transfer from old repo

2026-08-19 09:27:27 +02:00 · 2026-08-19 09:27:27 +02:00 · 277e2b8cf3
commit 277e2b8cf3
parent cfa4a5f9cc
1111 changed files with 83736 additions and 0 deletions
--- a/apps/.DS_Store
+++ b/apps/.DS_Store
--- a/apps/Assignment/assign_sample.csv
+++ b/apps/Assignment/assign_sample.csv
@ -0,0 +1,134 @@
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--- a/apps/Assignment/assign_sample.xlsx
+++ b/apps/Assignment/assign_sample.xlsx
--- a/apps/Assignment/group_assign.R
+++ b/apps/Assignment/group_assign.R
@ -0,0 +1,188 @@
+group_assignment <-
+  function(ds,
+           cap_classes = NULL,
+           excess_space = NULL,
+           pre_assign = NULL) {
+    require(dplyr)
+    require(tidyr)
+    require(ROI)
+    require(ROI.plugin.symphony)
+    require(ompr)
+    require(ompr.roi)
+    
+    if (!is.data.frame(ds)){
+      stop("Supplied data has to be a data frame, with each row
+           are subjects and columns are groups, with the first column being
+           subject identifiers")}
+    
+    ## This program very much trust the user to supply correctly formatted data
+    cost <- t(ds[,-1]) #Transpose converts to matrix
+    colnames(cost) <- ds[,1]
+    
+    num_groups <- dim(cost)[1]
+    num_sub <- dim(cost)[2]
+    
+    ## Adding the option to introduce a bit of head room to the classes by
+    ## the groups to a little bigger than the smallest possible
+    ## Default is to allow for an extra 20 % fill
+    if (is.null(excess_space)) {
+      excess <- 1.2
+    } else {
+      excess <- excess_space
+    }
+    
+    # generous round up of capacities
+    if (is.null(cap_classes)) {
+      capacity <- rep(ceiling(excess*num_sub/num_groups), num_groups)
+    # } else if (!is.numeric(cap_classes)) {
+    #   stop("cap_classes has to be numeric")
+    } else if (length(cap_classes)==1){
+     capacity <- ceiling(rep(cap_classes,num_groups)*excess)
+    } else if (length(cap_classes)==num_groups){
+      capacity <- ceiling(cap_classes*excess)
+    } else {
+      stop("cap_classes has to be either length 1 or same as number of groups")
+    }
+    
+    ## This test should be a little more elegant
+    ## pre_assign should be a data.frame or matrix with an ID and assignment column
+    with_pre_assign <- FALSE
+    if (!is.null(pre_assign)){
+      # Setting flag for later and export list
+      with_pre_assign <- TRUE
+      # Splitting to list for later merging
+      pre <- split(pre_assign[,1],factor(pre_assign[,2],levels = seq_len(num_groups)))
+      # Subtracting capacity numbers, to reflect already filled spots
+      capacity <- capacity-lengths(pre)
+      # Making sure pre_assigned are removed from main data set
+      ds <- ds[!ds[[1]] %in% pre_assign[[1]],]
+      
+      cost <- t(ds[,-1])
+      colnames(cost) <- ds[,1]
+      
+      num_groups <- dim(cost)[1]
+      num_sub <- dim(cost)[2]
+    }
+    
+    ## Simple NA handling. Better to handle NAs yourself!
