Usage with leafletProxy
In leaflet.multiopacity: Leaflet Multiple Opacity Controls for R

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

library(leaflet)
library(leaflet.multiopacity)
library(raster)

If you intend to use leaflet.multiopacity with Shiny, it is possible that you use the leafletProxy() function instead of only one call to leaflet() function. If this is your case, and you want to use the opacity controls of this package, you need to set the renderOnLayerAdd argument to TRUE.

ui <- shiny::fluidPage(
  leaflet::leafletOutput("map"),
  shiny::actionButton("addLayers", "Add Layers")
)

server <- function(input, output, session) {

  # Create a map inside of your server function
  output$map <- leaflet::renderLeaflet({
    # Create raster example
    r <- raster::raster(xmn = -2.8, xmx = -2.79,
                        ymn = 54.04, ymx = 54.05,
                        nrows = 30, ncols = 30)
    raster::values(r) <- matrix(1:900, nrow(r), ncol(r), byrow = TRUE)
    raster::crs(r) <- raster::crs("+init=epsg:4326")

    leaflet::leaflet() %>% 
      leaflet::setView(lng = -2.79545, lat = 54.04321, zoom = 14) %>% 
      leaflet::addProviderTiles("OpenStreetMap", layerId = "osm") %>%
      leaflet.multiopacity::addOpacityControls(group = "layersToAdd", 
                                               renderOnLayerAdd = TRUE)

  })

  # Observer that trigger a map update
  shiny::observeEvent(input$addLayers, {
    leaflet::leafletProxy("map", session) %>%
      leaflet::addRasterImage(r, colors = "viridis",
                              layerId = "raster1",
                              group = "layersToAdd") %>%
      leaflet::addRasterImage(r, colors = "Spectral",
                              layerId = "raster2",
                              group = "layersToAdd") %>% 
      leaflet::addAwesomeMarkers(lng = -2.79545, lat = 54.04321, 
                                 layerId = "hospital", 
                                 label = "Hospital",
                                 group = "layersToAdd")
  })

}

shiny::shinyApp(ui, server)

Please note that you need to use this with the first leaflet() call, not with leafletProxy() call. Some leaflet plugins don't work with the current R leaflet version when called after a leafletProxy() call.

What the renderOnLayerAdd argument does, is to associate the function of creating the opacity controls to the layerAdd event. This way, every time a new layer is added by a leafletProxy() call, the controls will be updated.