The digitize Package: Extracting Numerical Data from ... - The R Journal
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The digitize Package: Extracting Numerical Data from ... - The R Journal
traction of data from a graph whose source is not available. The package digitize, that I present here, allows a ... gra
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The digitize Package: Extracting Numerical Data from Scatterplots by Timothée Poisot Abstract I present the small R package digitize, designed to extract data from scatterplots with a simple method and suited to small datasets. I present an application of this method to the extraction of data from a graph whose source is not available. The package digitize, that I present here, allows a user to load a graphical file of a scatterplot (with the help of the read.jpeg function of the ReadImages package) in the graphical window of R, and to use the locator function to calibrate and extract the data. Calibration is done by setting four reference points on the original graph axis, two for the x values and two for the y values. The use of four points for calibration is justified by the fact that it makes calibrations on the axis possible, as y data are not taken into account for calibration of the x axis, and vice versa. This is useful when working on data that are not available in digital form, e.g. when integrating old papers in meta-analyses. Several commercial or free software packages allow a user to extract data from a plot in image format, among which we can cite PlotDigitizer (http://plotdigitizer.sourceforge. net/) or the commercial package GraphClick (http: //www.arizona-software.ch/graphclick/). While these programs are powerful and quite ergonomic, for some lightweight use, one may want to load the graph directly into R, and as a result get the data directly in R format. This paper presents a rapid digitization of a scatterplot and subsequent statistical analysis of the data. As an example, we will use the data presented by Jacques Monod in a seminal microbiology paper (Monod, 1949). The original paper presents the growth rate (in terms of divisions per hour) of the bacterium Escherichia coli in media of increasing glucose concentration. Such a hyperbolic relationship is best represented by the equation R = RK
C , C1 + C
where R is the growth rate at a given concentration of nutrients C, RK is the maximal growth rate, C1 is the concentration of nutrients at which R = 0.5RK . In R, this function is written as MonodGrowth
