Epidemiology is the study of the occurrence and distribution of health-related events, states, and processes in specified populations, including the study of the determinants influencing such processes, and the application of this knowledge to control relevant health problems (Centers for Disease Control and Prevention 2006; Porta, Greenland, and Last 2014).
This vignette provides instruction on the use of R and
epiR
for descriptive epidemiological analyses, that is, to
describe how the frequency of disease varies by individual, place and
time.
The EpiToolbox app for iPhone
and Android
devices provides access to many of the descriptive and analytical
functions in epiR
using a smart phone.
The frequency of disease can be reported in terms of either prevalence or incidence.
Some definitions. Strictly speaking, ‘prevalence’ equals the number of cases of a given disease or attribute that exists in a population at a specified point in time. Prevalence risk is the proportion of a population that has a given disease or attribute at a specified point in time. Many authors use the term ‘prevalence’ when they really mean prevalence risk, and this vignette will follow this convention.
Two types of prevalence are reported in the literature: (1) point prevalence equals the proportion of a population in a diseased state at a single point in time; (2) period prevalence equals the proportion of a population with a given disease or condition over a specific period of time (i.e., the number of existing cases at the start of a follow-up period plus the number of incident cases that occur during the follow-up period).
Incidence provides a measure of how frequently susceptible individuals become disease cases as they are observed over time. An incident case occurs when an individual changes from being susceptible to being diseased. The count of incident cases is the number of such events that occur in a population over a defined follow-up period. There are two ways to express incidence:
Incidence risk (also known as cumulative incidence) is the proportion of initially susceptible individuals in a population that become new cases over a defined follow-up period.
Incidence rate (also known as incidence density) is the number of new cases of disease that occur per unit of individual time at risk over a defined follow-up period.
In addition to reporting the point estimate of disease frequency, it
is important to provide an indication of the uncertainty around that
point estimate. The epi.conf
function in the
epiR
package allows you to calculate confidence intervals
for prevalence, incidence risks and incidence rates.
Let’s say we’re interested in the prevalence of disease X in a population comprised of 1000 individuals. Two hundred are tested and four returned a positive result. Assuming 100% diagnostic test sensitivity and specificity, what is the estimated prevalence of disease X in this population?
library(epiR); library(ggplot2); library(scales); library(zoo)
ncas <- 4; npop <- 200
tmp <- as.matrix(cbind(ncas, npop))
epi.conf(tmp, ctype = "prevalence", method = "exact", N = 1000, design = 1,
conf.level = 0.95) * 100
#> est lower upper
#> 1 2 0.5475566 5.041361
The estimated prevalence of disease X in this population is 2.0 (95% confidence interval [CI] 0.55 to 5.0) cases per 100 individuals at risk.
Another example. A study was conducted by Feychting, Osterlund, and Ahlbom (1998) to report the frequency of cancer among the blind. A total of 136 diagnoses of cancer were made from 22,050 person-years at risk. What was the incidence rate of cancer in this population?
ncas <- 136; ntar <- 22050
tmp <- as.matrix(cbind(ncas, ntar))
epi.conf(tmp, ctype = "inc.rate", method = "exact", N = 1000, design = 1,
conf.level = 0.95) * 1000
#> est lower upper
#> ncas 6.1678 5.174806 7.295817
The incidence rate of cancer in this population was 6.2 (95% CI 5.2 to 7.3) cases per 1000 person-years at risk.
