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Perhaps a basic question, but can php code be used in editing the CartoDB infowindow HTML? We want to show or hide a category depending on the value.

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Yes, you can do it. Just render the HTML you need in the view and "inject" that code in the visualization infowindow template. For example:

...
   layer.infowindow.set('template', document.getElementById('infowindow_template'));
...

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