+    cost[is.na(cost)] <- num_groups
+    
+    i_m <- seq_len(num_groups)
+    j_m <- seq_len(num_sub)
+    
+    m <- MIPModel() %>%
+      add_variable(grp[i, j],
+                   i = i_m,
+                   j = j_m,
+                   type = "binary") %>%
+      ## The first constraint says that group size should not exceed capacity
+      add_constraint(sum_expr(grp[i, j], j = j_m) <= capacity[i],
+                     i = i_m) %>%
+      ## The second constraint says each subject can only be in one group
+      add_constraint(sum_expr(grp[i, j], i = i_m) == 1, j = j_m) %>%
+      ## The objective is set to minimize the cost of the assignments
+      ## Giving subjects the group with the highest possible ranking
+      set_objective(sum_expr(
+        cost[i, j] * grp[i, j],
+        i = i_m,
+        j = j_m
+      ),
+      "min") %>%
+      solve_model(with_ROI(solver = "symphony", verbosity = 1))
+    
+    ## Getting assignments
+    solution <- get_solution(m, grp[i, j]) %>% filter(value > 0)
+    
+    assign <- solution |> select(i,j)
+    
+    if (!is.null(rownames(cost))){
+      assign$i <- rownames(cost)[assign$i]
+    }
+
+    if (!is.null(colnames(cost))){
+      assign$j <- colnames(cost)[assign$j]
+    }
+    
+    ## Splitting into groups based on assignment
+    assign_ls <- split(assign$j,assign$i)
+    
+    
+    ## Extracting subject cost for the final assignment for evaluation
+    if (is.null(rownames(cost))){
+      rownames(cost) <- seq_len(nrow(cost))
+    }
+    
+    if (is.null(colnames(cost))){
+      colnames(cost) <- seq_len(ncol(cost))
+    }
+    
+    eval <- lapply(seq_len(length(assign_ls)),function(i){
+      ndx <- match(names(assign_ls)[i],rownames(cost))
+      cost[ndx,assign_ls[[i]]]
+    })
+    names(eval) <- names(assign_ls)
+    
+    if (with_pre_assign){
+      names(pre) <- names(assign_ls)
+      assign_all <- mapply(c, assign_ls, pre, SIMPLIFY=FALSE)
+      
+      out <- list(all_assigned=assign_all)
+    } else {
+      out <- list(all_assigned=assign_ls)
+    }
+    
+    export <- do.call(rbind,lapply(seq_along(out[[1]]),function(i){
+      cbind("ID"=out[[1]][[i]],"Group"=names(out[[1]])[i])
+    }))
+    
+    out <- append(out,
+                  list(evaluation=eval,
+                       assigned=assign_ls,
+                       solution = solution,
+                       capacity = capacity,
+                       excess = excess,
+                       pre_assign = with_pre_assign,
+                       cost_scale = levels(factor(cost)),
+                       input=ds,
+                       export=export))
+    # exists("excess")
+    return(out)
+  }
+
+
+## Assessment performance overview
+## The function plots costs of assignment for each subject in every group
+assignment_plot <- function(lst){
+  
+  dl <- lst[[2]]
+  cost_scale <- unique(lst[[8]])
+  cap <- lst[[5]]
+  cnts_ls <- lapply(dl,function(i){
+    factor(i,levels=cost_scale)
+  })
+  require(ggplot2)
+  require(patchwork)
+  require(viridisLite)
+  
+  y_max <- max(lengths(dl))
+  
+  wrap_plots(lapply(seq_along(dl),function(i){
+    ttl <- names(dl)[i]
+    ns <- length(dl[[i]])
+    cnts <- cnts_ls[[i]]
+    ggplot() + geom_bar(aes(cnts,fill=cnts)) +
+      scale_x_discrete(name = NULL, breaks=cost_scale, drop=FALSE) +
+      scale_y_continuous(name = NULL, limits = c(0,y_max)) + 
+      scale_fill_manual(values = viridisLite::viridis(length(cost_scale), direction = -1)) +
+      guides(fill=FALSE) + labs(title=paste0(ttl," (fill=",round(ns/cap[[i]],1),";m=",round(mean(dl[[i]]),1),";n=",ns ,")"))
+  })) 
+}
+
+
+## Helper function for Shiny
+file_extension <- function(filenames) {
+  sub(pattern = "^(.*\\.|[^.]+)(?=[^.]*)", replacement = "", filenames, perl = TRUE)
+}
+
+
+
--- a/apps/Assignment/pre_grouped.csv
