diff --git a/DESCRIPTION b/DESCRIPTION
index 8fc6d1c..7c28853 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -17,23 +17,25 @@ Depends:
     R (>= 4.1.0),
     shiny (>= 1.7.0)
 Imports:
-    lpSolveAPI (>= 5.5.2),
+    bslib (>= 0.5.1),
+    cli (>= 3.6.0),
+    ggplot2 (>= 3.3.0),
     haven (>= 2.5.0),
+    htmltools,
+    lpSolveAPI (>= 5.5.2),
     markdown,
     productivity (>= 1.1.0),
-    readxl,
-    writexl,
-    bslib (>= 0.5.1),
-    ggplot2 (>= 3.3.0),
     reactable (>= 0.4.0),
-    cli (>= 3.6.0)
+    readxl,
+    rlang (>= 1.1.0),
+    scales,
+    writexl
 Suggests:
     Benchmarking (>= 0.30),
     data.table,
     rmarkdown,
     knitr,
-    scales,
-    rlang,
+    magick,
     testthat (>= 3.0.0),
     tibble,
     withr
diff --git a/NAMESPACE b/NAMESPACE
index a0a84f4..0a3f884 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -19,3 +19,9 @@ import(reactable)
 import(readxl)
 import(shiny)
 import(writexl)
+importFrom(stats,complete.cases)
+importFrom(stats,median)
+importFrom(stats,quantile)
+importFrom(stats,rnorm)
+importFrom(stats,sd)
+importFrom(stats,var)
diff --git a/NEWS.md b/NEWS.md
index d26c1d2..dd4f00d 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -4,6 +4,7 @@
 
 - Updated documentation for `run_pioneer()`
 - Added custom functions for DEA calculations in order to remove `{Benchmarking}` as a dependency (#80)
+- All R functions - including `server()` and `ui()` - have now been moved to the `R` directory with benefits to how internal functions are accessed. In additions, the global environment should be untouched when the app is run (#87)
 
 ## Bug fixes
 
diff --git a/inst/app/R/fct_dea-bootstrap.R b/R/fct_dea-bootstrap.R
similarity index 80%
rename from inst/app/R/fct_dea-bootstrap.R
rename to R/fct_dea-bootstrap.R
index 81b110a..e2d3a72 100644
--- a/inst/app/R/fct_dea-bootstrap.R
+++ b/R/fct_dea-bootstrap.R
@@ -1,3 +1,6 @@
+#' @importFrom stats complete.cases median quantile rnorm sd var
+NULL
+
 bw_rule <- function(delta, rule = 'ucv') {
   # Values must be in range 1, Inf. Take inverse if values are in range 0, 1
   if (min(delta) < 1) {
@@ -8,10 +11,10 @@ bw_rule <- function(delta, rule = 'ucv') {
   delta_2m <- c(delta_m, 2 - delta_m)
   # See Daraio & Wilson (2007) for a discussion on methods for determining bandwidth
   h <- switch(rule,
-    silverman = bw.nrd0(delta_2m),
-    scott = bw.nrd(delta_2m),
-    ucv = suppressWarnings({ h <- bw.ucv(delta_2m) }),
-    suppressWarnings({ h <- bw.ucv(delta_2m) })
+    silverman = stats::bw.nrd0(delta_2m),
+    scott = stats::bw.nrd(delta_2m),
+    ucv = suppressWarnings({ h <- stats::bw.ucv(delta_2m) }),
+    suppressWarnings({ h <- stats::bw.ucv(delta_2m) })
   )
   # See Daraio & Wilson (2007), p. 61, eq. 3.26
   h <- h * 2^(1/5) * (length(delta_m)/length(delta))^(1/5) * (sd(delta)/sd(delta_2m))
@@ -38,11 +41,11 @@ perform_boot <- function(x, y, rts, orientation, i, h, theta, boot) {
   beta <- bootstrap_sample(theta, h = h)
   if (orientation == 'in') {
     x_ref <- (theta / beta) * x
-    boot[, i] <- pioneeR:::compute_efficiency(x, y, rts = rts, orientation = orientation, xref = x_ref, yref = y, values_only = TRUE)$values
+    boot[, i] <- compute_efficiency(x, y, rts = rts, orientation = orientation, xref = x_ref, yref = y, values_only = TRUE)$values
   } else if (orientation == 'out') {
     beta <- 1 / beta
     y_ref <- (theta / beta) * y
-    boot[, i] <- pioneeR:::compute_efficiency(x, y, rts = rts, orientation = orientation, xref = x, yref = y_ref, values_only = TRUE)$values
+    boot[, i] <- compute_efficiency(x, y, rts = rts, orientation = orientation, xref = x, yref = y_ref, values_only = TRUE)$values
   }
   return(invisible(boot))
 }
diff --git a/inst/app/R/fct_file-functions.R b/R/fct_file-functions.R
similarity index 90%
rename from inst/app/R/fct_file-functions.R
rename to R/fct_file-functions.R
index fcc2e4c..3df439b 100644
--- a/inst/app/R/fct_file-functions.R
+++ b/R/fct_file-functions.R
@@ -1,3 +1,5 @@
+#' Check user provided file
+#' @noRd 
 check_file <- function(file) {
 
   check_missing <- sapply(1:nrow(file), function(i) all(is.na(file[i,])))
@@ -28,6 +30,8 @@ check_file <- function(file) {
 
