#' @import scales
#' @author Daniel Gardiner (daniel.gardiner@@phe.gov.uk)
#'
#' @param x a data.frame
#' @param date.col a character specifying the column containing dates
#' @param time.period a character of the desired time period for the epicurve, this can either be day, year, month, year.month, iso.year, iso.week, iso.year.week, use.date.col.as.is NOTE: if time.period = use.date.col.as.is the date.col will be treated as a factor and will be used as the x-axis
#' @param fill.by a character specifying the column to stratify by using colour
#' @param split.by a character specifying the column to facet by
#' @param shade.by a character specifying the column to stratify by using shading
#' @param start.at a character in the format "yyyy-mm-dd" to specify the start date for the epicurve
#' @param stop.at a character in the format "yyyy-mm-dd" to specify the stop date for the epicurve
#' @param xlab a character specifying the x-axis label for the epicurve
#' @param ylab a character specifying the y-axis label for the epicurve
#' @param fill.by.legend.title a character specifying the fill legend title
#' @param shade.by.legend.title a character specifying the shade legend title
#' @param angle a numeric to specify the x-axis label angel for the epicurve
#' @param col.pal a numeric specifying the colour palette (range 1-8 inclusive) OR a character stating 'phe' to use the phe colour palette
#' @param label.breaks a numeric specifying the interval for x-axis label breaks
#' @param epi.squares a logical specifying if episquares should be used on the epicurve
#' @param blank.background a logical specifying if the figure background should be blank
#' @param na.rm a logical specifying if missing dates should be removed from the epicurve
#'
#' @return an epicurve
#'
#' @examples
#' # set dummy data
#'
#' set.seed(2)
#'
#' data = data.frame(dates = sample(seq(as.Date('2014-01-01'), as.Date('2016-04-01'), by="day"), 200, replace = TRUE),
#' sex = c("Male", "Female"),
#' conf = sample(c("Confirmed", "Probable", "possible"), 200, replace = TRUE),
#' status = sample(c("Student", "Staff"), 200, replace = TRUE))
#'
#'
#' # use function
#'
#' epicurve(data,
#' date.col = "dates")
#'
#' epicurve(data,
#' date.col = "dates",
#' start.at = "2015-01-01",
#' stop.at = "2016-05-15")
#'
#' epicurve(data,
#' date.col = "dates",
#' start.at = "2015-01-01",
#' stop.at = "2016-05-15",
#' time.period = "iso.year.week",
#' label.breaks = 2)
#'
#' epicurve(data,
#' date.col = "dates",
#' time.period = "month",
#' xlab = "Month",
#' angle = 0)
#'
#' epicurve(data,
#' date.col = "dates",
#' time.period = "month",
#' shade.by = "sex",
#' xlab = "Month",
#' angle = 0)
#'
#' epicurve(data,
#' date.col = "dates",
#' time.period = "month",
#' fill.by = "sex",
#' xlab = "month",
#' angle = 0)
#'
#' epicurve(data,
#' date.col = "dates",
#' fill.by = "conf",
#' split.by = "sex")
#'
#' epicurve(data,
#' date.col = "dates",
#' time.period = "month",
#' start.at = "2014-01-01",
#' stop.at = "2016-04-20",
#' fill.by = "sex",
#' split.by = NULL,
#' shade.by = "conf",
#' xlab=NULL,
#' ylab="Count",
#' fill.by.legend.title = "Sex",
#' shade.by.legend.title = NULL,
#' angle = 0 ,
#' col.pal = 6,
#' label.breaks = 0,
#' epi.squares = FALSE,
#' na.rm = TRUE)
#'
#' data$dates.year.month = factor(format(data$dates, "%Y_%m"),
#' levels = unique(format(seq(min(data$dates),
#' max(data$dates), 1), "%Y_%m")))
#'
#' epicurve(x = data,
#' date.col = "dates.year.month",
#' time.period = "use.date.col.as.is",
#' start.at = "2015-02-01",
#' stop.at = "2015-06-22",
#' fill.by ="status",
#' split.by = NULL,
#' shade.by = NULL,
#' xlab = "Year_week",
