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

May 2, 2012
By

(This article was first published on theBioBucket*, and kindly contributed to R-bloggers)

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OUTDATED!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 = ""))

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