 }
 
+#' Check if a cell in Excel has a value
+#' @noRd 
 has_value <- function(x) {
   if (length(x) > 1L) return(sapply(x, has_value, USE.NAMES = FALSE))
   if (is.null(x) || is.na(x)) return(FALSE)
diff --git a/inst/app/R/fct_ui-functions.R b/R/fct_ui-functions.R
similarity index 84%
rename from inst/app/R/fct_ui-functions.R
rename to R/fct_ui-functions.R
index 5f0016f..bf5a764 100644
--- a/inst/app/R/fct_ui-functions.R
+++ b/R/fct_ui-functions.R
@@ -1,3 +1,5 @@
+#' Create a bootstrap styled alert box
+#' @noRd
 alert <- function(..., color = 'primary', icon = NULL, dismissable = FALSE) {
 
   cls <- sprintf('alert alert-%s', color)
@@ -14,6 +16,8 @@ alert <- function(..., color = 'primary', icon = NULL, dismissable = FALSE) {
 
 }
 
+#' Create a bootstrap styled modal button
+#' @noRd
 bs_modal_button <- function(
     label = 'Close', color = 'default', size = c('normal', 'sm', 'lg'))
 {
@@ -23,6 +27,8 @@ bs_modal_button <- function(
   tags$button(type = 'button', class = cls, `data-bs-dismiss` = 'modal', label)
 }
 
+#' Create a content element with proper Bootstrap styling
+#' @noRd
 content_div <- function(...) {
   tags$div(
     class = 'container mt-1',
diff --git a/inst/app/R/mod_file-upload.R b/R/mod_file-upload.R
similarity index 97%
rename from inst/app/R/mod_file-upload.R
rename to R/mod_file-upload.R
index 03c559a..583e249 100644
--- a/inst/app/R/mod_file-upload.R
+++ b/R/mod_file-upload.R
@@ -1,5 +1,5 @@
-library(reactable)
-
+#' UI module for file upload function
+#' @noRd 
 file_upload_ui <- function(id, wrap = FALSE, ...) {
   ns <- NS(id)
   if (wrap) {
@@ -9,6 +9,8 @@ file_upload_ui <- function(id, wrap = FALSE, ...) {
   }
 }
 
+#' Server module for file upload function
+#' @noRd 
 file_upload_srv <- function(id) {
   moduleServer(
     id, function(input, output, session) {
@@ -76,7 +78,7 @@ file_upload_srv <- function(id) {
         if (ext %in% c('csv', 'tsv', 'dsv', 'txt')) {
           req(input$file_sep, input$file_dec)
           header <- if (is.null(input$file_header)) TRUE else as.logical(input$file_header)
-          clean_doc <- read.table(
+          clean_doc <- utils::read.table(
             textConnection(raw_file()),
             sep = input$file_sep,
             dec = input$file_dec,
diff --git a/R/pkg-utils.R b/R/pkg-utils.R
index 7caed29..2356097 100644
--- a/R/pkg-utils.R
+++ b/R/pkg-utils.R
@@ -1,3 +1,5 @@
+#' Create temporary data that can be used by pioneeR when run locally
+#' @noRd
 set_local_data <- function(x) {
 
   if (nzchar(Sys.getenv('PIONEER_DATA'))) {
@@ -28,12 +30,16 @@ set_local_data <- function(x) {
 
 }
 
+#' Get list of unsafe ports that are used in Chrome
+#' @noRd
 unsafe_ports <- function() {
   return(
     c(3659, 4045, 5060, 5061, 6000, 6566, 6665:6669, 6697)
   )
 }
 
+#' Checks if the specified port is inside the ranges that are considered safe
+#' @noRd
 check_for_unsafe_port <- function(port) {
   if (is.null(port)) return()
   port <- as.numeric(port)
diff --git a/inst/app/server.R b/R/server.R
similarity index 81%
rename from inst/app/server.R
rename to R/server.R
index 62782eb..fa9486c 100644
--- a/inst/app/server.R
+++ b/R/server.R
@@ -1,16 +1,10 @@
-# Load required packages
-require(readxl)
-require(ucminf)
-require(productivity)
-require(ggplot2)
-require(scales)
-require(haven)
-require(writexl)
-require(reactable)
-require(rlang)
-
-# Define server logic
-shinyServer(function(input, output, session) {
+#' @import reactable
+#' @import ggplot2
+NULL
+
+#' Define server logic for pioneeR
+#' @noRd
+server <- function(input, output, session) {
 
   reactable_opts <- list(
     compact = TRUE, sortable = TRUE, filterable = TRUE, striped = TRUE,
@@ -23,6 +17,7 @@ shinyServer(function(input, output, session) {
   load_data <- list(file = NULL, cols = NULL, error = NULL)
 
   # If we are running locally, and we have data, load the data
+  is_local <- !nzchar(Sys.getenv('SHINY_PORT'))
   if (is_local && nzchar(Sys.getenv('PIONEER_DATA'))) {
     local_data <- NULL
     if (file.exists(Sys.getenv('PIONEER_DATA'))) {
@@ -157,8 +152,6 @@ shinyServer(function(input, output, session) {
 
