Как сбросить все флажки на блестящей панели инструментов?

Вот решение, основанное на фиксированном соглашении об именах для ваших флажков (я добавил префикс "chk _")

Обновлено: различать updateCheckboxInput и updateCheckboxGroupInput

library(shiny)
library(shinydashboard) 
library(tidyverse)
library(magrittr)

header <- dashboardHeader(
  title = "My Dashboard",
  titleWidth = 500
)

siderbar <- dashboardSidebar(

  sidebarMenu(

    # Add buttons to choose the way you want to select your data
    radioButtons("select_by", "Select by:",
                 c("Food Type" = "Food",
                   "Gym Type" = "Gym",
                   "TV show" = "TV"))

  )   

)

body <- dashboardBody(

  fluidRow(
    uiOutput("Output_panel"),
    tabBox(title = "RESULTS", width = 12, 
           tabPanel("Visualisation",
                    br(),
                    width = 12, 
                    height = 800
           )
    ),
    column(12, actionButton(inputId  = "resetBtn", label = "Reset Selection", icon = icon("times-circle")))
  )
) 

ui <- dashboardPage(header, siderbar, body, skin = "purple")


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

  nodes_data_1 <- data.frame(id = 1:15, 
                             Food = as.character(c("Edibles", "Fried", "Home Cooked", "packaged", "vending machine")), 
                             Product_name = as.character(c("Bacon", "Cheese", "eggs", "chips", "beans", "oast", "oats and beans", "fried beans", "chickpeas", "broad beans", "garbanzo", "oat bars", "dog meat", "cat food", "horse meat")),
                             Gym_type = as.character(paste("Gym", 1:15)), TV = 
                               sample(LETTERS[1:3], 15, replace = TRUE))

  # build a edges dataframe

  edges_data_1 <- data.frame(from = trunc(runif (15)*(15-1))+1,
                             to = trunc(runif (15)*(15-1))+1)


  # create reactive of nodes 

  nodes_data_reactive <- reactive({
    nodes_data_1


  }) # end of reactive
  # create reacive of edges 

  edges_data_reactive <- reactive({

    edges_data_1

  }) # end of reactive



  # The output panel differs depending on the how the data is selected 
  # so it needs to be in the server section, not the UI section and created
  # with renderUI as it is reactive
  output$Output_panel <- renderUI({

    # When selecting by workstream and issues:
    if (input$select_by == "Food") {

      box(title = "Output PANEL", 
          collapsible = TRUE, 
          width = 12,

          do.call(tabsetPanel, c(id='t',lapply(1:length(unique(nodes_data_reactive()$Food)), function(i) {
            food <- unique(sort(as.character(nodes_data_reactive()$Food)))

            tabPanel(food[i], 
                     checkboxGroupInput(paste0("chkgrp_checkboxfood_", i), 
                                        label = NULL, 
                                        choices = nodes_data_reactive() %>% 
                                          filter(Food == food[i]) %>%
                                          select(Product_name) %>%
                                          unlist(use.names = FALSE)),
                     checkboxInput(paste0("chksingle_all_", i), "Select all", value = TRUE)
            )
          })))

      ) # end of Tab box



      # When selecting by the strength of links connected to the issues:  
    } else if (input$select_by == "Gym") {
      box(title = "Output PANEL", collapsible = TRUE, width = 12,
          checkboxGroupInput("chkgrp_select_gyms", "Select gyms you want to display", choices = unique(nodes_data_reactive()$Gym_type)
                             ,
                             selected = NULL,
                             inline = FALSE
          )# end of checkboxGroupInput
      ) # end of box  

    } else if (input$select_by == "TV") {
      box(title = "Output PANEL", collapsible = TRUE, width = 12,
          checkboxGroupInput("chkgrp_select_tvs", 
                             "Select the tv shows you want to see",choices = sort(unique(nodes_data_reactive()$TV)),
                             selected = NULL,
                             inline = FALSE
          )# end of checkboxGroupInput
      ) # end of box  

    }  # end of else if

  }) # end of renderUI

  observe({
    lapply(1:length(unique(nodes_data_reactive()$Food)), function(i) {
      food <- unique(sort(as.character(nodes_data_reactive()$Food)))
      product_choices <- nodes_data_reactive() %>% 
        filter(Food == food[i]) %>%
        select(Product_name) %>%
        unlist(use.names = FALSE)

      if (!is.null(input[[paste0("chksingle_all_", i)]])){
        if (input[[paste0("chksingle_all_", i)]] == TRUE) {
          updateCheckboxGroupInput(session,
                                   paste0("chkgrp_checkboxfood_", i), 
                                   label = NULL, 
                                   choices = product_choices,
                                   selected = product_choices)
        } else {
          updateCheckboxGroupInput(session,
                                   paste0("chkgrp_checkboxfood_", i), 
                                   label = NULL, 
                                   choices =product_choices)
        }
      }
    })
  })

  observeEvent(input$resetBtn, ignoreNULL = TRUE, ignoreInit = TRUE, {
    resetChksingleInputs <- names(input)[grepl("^chksingle*", names(input))]
    cat("Resetting single checkboxes:", resetChksingleInputs, sep = "\n")
    lapply(resetChksingleInputs, updateCheckboxInput, session=session, value = FALSE)

    resetChkgrpInputs <- names(input)[grepl("^chkgrp*", names(input))]
    cat("Resetting checkbox groups:", resetChkgrpInputs, sep = "\n")
    lapply(resetChkgrpInputs, updateCheckboxGroupInput , session=session, selected = character(0))

  })

} # end of server


# Run the application 
shinyApp(ui = ui, server = server)