We now want to compare the frequency of disease across several populations. An effective way to do this is to use a ranked error bar plot. With a ranked error bar plot the points represent the point estimate of the measure of disease frequency and the error bars indicate the 95% confidence interval around each estimate. With a ranked error bar plot the disease frequency estimates are plotted from lowest to highest. Generate some data:
ncas <- c(347,444,145,156,56,618,203,113,10,30,663,447,213,52,256,216,745,97,31,250,430,494,96,544,352)
npop <- c(477,515,1114,625,69,1301,309,840,68,100,1375,1290,1289,95,307,354,1393,307,35,364,494,1097,261,615,508)
rname <- paste("Region ", 1:length(npop), sep = "")
dat.df <- data.frame(rname,ncas,npop)
Calculate the prevalence of disease in each region and its 95%
confidence interval. The function epi.conf
provides several
options for confidence interval calculation methods for prevalence. For
this example we’ll use the exact method:
tmp <- as.matrix(cbind(dat.df$ncas, dat.df$npop))
tmp <- epi.conf(tmp, ctype = "prevalence", method = "exact", N = 1000, design = 1,
conf.level = 0.95) * 100
dat.df <- cbind(dat.df, tmp)
head(dat.df)
#> rname ncas npop est lower upper
#> 1 Region 1 347 477 72.74633 68.51271 76.69532
#> 2 Region 2 444 515 86.21359 82.93082 89.07325
#> 3 Region 3 145 1114 13.01616 11.09506 15.13489
#> 4 Region 4 156 625 24.96000 21.61207 28.54645
#> 5 Region 5 56 69 81.15942 69.93958 89.56878
#> 6 Region 6 618 1301 47.50192 44.75821 50.25695
Sort the data in order of variable est
, assign a 1 to
n
identifier as variable rank
and make a copy
of dat.df$rname
:
dat.df <- dat.df[sort.list(dat.df$est),]
dat.df$rank <- 1:nrow(dat.df)
dat.df$labels <- dat.df$rname
Create a ranked error bar plot. Because its useful to provide the region-area names on the horizontal axis rotate the horizontal axis labels by 90 degrees.
ggplot(data = dat.df, aes(x = rank, y = est)) +
theme_bw() +
geom_errorbar(aes(ymin = lower, ymax = upper), width = 0.1) +
geom_point() +
scale_x_continuous(limits = c(0,25), breaks = dat.df$rank, labels = dat.df$labels, name = "Region") +
scale_y_continuous(limits = c(0,100), name = "Cases per 100 individuals at risk") +
theme(axis.text.x = element_text(angle = 90, hjust = 1))
If you have a large number of regions the horizontal axis labels can
become crowded and difficult to read. Use the ndelete
function to drop every n
th region name.
ndelete <- function(x, n){
id <- seq(from = 1, to = length(x), by = n)
rval <- rep("", times = length(x))
rval[id] <- x[id]
rval
}
dat.df$labels <- ndelete(x = dat.df$rname, n = 2)
Re-draw the ranked error bar plot:
ggplot(data = dat.df, aes(x = rank, y = est)) +
theme_bw() +
geom_errorbar(aes(ymin = lower, ymax = upper), width = 0.1) +
geom_point() +
scale_x_continuous(limits = c(0,25), breaks = dat.df$rank, labels = dat.df$labels, name = "Region") +
scale_y_continuous(limits = c(0,100), name = "Cases per 100 individuals at risk") +
theme(axis.text.x = element_text(angle = 90, hjust = 1))
Epidemic curves are used to describe patterns of disease over time. Epidemic curve data are often presented in one of two formats:
One row for each individual identified as a case with an event date assigned to each.
One row for every event date with an integer representing the number of cases identified on that date.
In the notes that follow we provide details on how to produce an epidemic curve when you’re data are in these formats.
