source : stackoverflow.com
r – plot residuals in spatstat without overlaying points
The data points are not being “over-plotted” on top of the residuals: the residual measure includes an ‘atom’ of mass at each data point, together with a smooth density, so the plot is correct.
If the problem is that you can’t see the detail because the symbols representing the atoms are too large, then you could just reduce the scale of these symbols, using one of the arguments markscale or maxsize which will be passed to plot.ppp.
Then again, if there are a lot of data points, you might be better to just smooth the residual measure. If res is the residual measure you calculated, then try plot(Smooth(res)). See the help for Smooth.msr for further information.
If you really need to extract the smooth density component of the residual measure, you could follow Ege’s advice, or alternatively use with.msr. For example
with(res, Smooth(qlocations %mark% density))
gives an image representing the continuous component of the residual measure.
These comments only apply for the raw residuals, where all atoms have equal mass 1. For other types of residuals, the atoms have unequal masses, and it becomes more important to display them.
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