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In version 1.1 the numerical output can be read by the GNUPLOT plotting package to produce a fully graphical output, although other plotting routines can be easily adapted.
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These features add additional value to an already powerful data analysis and plotting software package.
For visual comparison of univariate data we used bean plots as a combination of one-dimensional scatter plots and density plots were generated using the bean plot package for R statistical software [ 17].
For the native and the gelatinized starches data points were fitted using the Sigma plot package (Systat Software Inc) to a two parameters model: f =ax/(b+x), where "x" is the time and f the extent of degradation; "a" can be regarded as maximum asymptote and "b" can be regarded as the time to reach half of the maximum (Table 4).
Finally, absence of positive spatial autocorrelation in the residuals from the best model was verified by computing Moran I statistics and plotting spline correlogramme (package spdep in R).
Additional file 1 These are.dat files used for plotting graphs using pgfplot package.
Diffusion maps were created using the diffusionMap package available in the CRAN R repository, and then plotted using scatterplot3d package available from CRAN.
The same results were obtained using alternative implementations of ML ancestral reconstruction in R the ace function in the ape package (plotted as pie graphs in fig. 1 C) and pml functions in the phangorn package.
The density in windows was plotting using the R packages gplots and RColorBrewer.
The data were plotted using SigmaPlot software package (Systat Software).
The data were corrected for artifacts and plotted with the software package Gwyddion.
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