Generate some data, with one row for every individual identified as a case:
n.males <- 100; n.females <- 50
odate <- seq(from = as.Date("2024-07-26"), to = as.Date("2024-12-13"), by = 1)
prob <- c(1:100, 41:1); prob <- prob / sum(prob)
modate <- sample(x = odate, size = n.males, replace = TRUE, p = prob)
fodate <- sample(x = odate, size = n.females, replace = TRUE)
dat.df <- data.frame(sex = c(rep("Male", n.males), rep("Female", n.females)),
odate = c(modate, fodate))
# Sort the data in order of odate:
dat.df <- dat.df[sort.list(dat.df$odate),]
Plot the epidemic curve using the ggplot2
and
scales
packages:
ggplot(data = dat.df, aes(x = as.Date(odate))) +
theme_bw() +
geom_histogram(binwidth = 7, colour = "gray", fill = "dark blue", linewidth = 0.1) +
scale_x_date(breaks = date_breaks("7 days"), labels = date_format("%d %b"),
name = "Date") +
scale_y_continuous(breaks = seq(from = 0, to = 30, by = 5), limits = c(0,30), name = "Number of cases") +
theme(axis.text.x = element_text(angle = 90, hjust = 1))
You may want to superimpose a smoothed line to better appreciate
trend. Do this using the geom_density
function in
ggplot2
:
ggplot(data = dat.df, aes(x = odate)) +
theme_bw() +
geom_histogram(binwidth = 7, colour = "gray", fill = "dark blue", linewidth = 0.1) +
geom_density(aes(y = after_stat(density) * (nrow(dat.df) * 7)), colour = "red") +
scale_x_date(breaks = date_breaks("7 days"), labels = date_format("%d %b"),
name = "Date") +
scale_y_continuous(breaks = seq(from = 0, to = 30, by = 5), limits = c(0,30), name = "Number of cases") +
theme(axis.text.x = element_text(angle = 90, hjust = 1))
Produce a separate epidemic curve for males and females using the
facet_grid
option in ggplot2
:
ggplot(data = dat.df, aes(x = as.Date(odate))) +
theme_bw() +
geom_histogram(binwidth = 7, colour = "gray", fill = "dark blue", linewidth = 0.1) +
scale_x_date(breaks = date_breaks("1 week"), labels = date_format("%d %b"),
name = "Date") +
scale_y_continuous(breaks = seq(from = 0, to = 30, by = 5), limits = c(0,30), name = "Number of cases") +
theme(axis.text.x = element_text(angle = 90, hjust = 1)) +
facet_grid( ~ sex)
Let’s say an event occurred on 31 October 2024. Mark this date on
your epidemic curve using geom_vline
:
ggplot(data = dat.df, aes(x = as.Date(odate))) +
theme_bw() +
geom_histogram(binwidth = 7, colour = "gray", fill = "dark blue", linewidth = 0.1) +
scale_x_date(breaks = date_breaks("1 week"), labels = date_format("%d %b"),
name = "Date") +
scale_y_continuous(breaks = seq(from = 0, to = 30, by = 5), limits = c(0,30), name = "Number of cases") +
theme(axis.text.x = element_text(angle = 90, hjust = 1)) +
facet_grid( ~ sex) +
geom_vline(aes(xintercept = as.numeric(as.Date("31/10/2024", format = "%d/%m/%Y"))),
linetype = "dashed")
Plot the total number of disease events by day, coloured according to sex:
ggplot(data = dat.df, aes(x = as.Date(odate), group = sex, fill = sex)) +
theme_bw() +
geom_histogram(binwidth = 7, colour = "gray", linewidth = 0.1) +
scale_x_date(breaks = date_breaks("1 week"), labels = date_format("%d %b"),
name = "Date") +
scale_y_continuous(breaks = seq(from = 0, to = 30, by = 5), limits = c(0,30), name = "Number of cases") +
theme(axis.text.x = element_text(angle = 90, hjust = 1)) +
geom_vline(aes(xintercept = as.numeric(as.Date("31/10/2024", format = "%d/%m/%Y"))),
linetype = "dashed") +
scale_fill_manual(values = c("#d46a6a", "#738ca6"), name = "Sex") +
theme(legend.position = c(0.90, 0.80))
#> Warning: A numeric `legend.position` argument in `theme()` was deprecated in ggplot2
#> 3.5.0.
#> ℹ Please use the `legend.position.inside` argument of `theme()` instead.
#> This warning is displayed once every 8 hours.
#> Call `lifecycle::last_lifecycle_warnings()` to see where this warning was
#> generated.
