Views vs. Citations for PLOS Biology Articles

# code for figure 3: Bubblechart views vs. citations for
# PLOS Biology articles published in 2010.

# Load required libraries
library(plyr)

# load May 20, 2013 ALM report
alm <- read.csv("../data/alm_report_plos_biology_2013-05-20.csv", stringsAsFactors=FALSE, na.strings=c("0"))

# only look at papers published in 2010
alm$publication_date <- as.Date(alm$publication_date)
alm <- subset(alm, alm$publication_date > "2010-01-01" & alm$publication_date <= "2010-12-31")

# make sure counter values are numbers
alm$counter_html <- as.numeric(alm$counter_html)

# lump all papers together that are not research articles
reassignType <- function(x) if (x == "Research Article") 1 else 0
alm$article_group <- aaply(alm$article_type, 1, reassignType)

# calculate article age in months
alm$age_in_months <- (Sys.Date() - alm$publication_date) / 365.25 * 12
start_age_in_months <- floor(as.numeric(Sys.Date() - as.Date(strptime("2010-12-31", format = "%Y-%m-%d"))) / 365.25 * 12)

# chart variables
x <- alm$age_in_months
y <- alm$counter
z <- alm$scopus

xlab <- "Age in Months"
ylab <- "Total Views"

labels <- alm$article_group
col.main <- "#1ebd21"
col <- "#666358"

# calculate bubble diameter
z <- sqrt( z / pi )

# calculate bubble color
getColor <- function(x) c("#c9c9c7", "#1ebd21")[x+1]
colors <- aaply(labels, 1, getColor)

# plot the chart
opar <- par(mai=c(0.5,.75,0.5,0.5), omi=c(0.25,0.1,0.25,0.1), mgp=c(3,.5,.5), fg="black", cex=1, cex.main=2, cex.lab=1.5, col="white", col.main=col.main, col.lab=col)

plot(x, y, type = "n", xlim=c(start_age_in_months,start_age_in_months+13), ylim=c(0,60000), xlab=NA, ylab=NA, las=1)
symbols(x, y, circles=z, inches=exp(1.3)/15, bg=colors, xlim=c(start_age_in_months,start_age_in_months+13), ylim=c(0,ymax), xlab=NA, ylab=NA, las=1, add=TRUE)
mtext(xlab, side=1, col=col.main, cex=1.25, outer=TRUE, adj=1, at=1)
mtext(ylab, side=2, col=col.main, cex=1.25, outer=TRUE, adj=0, at=1, las=1)

par(opar)