+++ b/apps/Assignment/pre_grouped.csv
@ -0,0 +1,11 @@
+"ID","group"
+"sub36",16
+"sub105",10
+"sub112",3
+"sub61",15
+"sub27",8
+"sub78",7
+"sub110",1
+"sub129",2
+"sub109",12
+"sub46",14
--- a/apps/Assignment/rsconnect/shinyapps.io/cognitiveindex/assignment.dcf
+++ b/apps/Assignment/rsconnect/shinyapps.io/cognitiveindex/assignment.dcf
@ -0,0 +1,10 @@
+name: assignment
+title:
+username: cognitiveindex
+account: cognitiveindex
+server: shinyapps.io
+hostUrl: https://api.shinyapps.io/v1
+appId: 9832455
+bundleId: 7671734
+url: https://cognitiveindex.shinyapps.io/assignment/
+version: 1
--- a/apps/Assignment/server.R
+++ b/apps/Assignment/server.R
@ -0,0 +1,96 @@
+server <- function(input, output, session) {
+  library(dplyr)
+  library(tidyr)
+  library(ROI)
+  library(ROI.plugin.symphony)
+  library(ompr)
+  library(ompr.roi)
+  library(magrittr)
+  library(ggplot2)
+  library(viridisLite)
+  library(patchwork)
+  library(openxlsx)
+  # source("https://git.nikohuru.dk/au-phd/PhysicalActivityandStrokeOutcome/raw/branch/main/side%20projects/assignment.R")
+  source("group_assign.R")
+  
+  dat <- reactive({
+    # input$file1 will be NULL initially. After the user selects
+    # and uploads a file, head of that data file by default,
+    # or all rows if selected, will be shown.
+    
+    req(input$file1)
+    # Make laoding dependent of file name extension (file_ext())
+    ext <- file_extension(input$file1$datapath)
+    
+    if (ext == "csv") {
+      df <- read.csv(input$file1$datapath,na.strings = c("NA", '""',""))
+    } else if (ext %in% c("xls", "xlsx")) {
+      df <- openxlsx::read.xlsx(input$file1$datapath,na.strings = c("NA", '""',""))
+      
+    } else {
+      stop("Input file format has to be either '.csv', '.xls' or '.xlsx'")
+    }
+    
+    return(df)
+  })
+  
+  dat_pre <- reactive({
+    
+    # req(input$file2)
+    # Make laoding dependent of file name extension (file_ext())
+    if (!is.null(input$file2$datapath)){
+      ext <- file_extension(input$file2$datapath)
+      
+      if (ext == "csv") {
+        df <- read.csv(input$file2$datapath,na.strings = c("NA", '""',""))
+      } else if (ext %in% c("xls", "xlsx")) {
+        df <- openxlsx::read.xlsx(input$file2$datapath,na.strings = c("NA", '""',""))
+        
+      } else {
+        stop("Input file format has to be either '.csv', '.xls' or '.xlsx'")
+      }
+      
+      return(df)
+    } else {
+      return(NULL)
+    }
+
+  })
+  
+  assign <-
+    reactive({
+      assigned <- group_assignment(
+        ds = dat(),
+        excess_space = input$ecxess,
+        pre_assign = dat_pre()
+      )
+      return(assigned)
+    })
+  
+  
+  output$raw.data.tbl <- renderTable({
+    assign()$export
+  })
+  
+  output$pre.assign <- renderTable({
+    dat_pre()
+  })
+  
+  output$input <- renderTable({
+    dat()
+  })
+  
+  output$assign.plt <- renderPlot({
+    assignment_plot(assign())
+  })
+  
+  # Downloadable csv of selected dataset ----
+  output$downloadData <- downloadHandler(
+    filename = "group_assignment.csv",
+
+    content = function(file) {
+      write.csv(assign()$export, file, row.names = FALSE)
+    }
+  )
+  
+}
--- a/apps/Assignment/ui.R
+++ b/apps/Assignment/ui.R
@ -0,0 +1,123 @@
+library(shiny)
+library(ggplot2)
+
+ui <- fluidPage(
+  ## -----------------------------------------------------------------------------
+  ## Application title
+  ## -----------------------------------------------------------------------------
+  
+  titlePanel("Assign groups based on costs/priorities.",
+             windowTitle = "Group assignment calculator"),
+  h5(
+    "Please note this calculator is only meant as a proof of concept for educational purposes,
+     and the author will take no responsibility for the results of the calculator.