It can be difficult to appreciate differences in male and female disease counts as a function of date with the above plot format so dodge the data instead:
ggplot(data = dat.df, aes(x = as.Date(odate), group = sex, fill = sex)) +
theme_bw() +
geom_histogram(binwidth = 7, colour = "gray", linewidth = 0.1, position = "dodge") +
scale_x_date(breaks = date_breaks("1 week"), labels = date_format("%d %b"),
name = "Date") +
scale_y_continuous(breaks = seq(from = 0, to = 30, by = 5), limits = c(0,30), name = "Number of cases") +
theme(axis.text.x = element_text(angle = 90, hjust = 1)) +
geom_vline(aes(xintercept = as.numeric(as.Date("31/10/2024", format = "%d/%m/%Y"))),
linetype = "dashed") +
scale_fill_manual(values = c("#d46a6a", "#738ca6"), name = "Sex") +
theme(legend.position = c(0.90, 0.80))
We now provide code to deal with the situation where the data are presented with one row for every date during an outbreak and an integer representing the number of cases identified on each date.
Actual outbreak data will be used for this example. In the code below
edate
represents the event date (i.e., the date of case
detection) and ncas
represents the number of cases
identified on each edate
.
edate <- seq(from = as.Date("2024-02-24"), to = as.Date("2024-07-20"), by = 1)
ncas <- c(1,0,0,1,0,1,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,2,0,0,1,0,0,0,0,2,
0,0,1,0,1,1,2,3,2,5,10,15,5,7,17,37,31,34,42,46,73,58,67,57,54,104,77,52,
90,59,64,61,21,26,25,32,24,14,11,23,6,8,9,4,5,7,14,14,1,5,1,1,5,3,3,1,3,3,
7,5,10,11,21,14,16,15,13,13,8,5,16,7,9,19,13,5,6,6,5,5,10,9,2,2,5,8,10,6,
8,8,4,9,7,8,3,1,4,2,0,4,8,5,8,10,12,8,20,16,11,25,19)
dat.df <- data.frame(edate, ncas)
dat.df$edate <- as.Date(dat.df$edate, format = "%Y-%m-%d")
head(dat.df)
#> edate ncas
#> 1 2024-02-24 1
#> 2 2024-02-25 0
#> 3 2024-02-26 0
#> 4 2024-02-27 1
#> 5 2024-02-28 0
#> 6 2024-02-29 1
Generate an epidemic curve. Note weight = ncas
in the
aesthetics argument for ggplot2
:
ggplot() +
theme_bw() +
geom_histogram(dat.df, mapping = aes(x = edate, weight = ncas), binwidth = 1, fill = "#738ca6", colour = "grey", linewidth = 0.1) +
scale_x_date(breaks = date_breaks("2 weeks"), labels = date_format("%b %Y"),
name = "Date") +
scale_y_continuous(limits = c(0,125), name = "Number of cases") +
theme(axis.text.x = element_text(angle = 90, hjust = 1))
This plot has features of a common point source epidemic for the period April 2024 to May 2024. After May 2024 the plot shows feature of a propagated epidemic pattern.
Add a line to the plot to show the cumulative number of cases
detected as a function of calendar date. The coding here requires some
thought. First question: What was the cumulative number of cases at the
end of the follow-up period? Use the cumsum
(cumulative
sum) function in base R:
max(cumsum(dat.df$ncas))
#> [1] 1834
At the end of the follow-up period the cumulative number of cases was
1834. What we need to do is to get our 0 to 1834 cumulative case numbers
to ‘fit’ into the 0 to 125 vertical axis limits of the epidemic curve. A
reasonable approach would be to: (1) divide cumulative case numbers by a
number so that the maximum cumulative case number divided by our
selected number roughly equals the maximum number of cases identified
per day; for this example, 15 would be a good choice (1834 / 15 = 122);
and (2) set sec.axis = sec_axis(~ . * 15)
to multiply the
values that appear on the primary vertical axis by 15 for the labels
that appear on the secondary vertical axis:
ggplot() +
theme_bw() +
geom_histogram(data = dat.df, mapping = aes(x = edate, weight = ncas), binwidth = 1, fill = "#738ca6", colour = "grey", linewidth = 0.1) +
geom_line(data = dat.df, mapping = aes(x = edate, y = cumsum(ncas) / 15)) +
scale_x_date(breaks = date_breaks("2 weeks"), labels = date_format("%b %Y"),
name = "Date") +
scale_y_continuous(limits = c(0,125), name = "Number of cases",
sec.axis = sec_axis(~ . * 15, name = "Cumulative number of cases")) +
guides(fill = "none") +
theme(axis.text.x = element_text(angle = 90, hjust = 1))
Finally, we might want to superimpose a line representing the rolling
average of case numbers. Calculate the 5-day rolling mean use the
rollmean
function in the contributed zoo
package:
dat.df$rncas <- rollmean(x = dat.df$ncas, k = 5, fill = NA)
ggplot() +
theme_bw() +
geom_histogram(data = dat.df, mapping = aes(x = edate, weight = ncas), binwidth = 1, fill = "#738ca6", colour = "grey", linewidth = 0.1) +
geom_line(data = dat.df, mapping = aes(x = edate, y = rncas), colour = "red") +
scale_x_date(breaks = date_breaks("2 weeks"), labels = date_format("%b %Y"),
name = "Date") +
scale_y_continuous(limits = c(0,125), name = "Number of cases") +
guides(fill = "none") +
theme(axis.text.x = element_text(angle = 90, hjust = 1))
#> Warning: Removed 4 rows containing missing values or values outside the scale range
#> (`geom_line()`).