   })
 
-  source('conditionalUI.R', local = TRUE, encoding = 'UTF-8')
-
   output$preview <- renderReactable({
     # Input file is required. If input is NULL, return NULL
     req(preview())
@@ -251,7 +244,7 @@ shinyServer(function(input, output, session) {
 
     req(data(), dea.in(), dea.out())
 
-    d <- pioneeR:::compute_efficiency(
+    d <- compute_efficiency(
       dea.in(), dea.out(), rts = model_params$rts,
       orientation = model_params$orientation)
 
@@ -261,7 +254,7 @@ shinyServer(function(input, output, session) {
 
   dea.slack <- reactive({
     x <- tryCatch({
-      pioneeR:::compute_slack(dea.in(), dea.out(), dea.prod())
+      compute_slack(dea.in(), dea.out(), dea.prod())
     }, warning = function(e) {
       NULL
     }, error = function(e) {
@@ -274,7 +267,7 @@ shinyServer(function(input, output, session) {
 
     req(data(), dea.in(), dea.out())
 
-    d <- pioneeR:::compute_super_efficiency(
+    d <- compute_super_efficiency(
       dea.in(), dea.out(), rts = model_params$rts,
       orientation = model_params$orientation
     )
@@ -306,8 +299,8 @@ shinyServer(function(input, output, session) {
       geom_point(color = '#084887') +
       xlab(paste('Inputs:\n', paste(params()$inputs, collapse = ', '))) +
       ylab(paste('Outputs:\n', paste(params()$outputs, collapse = ', '))) +
-      scale_y_continuous(labels = label_number(suffix = find_scale(d$x)[[1]], scale = find_scale(d$x)[[2]])) +
-      scale_x_continuous(labels = label_number(suffix = find_scale(d$y)[[1]], scale = find_scale(d$y)[[2]])) +
+      scale_y_continuous(labels = scales::label_number(suffix = find_scale(d$x)[[1]], scale = find_scale(d$x)[[2]])) +
+      scale_x_continuous(labels = scales::label_number(suffix = find_scale(d$y)[[1]], scale = find_scale(d$y)[[2]])) +
       theme_pioneer()
 
     # Add frontier line
@@ -316,21 +309,21 @@ shinyServer(function(input, output, session) {
         p <- p + geom_abline(intercept = 0, slope = max(d$y/d$x), color = '#f9ab55', linewidth = 1)
       } else {
         if (model_params$rts == 'vrs') {
-          # Use chull to find the points which lie on the convex hull
-          hpts <- chull(d$x, d$y)
-          hpts <- hpts[c(which(d$x[hpts] == min(d$x[hpts])), which(head(d$x[hpts], -1) < tail(d$x[hpts], -1)) + 1)]
+          # Use chull from grDevices to find the points which lie on the convex hull
+          hpts <- grDevices::chull(d$x, d$y)
+          hpts <- hpts[c(which(d$x[hpts] == min(d$x[hpts])), which(utils::head(d$x[hpts], -1) < utils::tail(d$x[hpts], -1)) + 1)]
           y <- c(0, d$y[hpts], max(d$y))
           x <- c(min(d$x), d$x[hpts], max(d$x))
         } else if (model_params$rts == 'drs') {
           # If we have NIRS, the front starts at origo, so we add origo to our coordinates
-          hpts <- chull(c(0, d$x), c(0, d$y))
+          hpts <- grDevices::chull(c(0, d$x), c(0, d$y))
           hpts <- hpts[hpts != 1]-1
-          hpts <- hpts[c(which(head(d$x[hpts], -1) < tail(d$x[hpts], -1)) + 1)]
+          hpts <- hpts[c(which(utils::head(d$x[hpts], -1) < utils::tail(d$x[hpts], -1)) + 1)]
           y <- c(0, d$y[hpts], max(d$y))
           x <- c(0, d$x[hpts], max(d$x))
         }
         # Remove observations where the value on the y-axis is reduced
-        rm <- c(TRUE, mapply(\(t1, t2) t2 < t1, t1 = tail(y, -1), t2 = head(y, -1)))
+        rm <- c(TRUE, mapply(\(t1, t2) t2 < t1, t1 = utils::tail(y, -1), t2 = utils::head(y, -1)))
         coords <- data.frame(y = y[rm], x = x[rm])
         p <- p + geom_line(data = coords, aes(x = x, y = y), color = '#f9ab55', linewidth = 1)
       }
@@ -417,12 +410,13 @@ shinyServer(function(input, output, session) {
 
     color <- sprintf('#%s', input$salter.color) # 'rgb(8,48,107)'
 
