Code to cleanup and read WHO immunization monitoring tables into R data frames.

who_immunization_tables.R

require(XML)
require(reshape2)

# node content cleanup
cleanup <- function(node) {
    val <- xmlValue(node)
    if(is.character(val) | is.factor(val)) {
        out <- gsub("'","", val, fixed=TRUE)
    } else {
        out <- val
    }
    gsub("\U3e32633c","", gsub("\xa0","", out, useBytes=TRUE))
}

# read table, parse, remove extraneous rows and put into a tidy data set
who2df <- function(url) {
    tbs <- readHTMLTable(doc=url, elFun=cleanup, trim=TRUE, stringsAsFactors=FALSE)
    df <- tbs[[2]][-c(1,2),]
    fields <- df[1,]
    df <- df[-1,]
    colnames(df) <- fields
    df <- df[-nrow(df),]
    df[df=="_"] <- NA
    for (fn in fields[-1]) {
        df[,fn] <- as.numeric(df[,fn])
    }
    df2 <- melt(df, id.vars="Diseases", variable.name="year", value.name="cases")
    df2$year <- as.numeric(as.character(df2$year))
    df2
}

# examples reading data for Peru (PER) and United States (USA)

url_who <- "http://apps.who.int/immunization_monitoring/globalsummary/incidences?c="
url_pe <- paste0(url_who, "PER")
url_us <- paste0(url_who, "USA")

df_pe <- who2df(url_pe)
df_us <- who2df(url_us)