The R code that follows appears as it would in your text editor. If you have 'epitools' installed and loaded in R on your computer, you can paste this code into your R program.
Step 1. Read in data set and try epicurve.dates function.
library(epitools)
wdat <- read.table("http://www.medepi.net/data/wnv/wnv2004-12-14.txt",
sep = ",", header = TRUE, as.is = TRUE)
##fig1
epicurve.dates(wdat$date.onset)
Step 2. Change default axis labeling.
##suppress default axis labels and then re-label
##fig2
xv <- epicurve.dates(wdat$date.onset, axisnames = FALSE)
axis(1, at = xv$xvals, labels = xv$cmday, tick = FALSE, line = 0)
axis(1, at = xv$xvals, labels = xv$cmonth, tick = FALSE, line = 1)
Step 3. Using colors.plot function, add some color to this plot. (See next example to see how colors.plot function works.) Also, suppress default x-axis labels and then specify the x-axis labels precisely.
##fig3
xv <- epicurve.dates(wdat$date.onset,
axisnames = FALSE, col = "royalblue1")
dd <- xv$cmday==1 | xv$cmday==15
dd2 <- xv$cmday==15
axis(1, at = xv$xvals[dd], labels = xv$cmday[dd], tick = FALSE, line = 0)
axis(1, at = xv$xvals[dd], labels = xv$cmonth[dd], tick = FALSE, line = 1)
Step 4. Try epicurve.weeks function, stratify by clinical syndrome, add default legend, and add titles, etc.
##fig4
xv <- epicurve.weeks(wdat$date.onset, strata = wdat$syndrome,
min.date = "2004-01-01", max.date = "2004-12-31",
axisnames = FALSE,
legend.text = TRUE)
axis(1, at = xv$xvals, labels = xv$cweek, tick = FALSE,
line = -0.5, cex.axis = 0.8)
axis(1, at = xv$xvals, labels = xv$cmonth, tick = FALSE,
line = 0.5, cex.axis = 0.8)
axis(1, at = median(xv$xvals), labels = "Disease Week & Calendar Month, 2004",
tick = FALSE, line = 1.5)
title(main = "West Nile Virus Human Cases Reported in California
by Disease Week as of December 14, 2004", ylab = "Cases")
Step 5. Use colorbrewer.display function to select sequential colors for 3 categories (similar to the sequential colors above).
colorbrewer.display(3, "seq")
Step 6. Use colorbrewer.palette function to create a palette and plot epidemic curve. Try red-like colors first.
seq3.r <- colorbrewer.palette(3, "seq", "r") ##red-like
seq3.a <- colorbrewer.palette(3, "seq", "a") ##blue-like
##Re-level syndrome categories using 'factor' function
##fig5
syndrome <- factor(wdat$syndrome, levels = c("WNND", "WNF", "Unknown"))
xv <- epicurve.weeks(wdat$date.onset, strata = syndrome,
min.date = "2004-01-01", max.date = "2004-12-31",
axisnames = FALSE, col = seq3.r[3:1],
legend.text = TRUE)
title(main = "West Nile Virus Human Cases Reported in California
by Disease Week as of December 14, 2004", ylab = "Cases")
axis(1, at = xv$xvals, labels = xv$cweek, tick = FALSE,
line = -0.5, cex.axis = 0.8)
axis(1, at = xv$xvals, labels = xv$cmonth, tick = FALSE,
line = 0.5, cex.axis = 0.8)
axis(1, at = median(xv$xvals), labels = "Disease Week & Calendar Month, 2004",
tick = FALSE, line = 1.5)
Step 7. Try blue-like colors and add annotations to the plot.
##fig6
syndrome <- factor(wdat$syndrome, levels = c("WNND", "WNF", "Unknown"))
xv <- epicurve.weeks(wdat$date.onset, strata = syndrome,
min.date = "2004-01-01", max.date = "2004-12-31",
axisnames = FALSE, col = seq3.a[3:1],
legend.text = TRUE)
title(main = "West Nile Virus Human Cases Reported in California
by Disease Week as of December 14, 2004", ylab = "Cases")
axis(1, at = xv$xvals, labels = xv$cweek, tick = FALSE,
line = -0.5, cex.axis = 0.8)
axis(1, at = xv$xvals, labels = xv$cmonth, tick = FALSE,
line = 0.5, cex.axis = 0.8)
axis(1, at = median(xv$xvals), labels = "Disease Week & Calendar Month, 2004",
tick = FALSE, line = 1.5)
##add arrows and annotations
zdates <- as.week(c("2004-02-24", "2004-04-14",
"2004-05-17", "2004-06-20"))
znames <- c("+ Bird\n2/24","+ Mosquito\n4/14",
"+ Chicken\n5/17","+ Horse\n6/20")
x0 <- c(xv$xvals[xv$cstratum==zdates$stratum[1]],
xv$xvals[xv$cstratum==zdates$stratum[2]],
xv$xvals[xv$cstratum==zdates$stratum[3]],
xv$xvals[xv$cstratum==zdates$stratum[4]])
y0 <- c(10,20,30,40)
x1 <- c(xv$xvals[xv$cstratum==zdates$stratum[1]],
xv$xvals[xv$cstratum==zdates$stratum[2]],
xv$xvals[xv$cstratum==zdates$stratum[3]],
xv$xvals[xv$cstratum==zdates$stratum[4]])
y1 <- c(0, 0, 6, 18)
arrows(x0, y0, x1, y1, length = 0.15)
text(x1, y0 + 5, znames, cex=.8)
Step 8.Try epicurve.months function. Which epidemic curve do you like best?
##fig7
syndrome <- factor(wdat$syndrome, levels = c("WNND", "WNF", "Unknown"))
xv <- epicurve.months(wdat$date.onset, strata = syndrome,
min.date = "2004-01-01", max.date = "2004-12-31",
axisnames = FALSE, col = seq3.a[3:1],
legend.text = TRUE)
title(main = "West Nile Virus Human Cases Reported in California
by Month as of December 14, 2004", ylab = "Cases")
axis(1, at = xv$xvals, labels = xv$cmonth, tick = FALSE, line = -0.5, cex.axis = 0.8)
axis(1, at = median(xv$xvals), labels = "Calendar 2004", tick = FALSE, line = 0.5)