-    g <- ggplot(d, aes(x = wt, y = eff, width = inputs, fill = as.character(row.names(d)))) +
+    # To avoid R CMD notes about no visible bindings, we use the .data pronoun
+    g <- ggplot(d, aes(x = .data$wt, y = .data$eff, width = .data$inputs, fill = as.character(row.names(d)))) +
       geom_bar(stat = 'identity', position = 'identity', show.legend = FALSE) +
       scale_fill_manual(values = rep(c('#084887', '#f9ab55'), length.out = nrow(d))) +
       labs(x = input$salter.xtitle, y = input$salter.ytitle) +
-      scale_x_continuous(labels = label_number(suffix = find_scale(d$wt)[[1]], scale = find_scale(d$wt)[[2]])) +
-      scale_y_continuous(labels = label_number(suffix = find_scale(d$eff)[[1]], scale = find_scale(d$eff)[[2]])) +
+      scale_x_continuous(labels = scales::label_number(suffix = find_scale(d$wt)[[1]], scale = find_scale(d$wt)[[2]])) +
+      scale_y_continuous(labels = scales::label_number(suffix = find_scale(d$eff)[[1]], scale = find_scale(d$eff)[[2]])) +
       theme_pioneer()
 
   })
@@ -549,7 +543,7 @@ shinyServer(function(input, output, session) {
         renderPlot({
           # Find to optimal number of bins using Freedman-Diaconis rule if N is less
           # than 200, and Sturge's rule if N is equal or greater than 200
-          n_bins <- if (length(eff) < 200) nclass.FD(eff) else nclass.Sturges(eff)
+          n_bins <- if (length(eff) < 200) grDevices::nclass.FD(eff) else grDevices::nclass.Sturges(eff)
           bins <- pretty(range(eff), n = n_bins, min.n = 1)
           ggplot(data.frame(eff = eff), aes(x = eff)) +
             stat_bin(fill = '#ee2255', color = '#eeeeee', breaks = bins) +
@@ -565,18 +559,6 @@ shinyServer(function(input, output, session) {
 
   })
 
-  observeEvent(input$exportplot, {
-
-    require(processx)
-
-    p <- plot.dea()
-
-    tmpFile <- tempfile(fileext = ".png")
-    export(p, file = tmpFile)
-    browseURL(tmpFile)
-
-  })
-
   dea.tbl <- reactive({
 
     deff <- matrix(dea.prod()$values, ncol = 1, dimnames = list(NULL, 'Efficiency'))
@@ -617,7 +599,7 @@ shinyServer(function(input, output, session) {
 
   output$dea.table <- renderReactable({
     df <- dea.tbl()
-    opts <- list2(!!!reactable_opts, data = df, columns = list(
+    opts <- rlang::list2(!!!reactable_opts, data = df, columns = list(
       DMU = colDef(sticky = 'left')
     ))
     do.call(reactable, opts)
@@ -627,15 +609,15 @@ shinyServer(function(input, output, session) {
     df <- round(dea.slack()$data, input$dea_round)
     colnames(df)[ncol(df)] <- 'Total'
 
-    opts <- list2(!!!reactable_opts, data = df)
+    opts <- rlang::list2(!!!reactable_opts, data = df)
     do.call(reactable, opts)
   })
 
   output$peers.table <- renderReactable({
-    df <- pioneeR:::get_peers(dea.prod(), ids = selection()[, input$dea_id], threshold = 0)
+    df <- get_peers(dea.prod(), ids = selection()[, input$dea_id], threshold = 0)
     colnames(df)[1] <- 'DMU'
 
-    opts <- list2(!!!reactable_opts, data = df, columns = list(
+    opts <- rlang::list2(!!!reactable_opts, data = df, columns = list(
       DMU = colDef(sticky = 'left')
     ))
     do.call(reactable, opts)
@@ -657,7 +639,7 @@ shinyServer(function(input, output, session) {
       } else if (input$exportfileformat == 'xlsx') {
         writexl::write_xlsx(df, file)
       } else if (input$exportfileformat == 'csv') {
-        write.csv2(df, file, fileEncoding = 'CP1252', row.names = FALSE)
+        utils::write.csv2(df, file, fileEncoding = 'CP1252', row.names = FALSE)
       }
     }
   )
@@ -667,7 +649,7 @@ shinyServer(function(input, output, session) {
     num_cols <- which(sapply(df, is.numeric, USE.NAMES = FALSE))
     df[, num_cols] <- round(df[, num_cols], input$dea_round)
 
-    opts <- list2(!!!reactable_opts, data = df, columns = list(
+    opts <- rlang::list2(!!!reactable_opts, data = df, columns = list(
       DMU = colDef(sticky = 'left'),
       Scale.eff. = colDef(name = 'Scale eff.'),
       VRS.NIRS.ratio = colDef(
@@ -901,7 +883,7 @@ shinyServer(function(input, output, session) {
     # Add DMU names and round inputs
     df <- cbind(data.frame(DMU = names(dea.prod()$values)), round(res$tbl, input$boot_round))
 
-    opts <- list2(!!!reactable_opts, data = df, columns = list(
+    opts <- rlang::list2(!!!reactable_opts, data = df, columns = list(
       eff = colDef(show = input$boot_show_eff, name = 'Efficiency'),
       bias = colDef(show = input$boot_show_bias, name = 'Bias'),
       eff_bc = colDef(name = 'Bias corr. score'),
@@ -947,7 +929,7 @@ shinyServer(function(input, output, session) {
       } else if (input$boot_fileformat == 'xlsx') {
         writexl::write_xlsx(df, file)
       } else if (input$boot_fileformat == 'csv') {
-        write.csv2(df, file, fileEncoding = 'CP1252', row.names = FALSE)
+        utils::write.csv2(df, file, fileEncoding = 'CP1252', row.names = FALSE)
       }
     }
   )
@@ -958,7 +940,7 @@ shinyServer(function(input, output, session) {
 
     req(data(), params()$year)
 