Two types of maps are often used when describing patterns of disease by place:
Choropleth maps. Choropleth mapping involves producing a summary statistic of the outcome of interest (e.g. count of disease events, prevalence, incidence) for each component area within a study region. A map is created by ‘filling’ (i.e. colouring) each component area with colour, providing an indication of the magnitude of the variable of interest and how it varies geographically.
Point maps.
Choropleth maps
For illustration we make a choropleth map of the percentage of
individuals aged greater than 65 years in an area of New York, USA.
These data are taken from the data sets supporting Waller and Gotway (2004). In the code that follows
ny
refers to New York, age65
refers to
individuals aged greater than 65 years and utm
refers to
the spatial projection of the sf
object (Universal
Transverse Mercator). The object name suffix .sf
tells you
that this is a spatial features object.
library(sf); library(spData); library(plyr); library(RColorBrewer); library(sp); library(spatstat)
nyage65utm.sf <- st_read(dsn = system.file("shapes/NY8_bna_utm18.gpkg", package = "spData")[1])
#> Reading layer `sf_bna2_utm18' from data source
#> `C:\Users\marks1\AppData\Local\R\win-library\4.4\spData\shapes\NY8_bna_utm18.gpkg'
#> using driver `GPKG'
#> Simple feature collection with 281 features and 12 fields
#> Geometry type: MULTIPOLYGON
#> Dimension: XY
#> Bounding box: xmin: 357628 ymin: 4649538 xmax: 480360.3 ymax: 4808317
#> Projected CRS: UTM Zone 18, Northern Hemisphere
head(nyage65utm.sf)
#> Simple feature collection with 6 features and 12 fields
#> Geometry type: MULTIPOLYGON
#> Dimension: XY
#> Bounding box: xmin: 421391.6 ymin: 4661130 xmax: 427059.6 ymax: 4664600
#> Projected CRS: UTM Zone 18, Northern Hemisphere
#> AREAKEY AREANAME X Y POP8 TRACTCAS PROPCAS
#> 1 36007000100 Binghamton city 4.069397 -67.3533 3540 3.08 0.000870
#> 2 36007000200 Binghamton city 4.639371 -66.8619 3560 4.08 0.001146
#> 3 36007000300 Binghamton city 5.709063 -66.9775 3739 1.09 0.000292
#> 4 36007000400 Binghamton city 7.613831 -65.9958 2784 1.07 0.000384
#> 5 36007000500 Binghamton city 7.315968 -67.3183 2571 3.06 0.001190
#> 6 36007000600 Binghamton city 8.558753 -66.9344 2729 1.06 0.000388
#> PCTOWNHOME PCTAGE65P Z AVGIDIST PEXPOSURE
#> 1 0.3277311 0.1466102 0.14197 0.2373852 3.167099
#> 2 0.4268293 0.2351124 0.35555 0.2087413 3.038511
#> 3 0.3377396 0.1380048 -0.58165 0.1708548 2.838229
#> 4 0.4616048 0.1188937 -0.29634 0.1406045 2.643366
#> 5 0.1924370 0.1415791 0.45689 0.1577753 2.758587
#> 6 0.3651786 0.1410773 -0.28123 0.1726033 2.848411
#> geom
#> 1 MULTIPOLYGON (((421808.5 46...
