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‎DESCRIPTION

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Package: shinysse
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Type: Package
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Title: What the Package Does (Title Case)
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Version: 0.1.2
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Author: Milica Markovic
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Maintainer: Milica Markovic <[email protected]>
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Description: Shiny package providing a sample size estimation (sse) web app
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License: What license is it under?
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Depends:
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shiny,
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shinydashboard,
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dplyr,
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sse,
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purrr,
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ggplot2
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Encoding: UTF-8
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LazyData: true
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RoxygenNote: 7.0.2

‎NAMESPACE

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# Generated by roxygen2: do not edit by hand
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export(app_server)
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export(app_ui)
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export(dash)
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export(fun_calc_prop)
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export(fun_calc_t)
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export(run_shiny)

‎R/app.R

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#' Runs the shinysse Shiny application
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#'
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#' This runs the shinysse Shiny web application. You can run the application by
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#' calling the run_shiny() function.
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#'
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#' @seealso \code{\link{app}},\code{\link{app_ui}}
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#' @export
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#'
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run_shiny <- function(){
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## with addResourcePath, one can make resources available in the global environment
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## this is needed for www since we keep it at a non-standard location for shiny term
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addResourcePath('www', system.file('www', package = 'shinysse'))
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shinyApp(ui = app_ui, server = app_server)
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}

‎R/app_server.R

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#' Shiny main app server function for shinysse
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#'
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#' Calls modules defined in app_ui, and passes on relevant data.
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#'
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#' @seealso \code{\link{app_ui}}, \code{\link{run_shiny}}
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#' @export
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#'
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app_server <- function(input, output) {
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# data
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calc_t_twosample <- readRDS(system.file("extdata", "calc_t_test_twosample.rds", package = "shinysse"))
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calc_t_paired <- readRDS(system.file("extdata/calc_t_test_paired.rds", package = "shinysse"))
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calc_prop <- readRDS(system.file("extdata/calc_prop_test.rds", package = "shinysse"))
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# modules
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mod <- fun_get_mods()
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callModule(dash, mod$dash)
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callModule(sseBasic, mod$sse_basic, calc_t_twosample, calc_t_paired)
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callModule(ssePlus, mod$sse_plus, calc_t_twosample)
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callModule(ssePlus, mod$sse_plus_paired, calc_t_paired)
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callModule(sseProp, mod$sse_prop, calc_prop)
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}

‎R/app_ui.R

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#' Shiny main app UI function for shinysse
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#'
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#' Controls the general appearance, header, sidebar, body, modules, etc.
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#'
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#' @seealso \code{\link{app}}
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#' @export
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#'
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app_ui <- function(){
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mod <- fun_get_mods()
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dashboardPage(
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header_unibas("SSE app"),
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dashboardSidebar(
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div(p(" ")),
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sidebarMenu(
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menuItem("Introduction", tabName = mod$dash, icon = icon("info")),
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menuItem("Two sample t-Test SSE", tabName = mod$sse_basic, icon = icon("text-size", lib = "glyphicon")),
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menuItem("Two sample t-Test SSE + input", tabName = mod$sse_plus, icon = icon("text-size", lib = "glyphicon")),
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menuItem("Paired t-Test SSE + input", tabName = mod$sse_plus_paired, icon = icon("text-size", lib = "glyphicon")),
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menuItem("Proportion Test SSE", tabName = mod$sse_prop, icon = icon("percentage"))
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)
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),
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dashboardBody(
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tags$head(
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tags$link(rel = "stylesheet", type = "text/css", href = "www/custom.css")
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),
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tabItems(
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dashUI(mod$dash, label = mod$dash),
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sseBasicUI(mod$sse_basic, label = mod$sse_basic),
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ssePlusUI(mod$sse_plus, label = mod$sse_plus),
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ssePlusUI(mod$sse_plus_paired, label = mod$sse_plus_paired),
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ssePropUI(mod$sse_prop, label = mod$sse_prop)
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)
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)
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)
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}