-    df <- checkBalance(selection(), params()$id, params()$year)
+    df <- check_balance(selection(), params()$id, params()$year)
     if (nrow(df$data) == 0) {
       out <- alert(
         color = 'danger', icon = 'danger',
@@ -982,9 +964,9 @@ shinyServer(function(input, output, session) {
 
     req(selection())
 
-    df <- checkBalance(selection(), params()$id, params()$year)
+    df <- check_balance(selection(), params()$id, params()$year)
 
-    malmquist <- malm(
+    malmquist <- productivity::malm(
       data = df$data, id.var = params()$id, time.var = params()$year,
       x.vars = params()$inputs, y.vars = params()$outputs,
       rts = input$malm_rts, orientation = input$malm_orientation, scaled = TRUE)
@@ -1028,7 +1010,7 @@ shinyServer(function(input, output, session) {
       } else if (input$malm.fileformat == 'xlsx') {
         writexl::write_xlsx(df, file)
       } else if (input$malm.fileformat == 'csv') {
-        write.csv2(df, file, fileEncoding = 'CP1252', row.names = FALSE)
+        utils::write.csv2(df, file, fileEncoding = 'CP1252', row.names = FALSE)
       }
     }
   )
@@ -1048,8 +1030,9 @@ shinyServer(function(input, output, session) {
       sprintf('dea-model-%s-%s.pdf', model_params$rts, model_params$orientation)
     },
     content = function(file) {
+      template <- system.file('files', 'dea_analysis.Rmd', package = 'pioneeR')
       tempReport <- file.path(tempdir(), 'dea_analysis.Rmd')
-      file.copy('dea_analysis.Rmd', tempReport, overwrite = TRUE)
+      file.copy(template, tempReport, overwrite = TRUE)
 
       params <- list(
         data = selection(),
@@ -1082,8 +1065,140 @@ shinyServer(function(input, output, session) {
     stopApp(x)
   })
 
+  # From conditionalUI.R
+  # Functions to render the UI based on other input
+
+  output$ui_id <- renderUI({
+
+    req(data())
+
+    if (is.null(data()$file)) return(NULL)
+
+    choices <- colnames(data()$file)
+    selectInput('dea_id', 'Firm ID', choices = choices, multiple = FALSE)
+
+  })
+
+  output$ui_inputs <- renderUI({
+
+    req(data())
+
+    if (is.null(data()$file)) return(NULL)
+
+    # Restore input if we are restoring previous state
+    selected <- if (!is.null(restoreVals$inputs)) restoreVals$inputs else NULL
+    choices <- data()$cols[sapply(data()$file, is.numeric, USE.NAMES = FALSE)]
+
+    selectInput('dea_input', 'Inputs', choices = choices, selected = selected, multiple = TRUE)
+
+  })
+
+  observeEvent(input$dea_input, {
+    selected_inputs <- input$dea_input
+    selected <- input$dea_output
+    choices <- data()$cols[sapply(data()$file, is.numeric, USE.NAMES = FALSE)]
+    if (length(selected_inputs) > 0) {
+      choices <- choices[!(choices %in% selected_inputs)]
+    }
+    if (!is.null(selected) && any(selected %in% selected_inputs)) {
+      selected <- selected[!(selected %in% selected_inputs)]
+    }
+    updateSelectInput(session, 'dea_output', choices = choices, selected = selected)
+  })
+
+  output$ui_outputs <- renderUI({
+
+    req(data())
+
+    if (is.null(data()$file)) return(NULL)
+
+    # Restore input if we are restoring previous state
+    selected <- if (!is.null(restoreVals$outputs)) restoreVals$outputs else NULL
+    choices <- data()$cols[sapply(data()$file, is.numeric, USE.NAMES = FALSE)]
+
+    selectInput('dea_output', 'Outputs', choices = choices, selected = selected, multiple = TRUE)
+
+  })
+
+  observeEvent(input$dea_output, {
+    selected_outputs <- input$dea_output
+    selected <- input$dea_input
+    choices <- data()$cols[sapply(data()$file, is.numeric, USE.NAMES = FALSE)]
+    if (length(selected_outputs) > 0) {
+      choices <- choices[!(choices %in% selected_outputs)]
+    }
+    if (!is.null(selected) && any(selected %in% selected_outputs)) {
+      selected <- selected[!(selected %in% selected_outputs)]
+    }
+    updateSelectInput(session, 'dea_input', choices = choices, selected = selected)
+  })
+
+  output$ui_timeseries <- renderUI({
+
+    req(data()$file)
+
+    checkboxInput('hasyear', 'Time series data', value = FALSE)
+
+  })
+
+  output$ui_year <- renderUI({
+
+    req(data(), input$hasyear)
+
+    # We only want to show the input if we have time series data
+    if (!input$hasyear) return(NULL)
+
+    df <- data()$file
+
+    identify_year_variable <- \(x) {
+      if (!is.atomic(x) || !is.numeric(x) || any(is.na(x))) {
+        return(FALSE)
+      }
+      return(all(abs(2000 - range(x)) < 100))
+    }
+
+    choices <- data()$cols
+    year_variable <- df[names(df[(which(sapply(df, identify_year_variable)))])]
+    selected <- ifelse(length(year_variable) >= 1, names(year_variable[1]), choices[[1]])
+    selectInput('dea_year', 'Time series variable', choices = choices, selected = selected, multiple = FALSE)
+
+  })
+
+  output$ui_subset <- renderUI({
+
+    req(data()$file)
+
+    tagList(
+      checkboxInput('data.subset', 'Subset data', value = FALSE)
+    )
+
+  })
+
+  output$ui_subset_info <- renderUI({
+
+    req(data()$file)
+
+    n_rows <- length(preview_selected())
+    t_rows <- nrow(data()$file)
+    one <- n_rows == 1
+
+    tagList(
+      p(
+        class = 'small', helpText(sprintf(
+          'Click to subset data. You can select the rows to include in the analysis by
+        clicking the rows in the table. Currently %s %s of %s %s selected',
+          n_rows, if (one) 'row' else 'rows', t_rows, if (one) 'is' else 'are'
+        ))
+      ),
+      actionButton('data.subset.select', 'Select all'),
+      actionButton('data.subset.deselect', 'Deselect all')
+    )
+
+  })
+  # Stop from conditionalUI.R
+
   onStop(function() {
     Sys.unsetenv('PIONEER_DATA')
   })
 