#' ylab="Count",
#' fill.by.legend.title = "",
#' shade.by.legend.title = NULL,
#' angle = 90,
#' col.pal = 1,
#' label.breaks = 0,
#' epi.squares = TRUE,
#' na.rm = TRUE)
#'
#' @export
epicurve <- function(x,
date.col,
time.period = NULL,
start.at = NULL,
stop.at = NULL,
fill.by = NULL,
split.by = NULL,
shade.by = NULL,
xlab = NULL,
ylab = "Number of cases",
fill.by.legend.title = NULL,
shade.by.legend.title = NULL,
angle = 90,
col.pal = "phe",
label.breaks = 0,
epi.squares = TRUE,
blank.background = TRUE,
na.rm = TRUE) {
# make sure x is a data.frame
x = as.data.frame(x)
# check values supplied to col.pal argument
if(!(col.pal == "phe" | (col.pal >= 0 & col.pal <= 8))) {
col.pal = "phe"
warning("col.pal must either be an integer from 1 to 8 or 'phe',
setting col.pal='phe'")
}
# check values supplied to time.period argument
if(is.null(time.period)){
NULL
} else if(!(time.period %in% c("day", "year", "month", "quarter", "year.month",
"year.quarter", "iso.year", "iso.week",
"iso.year.week", "use.date.col.as.is"))){
stop("time.period must be either: day, year, quarter, month, year.quarter, year.month, iso.year, iso.week, iso.year.week, use.date.col.as.is, NULL")
} else {
NULL
}
##############################################################################
# Define factor column (date.col.temp) to be used along the x-axis
# if time.period argument is use.date.col.as.is then use date.col along the x-axis
time.period = ifelse(is.null(time.period), "NULL", time.period)
if (time.period == "use.date.col.as.is") {
x$date.col.temp = x[, date.col]
# otherwise convert the date provided in date.col to the time period specified
# in the time.period argument
} else {
# load get.dates function
get.dates = function(x){
if(class(x) == "Date"){
NULL
} else {
stop("x is not a date")
}
df = data.frame(day = as.character(x),
year = format(x, "%Y"),
month = format(x, "%m"))
df$year.month = paste0(df$year, df$month)
df$iso.year = sapply(strsplit(ISOweek(x), "-W"), function(x) x[1])
df$iso.week = sapply(strsplit(ISOweek(x), "-W"), function(x) x[2])
df$iso.year.week = gsub("-W", "", ISOweek(x))
df$quarter = NA
df$quarter[!is.na(df$day)] = sprintf("%02d", ceiling(as.numeric(as.character(df$month[!is.na(df$day)]))/3))
df$year.quarter = paste0(df$year, df$quarter)
df[is.na(df$day), ] = NA
df
}
# append the get.dates data.frame to the data.frame provided
x = data.frame(x, get.dates(x[, date.col]))
# create a new factor column for the x-axis (levels of the factor contain
# dates ranging from start.at to stop.at)
# if start.at and stop.at are not defined by user (i.e. are NULL) then
# auto generate start.at/stop.at
if(is.null(start.at)){
start.at = min(x[, date.col]) - 5
} else {
start.at = as.Date(start.at)
}
if(is.null(stop.at)){
stop.at = max(x[, date.col]) + 5
} else {
stop.at = as.Date(stop.at)
}
# if time.period are not defined by user (i.e. is NULL) then auto generate
# time.period
if(time.period == "NULL"){
n.days = length(seq(start.at, stop.at, 1))
if(n.days < 31*2){
time.period = "day"
if(is.null(xlab)) xlab = "Day"
} else if (n.days < 365) {
time.period = "iso.year.week"
if(is.null(xlab)) xlab = "ISO Year Week"
} else {
time.period = "year.month"
if(is.null(xlab)) xlab = "Year - Month"
}
} else {
NULL
}
all.dates = get.dates(seq(start.at, stop.at, 1))
all.dates = unique(all.dates[, time.period])
x$date.col.temp = factor(x[, time.period],
levels = all.dates)
# recode dates that fall outside of start.at/stop.at to NA
x[!(as.character(x[, date.col]) %in%
as.character(get.dates(seq(start.at, stop.at, 1))$day)), "date.col.temp"] = NA
## REMOVE MISSING DATES ##
message(paste(sum(is.na(x$date.col.temp)), "rows have missing dates OR dates outside of the start/stop period"))
