2 May 2012

knitr-Example: Use World Bank Data to Generate Report for Threatened Bird Species

I'll use the below script that retrieves data for threatened bird species from the World Bank via its API and does some processing, plotting and analysis. There is a package (WDI) that allows you to access the data easily.









# world bank indicators for species - 
# I'll check bird species:
code <- as.character(WDIsearch("bird")[1,1])
bird_data <- WDI(country="all", indicator=code, start=2010, end=2012)

# remove NAs and select values in the range 50 - 1000:
bird_data_sub <- bird_data[!is.na(bird_data$EN.BIR.THRD.NO)&
                           bird_data$EN.BIR.THRD.NO < 1000&
                           bird_data$EN.BIR.THRD.NO > 50, ]

# change in numbers across years 2010 and 2011:
change.no <- aggregate(EN.BIR.THRD.NO ~ country, diff,
                       data = bird_data_sub)
# plot:
par(mar = c(3, 3, 5, 1))
plot(x = change.no[,2], y = 1:nrow(change.no),
     xlim = c(-12, 12), xlab = "", ylab = "",
     yaxt = "n")
abline(v = 0, lty = 2, col = "grey80")
title(main = "Change in Threatened Bird Species in\nCountries with Rich Avifauna (>50)")
text(y = 1:nrow(change.no), 
     x = -2, adj = 1,
     labels = change.no$country)
segments(x0 = 0, y0 = 1:nrow(change.no),
         x1 = change.no[, 2], y1 =  1:nrow(change.no))

# test hypothesis that probability of species decrease is
# equal to probability of increase:
binom.test(sum(change.no < 0), sum(change.no != 0))
For generating the report you can source the script from dropbox.com and stitch it in this fashion:
stitch("http://dl.dropbox.com/s/ga0qbk1o17n17jj/Change_threatened_species.R")
..this is one line of code - can you dig it?..
BTW, for simplicity I use knitr::stitch with its default template...

You should get something like THIS PDF.

EDIT, MARCH 2013
OUTDATED! you can use this approach instead:

library(knitr); library(RCurl); library(WDI)

destfile = "script.txt"
x = getBinaryURL("https://dl.dropbox.com/s/ga0qbk1o17n17jj/Change_threatened_species.R", followlocation = TRUE, ssl.verifypeer = FALSE)
writeBin(x, destfile, useBytes = TRUE)
source(paste(tempdir(), "/script.txt", sep = ""))

stitch(paste(tempdir(), "/script.txt", sep = ""))

4 comments :

  1. Dear Kay, thanks for your interesting example. I am curious that how the font/fig size could be controlled with kintr. And, how about choosing different fonts, colors for texts?

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    Replies
    1. You would set the parameters in the template (the .Rnw file)
      please also see:
      ?knitr::stitch

      The .Rnw that I used (default) can be viewed by:

      shell.exec(system.file("examples", "knitr-minimal.Rnw", package = "knitr"))

      Note that you need to define a standard program for opening files with the .Rnw extension (Word-Pad, i.e.)

      Yours,
      Kay

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    2. Vincent Arel-Bundock3 May 2012 17:09

      Glad to see I'm not the only one using WDI() :)

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    3. Of course I'm using it! BTW, many thanks for contributing your valueable work to the R-community!

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