-})
+}
diff --git a/R/shiny-functions.R b/R/shiny-functions.R
index 2f158c7..0a366a6 100644
--- a/R/shiny-functions.R
+++ b/R/shiny-functions.R
@@ -9,6 +9,19 @@
 #' @import writexl
 NULL
 
+#' Function to add JS and CSS dependencies to the app
+#' @noRd
+pioneer_scripts <- function() {
+  htmltools::htmlDependency(
+    name = 'pioneer-assets',
+    version = utils::packageVersion('pioneeR'),
+    package = 'pioneeR',
+    src = 'www',
+    script = 'pioneer.js',
+    style = 'style.css'
+  )
+}
+
 #' Run pioneeR
 #'
 #' Run the pioneeR app on your local machine.
@@ -38,7 +51,17 @@ run_pioneer <- function(x = NULL, port = NULL, ...) {
     port <- check_for_unsafe_port(port)
   }
 
-  shiny::runApp(system.file('app', package = 'pioneeR'), port = port, ...)
+  pioneer_env <- new.env()
+  environment(ui) <- pioneer_env
+  environment(server) <- pioneer_env
+
+  # shiny::runApp(system.file('app', package = 'pioneeR'), port = port, ...)
+  shiny::shinyApp(
+    ui,
+    server,
+    enableBookmarking = 'server',
+    ...
+  )
 
 }
 
@@ -52,3 +75,31 @@ runPioneeR <- run_pioneer
 #'
 #' @export
 unset_env_vars <- \() Sys.unsetenv('PIONEER_DATA')
+
+#' Check if time series data is balanced for use in Malmquist models
+#' @noRd
+check_balance <- function(data, id_var, time_var) {
+
+  units <- unique(data[, id_var])
+  time <- unique(data[, time_var])
+
+  miss <- sapply(units, function(u) {
+    unit_time <- unique(data[data[,id_var] == u, time_var])
+    all(sapply(time, function(t) t %in% unit_time))
+  })
+
+  r <- list()
+
+  if (!all(miss)) {
+    r$data <- data[data[,id_var] %in% units[miss],]
+    r$listwise <- TRUE
+    r$message <- 'Data was not balanced, listwise deleting has been performed'
+  } else {
+    r$data <- data
+    r$listwise <- FALSE
+    r$message <- NULL
+  }
+
+  r
+
+}
diff --git a/inst/app/ui.R b/R/ui.R
similarity index 96%
rename from inst/app/ui.R
rename to R/ui.R
index 9bcb582..1aa5708 100644
--- a/inst/app/ui.R
+++ b/R/ui.R
@@ -1,9 +1,6 @@
 # Load required packages
-require(data.table)
-require(reactable)
-require(bslib)
-
 ver <- utils::packageVersion('pioneeR')
+bs_ver <- 5
 
 sidebar_width <- 400
 
@@ -21,7 +18,8 @@ if (utils::packageVersion('bslib') > '0.5.1') {
   theme_args = list(version = bs_ver)
 }
 
-# Define UI for application that draws a histogram
+#' Define the user interface for pioneeR
+#' @noRd
 ui <- function(request) { page_navbar(
 
   title = 'pioneeR',
@@ -30,10 +28,7 @@ ui <- function(request) { page_navbar(
   fluid = TRUE,
 
   # Add custom CSS
-  header = tags$head(
-    tags$link(rel = 'stylesheet', type = 'text/css', href = 'style.css'),
-    tags$script(src = 'pioneer.js') # pioneer.min.js
-  ),
+  header = pioneer_scripts(),
 
   tabPanel(
     'Data', value = 'pioneer_upload',
@@ -293,7 +288,7 @@ ui <- function(request) { page_navbar(
   tabPanel(
     'About', value = 'pioneeR_about',
     content_div(
-      includeMarkdown('about.md')
+      includeMarkdown(system.file('files', 'about.md', package = 'pioneeR'))
     )
   ),
 
@@ -303,7 +298,7 @@ ui <- function(request) { page_navbar(
       Norway](https://www.riksrevisjonen.no/en)**.
 
