The digitize package: extracting numerical data from scatterplots

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Authors Timothée Poisot
Journal/Conference Name The R Journal
Paper Category
Paper 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 ex- traction 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 cal- ibration is justified by the fact that it makes calibra- tions 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 di- rectly in R format. This paper presents a rapid dig- itization 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 mi- crobiology paper (Monod, 1949). The original paper presents the growth rate (in terms of divisions per hour) of the bacterium Es- cherichia coli in media of increasing glucose concen- tration. Such a hyperbolic relationship is best repre- sented by the equation
Date of publication 2011
Code Programming Language R
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