if(na.rm) x = x[!is.na(x$date.col.temp), ]
# order the levels of the date.col.temp column
x$date.col.temp = factor(x$date.col.temp,
levels = sort(levels(x$date.col.temp)))
}
# we have now defined the factor column (date.col.temp) to be used along the x-axis
##############################################################################
# order data for plotting
if(!is.null(fill.by) & !is.null(shade.by)){
x = x[order(x[, fill.by], x[, shade.by]), ]
} else if(!is.null(fill.by)){
x = x[order(x[, fill.by]), ]
} else if(!is.null(shade.by)){
x = x[order(x[, shade.by]), ]
} else{
NULL
}
# add dummy fill.by column if fill.by = NULL
if(is.null(fill.by)){
fill.by = ".dummy"
x$.dummy = "dummy"
} else {
NULL
}
# create blocks column (this is to allow for epi squares to be added)
x$blocks = 1:nrow(x)
##############################################################################
# generate plot
# generate main body of plot
p = ggplot(x)
# add geom_bar layer with either epi-squares or no epi-squares
if(epi.squares){
p = p + geom_bar(aes_string(x = "date.col.temp", fill = fill.by, alpha = shade.by, group = "blocks"),
colour = "black")
} else {
p = p + geom_bar(aes_string(x = "date.col.temp", fill = fill.by, alpha = shade.by),
colour = "black")
}
# add labs
p = p + labs(x = xlab, y = ylab)
# add x-axis label breaks
p = p + scale_x_discrete(breaks = levels(x$date.col.temp)[c(T, rep(F, label.breaks))],
drop = FALSE)
# format y-axis breaks
p = p + scale_y_continuous(breaks = function(x) unique(floor(pretty(seq(0, (max(x) + 1)*1.1)))),
expand = c(0,0))
# add a solid line running across the bottom of the figure
p = p + geom_hline(aes(yintercept = 0))
# add theme aesthetics
p = p + theme(title = element_text(size = 11, colour = "black", face = "bold"),
axis.title.x = element_text(size = 13, face = "bold", margin = margin(t = 20, r = 0, b = 0, l = 0)),
axis.title.y = element_text(size = 13, face = "bold", margin = margin(t = 0, r = 20, b = 0, l = 0)),
axis.text.x = element_text(angle = angle, hjust = 0.5, vjust = 0, size = 11, face = "plain", colour = "black"),
axis.text.y = element_text(hjust = 0, vjust = 0.5, size = 11, face = "plain", colour = "black"),
legend.title = element_text(size = 11, face = "bold", colour = "black"),
legend.text= element_text(hjust = 1, size = 11, face = "plain", colour = "black"),
legend.position = "right",
legend.justification = c(0.018,0.975),
legend.text.align = 0,
strip.text.y = element_text(hjust = 1, size = 13, colour = "black", face = "bold"),
plot.margin = (unit(c(0.5, 0.5, 0.5, 0.5), "cm")))
# remove background if specified in blank.background argument
if (blank.background) {
p = p + theme(panel.background = element_blank())
} else {
NULL
}
# add labels for the fill.by and shade.by legends
p = p + labs(fill = fill.by.legend.title,
alpha = shade.by.legend.title)
# specify a range for the shady.by level
p = p + scale_alpha_discrete(range = c(0.35, 1))
# facet using split.by
if (!is.null(split.by)) p = p + facet_grid(paste(split.by, ".", sep = "~"),
drop = FALSE)
# add the phe colour palette or a generic colour palette
if (col.pal == "phe") {
phe.cols = c("#822433", "#00B092", "#002776", "#EAAB00", "#8CB8C6",
"#E9994A", "#00A551", "#A4AEB5", "#00549F", "#DAD7CB")
p = p + scale_fill_manual(values = phe.cols, drop = FALSE)
} else if (!is.null(col.pal)) {
p = p + scale_fill_brewer(type = "qual",
palette = col.pal, drop = FALSE)
} else {
NULL
}
# remove dummy legend if fill.by = NULL
if(fill.by == ".dummy"){
p = p + theme(legend.position = "none")
} else {
NULL
}
# return the final output
p
}
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