       &copy; %s Office of the Auditor General of Norway &#8212; Version %s with bslib %s',
-      format(Sys.Date(), '%Y'), ver, packageVersion('bslib')
+      format(Sys.Date(), '%Y'), ver, utils::packageVersion('bslib')
     ))
   )
 
diff --git a/inst/app/R/utils.R b/R/utils.R
similarity index 94%
rename from inst/app/R/utils.R
rename to R/utils.R
index 7b69cf8..772de55 100644
--- a/inst/app/R/utils.R
+++ b/R/utils.R
@@ -1,4 +1,3 @@
-
 #' Create Bootstrap dropdown button with custom UI
 #'
 #' @param title The name of the dropdown button
@@ -11,7 +10,7 @@
 #' @param direction The direction of the dropdown Default value \code{'down'}.
 #' @param autoclose If \code{TRUE} the dropdown will close when the user clicks inside it
 #'
-#' @export
+#' @noRd
 dropdown_button <- function(
     title, ..., color = 'primary', outline = FALSE, size = c('normal', 'sm', 'lg'),
     width = 400, direction = c('down', 'right', 'up', 'left'), autoclose = TRUE)
@@ -39,6 +38,8 @@ dropdown_button <- function(
 
 }
 
+#' Automatically assign a scale for large numbers in ggplot2
+#' @noRd
 find_scale <- function(x) {
   m <- abs(max(x))
   i <- c(0, 1e3, 1e6, 1e9, 1e12)
@@ -47,7 +48,9 @@ find_scale <- function(x) {
   return(list(names(i)[findInterval(m, i)], x[findInterval(m, i)]))
 }
 
-theme_pioneer <- function(){
+#' Theme for ggplot2
+#' @noRd
+theme_pioneer <- function() {
   theme(
     axis.text.x = element_text(
       angle = 0, color = '#183271', vjust = 0.5,
@@ -91,6 +94,8 @@ theme_pioneer <- function(){
     panel.spacing = unit(2, "lines"))
 }
 
+#' Save function for ggplot2 objects
+#' @noRd
 ggsave_ <- function(filename, plot, format = 'png', size = c('A5', 'A4', 'A3')) {
   size <- match.arg(size)
   dims <- switch(
@@ -106,6 +111,8 @@ ggsave_ <- function(filename, plot, format = 'png', size = c('A5', 'A4', 'A3'))
     ))
 }
 
