Epidemiological epicurve

[Yuster Ronoh]

Dear list members I have the dataset  and I want to construct the epicurve similar to this. 

This is the code I used

>flu <- read.csv("C:/Users/symon/Desktop/flu epicurve.csv")

> require(date)

 # Format the date

> flu$Date_epi <- strptime(flu$Date_epi, format= "%d/%m/%Y")

>format(flu$Date_epi, format="%Y-%m-%d")

> str(flu)

# plot the epicurve

> hist(flu$Date_epi[(flu$Sex=="F")], "weeks", 

    format = "%d %b %Y", freq=T, col=rgb(0,0,0,1), axes=F, main="")

> hist(flu$Date_epi[(flu$Sex=="M")], "weeks", 

     format = "%d %b %y", freq=T, col=rgb(0,0,0,1), axes=F, main="")

> axis.Date(1, at=seq(as.Date("2014-06-03"), as.Date("2014-07-19"), by="1 week"), format="%d %b %y")

> axis.Date(1, at=seq(as.Date("2014-06-03"), as.Date("2014-07-19"), by="weeks"), 

          labels=F, tcl= -0.5)

But this is what I obtain(two different graph) than what I expected) could anyone help me plot the epicurve similar to the above

​​

[Roman Luštrik]

What about something like this?

flu$Date_epi <- strptime(flu$Date_epi, format= "%Y-%m-%d")

library(ggplot2)

ggplot(flu, aes(x = Date_epi, fill = Classification)) +

  theme_bw() +

  geom_histogram(position = "dodge")

I don't know which variable you want to use to group the data, I chose Classification.

Cheers,

Roman

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[Yuster Ronoh]

Thanks Roman for swift reply. The variables I am intending to use are Date_epi for epidemiological weeks by Sex since the data was abstracted from all patients tested positive Influenza A.

I ran the code but I run to an error and could not figured it out to manouver it.

> ggplot(flu, aes(x = Date_epi, fill = Classification)) +

+   theme_bw() +

+   geom_histogram(position = "dodge")

stat_bin: binwidth defaulted to range/30. Use 'binwidth = x' to adjust this.

Error in exists(name, envir = env, mode = mode) : 

  argument "env" is missing, with no default