#> 2 MULTIPOLYGON (((421794.6 46...
#> 3 MULTIPOLYGON (((423127.5 46...
#> 4 MULTIPOLYGON (((425229.9 46...
#> 5 MULTIPOLYGON (((425001.4 46...
#> 6 MULTIPOLYGON (((426143.9 46...
The nyage65utm.sf
simple features object lists for each
census tract the percentage of individuals aged greater than 65
years:
ggplot() +
theme_bw() +
geom_sf(data = nyage65utm.sf, aes(fill = PCTAGE65P), colour = "dark grey") +
scale_fill_gradientn(limits = c(0,0.5), colours = brewer.pal(n = 5, "Reds"), guide = "colourbar") +
scale_x_continuous(name = "Longitude") +
scale_y_continuous(name = "Latitude") +
labs(fill = "Age >65 years")
Point maps
Between 1972 and 1980 an industrial waste incinerator operated at a site about 2 kilometres southwest of the town of Coppull in Lancashire, England. Addressing community concerns that there were greater than expected numbers of laryngeal cancer cases in close proximity to the incinerator Diggle (1990) conducted a study investigating risks for laryngeal cancer, using recorded cases of lung cancer as controls. The study area is 20 km x 20 km in size and includes location of residence of patients diagnosed with each cancer type from 1974 to 1983.
Load the chorley
data set from the spatstat
package. The point locations in this data are projected using the
British National Grid coordinate reference system (EPSG code 27700).
Create an observation window for the data as coppull.ow
and
a ppp
object for plotting:
data(chorley)
chorley.df <- data.frame(xcoord = chorley$x * 1000, ycoord = chorley$y * 1000, status = chorley$marks)
chorley.df$status <- factor(chorley.df$status, levels = c("lung","larynx"), labels = c("Lung","Larynx"))
chlarynxbng.sf <- st_as_sf(chorley.df, coords = c("xcoord","ycoord"), remove = FALSE)
st_crs(chlarynxbng.sf) <- 27700
chlarynxbng.ow <- chorley$window
Create a simple features polygon object from coppull.ow
.
First we convert chlarynxbng.ow
to a
SpatialPolygonsDataFrame
object:
coords <- matrix(c(chlarynxbng.ow$bdry[[1]]$x * 1000, chlarynxbng.ow$bdry[[1]]$y * 1000), ncol = 2, byrow = FALSE)
pol <- Polygon(coords, hole = FALSE)
pol <- Polygons(list(pol),1)
pol <- SpatialPolygons(list(pol))
chpolbng.spdf <- SpatialPolygonsDataFrame(Sr = pol, data = data.frame(id = 1), match.ID = TRUE)
Convert the SpatialPolygonsDataFrame
to an
sf
object and set the coordinate reference system:
chpolbng.sf <- as(chpolbng.spdf, "sf")
st_crs(chpolbng.sf) <- 27700
The mformat
function is used to plot the axis labels in
kilometres (instead of metres):
mformat <- function(){
function(x) format(x / 1000, digits = 2)
}
ggplot() +
theme_bw() +
geom_sf(data = chlarynxbng.sf, aes(colour = status, shape = status)) +
geom_sf(data = chpolbng.sf, fill = "transparent", colour = "black") +
coord_sf(datum = st_crs(chpolbng.sf)) +
scale_colour_manual(name = "Type", values = c("grey","red")) +
scale_shape_manual(name = "Type", values = c(1,16)) +
scale_x_continuous(name = "Easting (km)", labels = mformat()) +
scale_y_continuous(name = "Northing (km)", labels = mformat()) +
theme(legend.position = c(0.10, 0.12))