‎R/fun_calc_prop.R

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#' Evaluates power -function for power.prop.test
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#'
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#' For all pre-set combinations of n, theta, xi and alpha, this function calculates a list of powPar (package: sse)
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#' objects and saves them at a pre-set location in inst/extdata. The function uses the stats::power.prop.test for
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#' this purpose. Make sure to re-build the package after running the function, in order to make it available
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#' with package installation.
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#'
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#' @return list of calculated powPar objects
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#' @export
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#'
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fun_calc_prop <- function(){
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## define range of significance levels
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alpha <- c(0.01, 0.025, 0.05)
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## defining the range of n and theta to be evaluated
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psi_prop <- powPar(n = seq(from = 3, to = 10000, by = 5), # possible range of sample sizes
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theta = c(seq(from = 0, to = 0.15, by = 0.0125),
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seq(from = 0.2, to = 0.5, by = 0.05)), # possible range of effect sizes
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xi = seq(from = 0.05, to = 1, by = 0.05)) # possible range of proportions
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## defining a power-function based on a power.prop.test
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powFuns_prop <- list()
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for(i in 1:length(alpha)){
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eval(parse(text = paste(paste0("powFuns_prop[[", paste0("'alpha", sub(".", "p", alpha[i], fixed = TRUE)), "']]", " <- function(psi)"),
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"{",
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"p1 = xi(psi)",
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"power.prop.test(n = sse::n(psi)/2,",
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"p1 = p1,",
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"p2 = p1-theta(psi),",
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paste0("sig.level = ", alpha[i], ","),
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"power = NULL",
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")$power",
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"}", sep = "\n")))
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}
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## evaulate power-function for all combinations of n, theta, xi and alpha
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calc_prop <- map(powFuns_prop, ~powCalc(psi_prop, .))
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## readRDS
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calc_prop <- readRDS("calc_prop_test.rds")
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calc_prop <- readRDS(system.file("extdata", "calc_prop_test.rds", package = "shinyssepkg"))
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## save calcs to be used in the shiny app
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save_path <- file.path("inst", "extdata", "calc_prop_test.rds")
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saveRDS(calc_prop, save_path)
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return(calc_prop)
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}

‎R/fun_calc_t.R

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#' Evaluates power -function for power.t.test
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#'
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#' For all pre-set combinations of n, theta, xi and alpha, this function calculates a list of powPar (package: sse)
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#' objects and saves them at a pre-set location in inst/extdata. The function uses the stats::power.t.test for
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#' this purpose. Make sure to re-build the package after running the function, in order to make it available
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#'
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#' @param type character string specifying the type of t test. options: "two.sample", "one.sample", "paired"
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#' @return list of calculated powPar objects
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#' @export
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#'
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fun_calc_t <- function(type = "two.sided"){
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print(type)
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## define range of significance levels
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alpha <- c(0.01, 0.025, 0.05)
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## defining the range of n and theta to be evaluated
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psi_t <- powPar(n = seq(from = 5, to = 2000, by = 5), # possible range of sample sizes
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theta = seq(from = 1, to = 50, by = 1), # possible range of effect sizes
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xi = seq(from = 1, to = 80, by = 1)) # possible range of standard deviations
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## defining a power-function based on a power.t.test
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powFuns_t <- list()
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for(i in 1:length(alpha)){
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eval(parse(text = paste(paste0("powFuns_t[[", paste0("'alpha", sub(".", "p", alpha[i], fixed = TRUE)), "']]", " <- function(psi)"),
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"{",
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"power.t.test(n = sse::n(psi)/2,",
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"delta = theta(psi),",
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"sd = xi(psi),",
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paste0("sig.level = ", alpha[i], ","),
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"power = NULL,",
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paste0("type = '", type, "'"),
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")$power",
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"}", sep = "\n")))
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}
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## evaulate power-function for all combinations of n, theta, xi and alpha
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calc_t <- map(powFuns_t, ~powCalc(psi_t, .))
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## save calcs to be used in the shiny app
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save_path <- file.path("inst", "extdata", paste0("calc_t_test_", type, ".rds"))
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saveRDS(calc_t, save_path)
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return(calc_t)
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}

‎R/fun_get_mods.R

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fun_get_mods <- function(){
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mod <- list()
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mod$dash <- "dashboard"
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mod$sse_basic <- "sse_basic"
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mod$sse_plus <- "sse_plus"
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mod$sse_plus_paired <- "sse_plus_paired"
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mod$sse_prop <- "sse_prop"
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return(mod)
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}

‎R/fun_header_unibas.R

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# define header
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header_unibas <- function(header_label){
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header <- dashboardHeader(
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title = header_label,
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tags$li(class = "dropdown"))
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header$children[[4]] <- header$children[[2]]
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header$children[[4]]$children[[1]] <- header$children[[2]]
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header$children[[4]]$children[[2]] <- header$children[[2]]
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header$children[[4]]$children[[2]]$children[[1]] <- header$children[[2]]
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header$children[[4]]$name <- "div"
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header$children[[4]]$attribs$class <- "custom-head"
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# uni basel header row
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header$children[[4]]$children[[1]]$name <- "aside"
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header$children[[4]]$children[[1]]$attribs$class <- "unibas"
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header$children[[4]]$children[[1]]$children <- NULL
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# dkf/faculty header row
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header$children[[4]]$children[[2]]$name <- "aside"
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header$children[[4]]$children[[2]]$attribs$class <- "dkf"
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header$children[[4]]$children[[2]]$children <- NULL
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return(header)
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}

‎R/fun_sidebar.R

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getSidebar <- function(){
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library(shinydashboard)
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side <- sidebarMenu(
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menuItem("Dashboard", tabName = mod$dash, icon = icon("dashboard")),
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menuItem("SSE Basic", tabName = mod$sse_basic, icon = icon("user-alt")),
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menuItem("SSE Plus", tabName = mod$sse_plus, icon = icon("user-plus"))
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)
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return(side)
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}

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