I am in the process of creating a Shiny dashboard application, where the dashboard body is supposed to show some maps. So far no problem to get the map expand over the entir
Another option is what jcheng5 and kent37 have described on GitHub
output$mymap = renderLeaflet({...make a map...}) leafletOutput('mymap', height=1000)
Works for me with a leaflet map in R flexdashboard
leaflet map
R flexdashboard