re-initialize r2d3() in shiny renderd3? about r2d3 HOT 2 OPEN

This is 6 months late, but it might help someone else with the same question. I think your problem is in your d3 script. For each draw-iteration you add points and lines, and you should also remove unused values from the prior iteration. The d3 update pattern (https://bl.ocks.org/mbostock/3808218) shows a select, then a data join, then a merge, then a remove. In my limited experience r2d3 doesn't make good use of the merge function so I find just the select, join, and remove to be the way to go, and (maybe incorrectly) I just go ahead and remove all elements before drawing new ones for each iteration.
for example, your lines are:

focus.selectAll('lines')
   .data(dById)
   .enter().append("path")
   .attr("class", "line")
   .attr("d", function(d) {
     return connectLine(d.values);
   })
   .attr("stroke", function(d) {
     return color(d.key);
   })
   .attr('stroke-width', 4);

To clear all existing lines and draw new ones you could try:

 // start with the svg object provided by r2d3
svg.selectAll('lines').remove();
focus.selectAll('lines')
   .data(dById)
   .enter().append("path")
   .attr("class", "line")
   .attr("d", function(d) {
     return connectLine(d.values);
   })
   .attr("stroke", function(d) {
     return color(d.key);
   })
   .attr('stroke-width', 4);

You might be able to simplify this even more by removing all g elements at the top of your d3 script.

from r2d3.

Just found this, which I think is the same issue: https://stackoverflow.com/questions/44348963/replace-existing-r-shiny-htmlwidget-data-with-new-data

The responses there didn't help me much though :/ I suspect that each call to r2d3 creates a new htmlwidget (each of them using the same set of bindings? given that the old instances respond to new input too?) and that what's needed is to delete either just the old widget or the widget plus the bindings from within shiny before making a new call to r2d3 - correct?

from r2d3.