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

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

Ill 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 - 
# Ill 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 Countries 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OUTDATED!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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