+#' Create a random ID
+#' @noRd
 rand_id <- function() {
   # For true random IDs, we should use uuid or openssl libraries, but this will do
   hex_digits <- c(0:9, letters[1:6])
diff --git a/inst/app/.gitignore b/inst/app/.gitignore
deleted file mode 100644
index eda8ee3..0000000
--- a/inst/app/.gitignore
+++ /dev/null
@@ -1,4 +0,0 @@
-shiny_bookmarks
-
-# VS code settings
-.vscode/settings.json
diff --git a/inst/app/conditionalUI.R b/inst/app/conditionalUI.R
deleted file mode 100644
index 02db80f..0000000
--- a/inst/app/conditionalUI.R
+++ /dev/null
@@ -1,129 +0,0 @@
-# Functions to render the UI based on other input
-
-output$ui_id <- renderUI({
-
-  req(data())
-
-  if (is.null(data()$file)) return(NULL)
-
-  choices <- colnames(data()$file)
-  selectInput('dea_id', 'Firm ID', choices = choices, multiple = FALSE)
-
-})
-
-output$ui_inputs <- renderUI({
-
-  req(data())
-
-  if (is.null(data()$file)) return(NULL)
-
-  # Restore input if we are restoring previous state
-  selected <- if (!is.null(restoreVals$inputs)) restoreVals$inputs else NULL
-  choices <- data()$cols[sapply(data()$file, is.numeric, USE.NAMES = FALSE)]
-
-  selectInput('dea_input', 'Inputs', choices = choices, selected = selected, multiple = TRUE)
-
-})
-
-observeEvent(input$dea_input, {
-  selected_inputs <- input$dea_input
-  selected <- input$dea_output
-  choices <- data()$cols[sapply(data()$file, is.numeric, USE.NAMES = FALSE)]
-  if (length(selected_inputs) > 0) {
-    choices <- choices[!(choices %in% selected_inputs)]
-  }
-  if (!is.null(selected) && any(selected %in% selected_inputs)) {
-    selected <- selected[!(selected %in% selected_inputs)]
-  }
-  updateSelectInput(session, 'dea_output', choices = choices, selected = selected)
-})
-
-output$ui_outputs <- renderUI({
-
-  req(data())
-
-  if (is.null(data()$file)) return(NULL)
-
-  # Restore input if we are restoring previous state
-  selected <- if (!is.null(restoreVals$outputs)) restoreVals$outputs else NULL
-  choices <- data()$cols[sapply(data()$file, is.numeric, USE.NAMES = FALSE)]
-
-  selectInput('dea_output', 'Outputs', choices = choices, selected = selected, multiple = TRUE)
-
-})
-
-observeEvent(input$dea_output, {
-  selected_outputs <- input$dea_output
-  selected <- input$dea_input
-  choices <- data()$cols[sapply(data()$file, is.numeric, USE.NAMES = FALSE)]
-  if (length(selected_outputs) > 0) {
-    choices <- choices[!(choices %in% selected_outputs)]
-  }
-  if (!is.null(selected) && any(selected %in% selected_outputs)) {
-    selected <- selected[!(selected %in% selected_outputs)]
-  }
-  updateSelectInput(session, 'dea_input', choices = choices, selected = selected)
-})
-
-output$ui_timeseries <- renderUI({
-
-  req(data()$file)
-
-  checkboxInput('hasyear', 'Time series data', value = FALSE)
-
-})
-
-output$ui_year <- renderUI({
-
-  req(data(), input$hasyear)
-
-  # We only want to show the input if we have time series data
-  if (!input$hasyear) return(NULL)
-
-  df <- data()$file
-
-  identify_year_variable <- \(x) {
-    if (!is.atomic(x) || !is.numeric(x) || any(is.na(x))) {
-      return(FALSE)
-    }
-    return(all(abs(2000 - range(x)) < 100))
-  }
-
-  choices <- data()$cols
-  year_variable <- df[names(df[(which(sapply(df, identify_year_variable)))])]
-  selected <- ifelse(length(year_variable) >= 1, names(year_variable[1]), choices[[1]])
-  selectInput('dea_year', 'Time series variable', choices = choices, selected = selected, multiple = FALSE)
-
-})
-
-output$ui_subset <- renderUI({
-
-  req(data()$file)
-
-  tagList(
-    checkboxInput('data.subset', 'Subset data', value = FALSE)
-  )
-
-})
-
-output$ui_subset_info <- renderUI({
-
-  req(data()$file)
-
-  n_rows <- length(preview_selected())
-  t_rows <- nrow(data()$file)
-  one <- n_rows == 1
-
-  tagList(
-    p(
-      class = 'small', helpText(sprintf(
-        'Click to subset data. You can select the rows to include in the analysis by
-        clicking the rows in the table. Currently %s %s of %s %s selected',
-        n_rows, if (one) 'row' else 'rows', t_rows, if (one) 'is' else 'are'
-      ))
-    ),
-    actionButton('data.subset.select', 'Select all'),
-    actionButton('data.subset.deselect', 'Deselect all')
-  )
-
-})
diff --git a/inst/app/global.R b/inst/app/global.R
deleted file mode 100644
index 6ab1034..0000000
--- a/inst/app/global.R
+++ /dev/null
@@ -1,39 +0,0 @@
-# Load packages
-library(pioneeR)
-library(shiny)
-library(bslib)
-source('R/utils.R')
-
-# Set Bootstrap version
-bs_ver <- 5
-
-enableBookmarking(store = 'server')
-
-# Check if we're running locally or on a server
-is_local <- !nzchar(Sys.getenv('SHINY_PORT'))
-
-checkBalance <- function(df, id.var, time.var) {
-
-  units <- unique(df[, id.var])
-  time <- unique(df[, time.var])
-
-  miss <- sapply(units, function(u) {
-    unit.time <- unique(df[df[,id.var] == u, time.var])
-    all(sapply(time, function(t) t %in% unit.time))
-  })
-
-  r <- list()
-
-  if (!all(miss)) {
-    r$data <- df[df[,id.var] %in% units[miss],]
-    r$listwise <- TRUE
-    r$message <- 'Data was not balanced, listwise deleting has been performed'
-  } else {
-    r$data <- df
-    r$listwise <- FALSE
-    r$message <- NULL
-  }
-
-  return(r)
-
-}
diff --git a/inst/app/about.md b/inst/files/about.md
similarity index 100%
rename from inst/app/about.md
rename to inst/files/about.md
diff --git a/inst/app/dea_analysis.Rmd b/inst/files/dea_analysis.Rmd
similarity index 100%
rename from inst/app/dea_analysis.Rmd
rename to inst/files/dea_analysis.Rmd
diff --git a/inst/app/www/pioneer.js b/inst/www/pioneer.js
similarity index 100%
rename from inst/app/www/pioneer.js
rename to inst/www/pioneer.js
diff --git a/inst/app/www/pioneer.min.js b/inst/www/pioneer.min.js
similarity index 100%
rename from inst/app/www/pioneer.min.js
rename to inst/www/pioneer.min.js
diff --git a/inst/app/www/style.css b/inst/www/style.css
similarity index 100%
rename from inst/app/www/style.css
rename to inst/www/style.css
diff --git a/inst/app/www/style.min.css b/inst/www/style.min.css
similarity index 100%
rename from inst/app/www/style.min.css
rename to inst/www/style.min.css