+     Uploaded data is not kept, but please, do not upload any sensitive data."
+  ),
+  
+  ## -----------------------------------------------------------------------------
+  ## Side panel
+  ## -----------------------------------------------------------------------------
+  
+  
+  ## -----------------------------------------------------------------------------
+  ## Single entry
+  ## -----------------------------------------------------------------------------
+  sidebarLayout(
+    sidebarPanel(
+      numericInput(
+        inputId = "ecxess",
+        label = "Excess space",
+        value = 1,
+        step = .05
+      ),
+      p("As default, the program will try to evenly distribute subjects in groups. 
+        This factor will add more capacity to each group, for an overall lesser cost, 
+        but more uneven group numbers. More adjustments can be performed with the source script."),
+      a(href='https://git.nikohuru.dk/au-phd/PhysicalActivityandStrokeOutcome/src/branch/main/apps/Assignment', "Source", target="_blank"),
+      ## -----------------------------------------------------------------------------
+      ## File upload
+      ## -----------------------------------------------------------------------------
+      
+      # Input: Select a file ----
+      
+      fileInput(
+        inputId = "file1",
+        label = "Choose main data file",
+        multiple = FALSE,
+        accept = c(
+          ".csv",".xls",".xlsx"
+        )
+      ),
+      strong("Columns: ID, group1, group2, ... groupN."),
+      strong("NOTE: 0s will be interpreted as lowest score."),
+      p("Cells should contain cost/priorities.
+         Lowest score, for highest priority.
+        Non-ranked should contain a number (eg lowest score+1).
+         Will handle missings but try to avoid."),
+      
+      fileInput(
+        inputId = "file2",
+        label = "Choose data file for pre-assigned subjects",
+        multiple = FALSE,
+        accept = c(
+          ".csv",".xls",".xlsx"
+        )
+      ),
+      h6("Columns: ID, group"),
+      
+      
+      
+      ## -----------------------------------------------------------------------------
+      ## Download output
+      ## -----------------------------------------------------------------------------
+      
+      # Horizontal line ----
+      tags$hr(),
+      
+      h4("Download results"),
+      
+      # Button
+      downloadButton("downloadData", "Download")
+    ),
+    
+    mainPanel(tabsetPanel(
+      ## -----------------------------------------------------------------------------
+      ## Plot tab
+      ## -----------------------------------------------------------------------------
+      
+      tabPanel(
+        "Summary",
+        h3("Assignment plot"),
+        p("These plots are to summarise simple performance meassures for the assignment. 
+          'f' is group fill fraction and 'm' is mean cost in group."),
+        
+        plotOutput("assign.plt")
+        
+      ),
+      
+      tabPanel(
+        "Results",
+        h3("Raw Results"),
+        p("This is identical to the downloaded file (see panel on left)"),
+        
+        htmlOutput("raw.data.tbl", container = span)
+        
+      ),
+      
+      tabPanel(
+        "Input data Results",
+        h3("Costs/prioritis overview"),
+        
+        
+        htmlOutput("input", container = span),
+        
+        h3("Pre-assigned groups"),
+        p("Appears empty if none is uploaded."),
+
+        htmlOutput("pre.assign", container = span)
+        
+      )
+      
+    ))
+  )
+)
--- a/apps/Cognitive
+++ b/apps/Cognitive
@ -0,0 +1,42 @@
+## -----------------------------------------------------------------------------
+## Cognitive Index app
+## -----------------------------------------------------------------------------
+## 
+## This app is created to demonstrate the index-lookup of a certain cognitive test.
+## The results a provided with no responsibility of validity.
+## Do not upload sensitive data when using the app.
+## 
+## /AG Damsbo 
+## 
+
+
+## -- START WITH THIS -- ##
+old_wd<-getwd()
+
+setwd(paste0(old_wd,"/apps/Index app"))
+shiny::runApp()
+
+source(paste0(old_wd,"/apps/app_deploy.R"))
+
+setwd(old_wd)
+
+## Poor mans changelog
+
+## 18aug2022 Its alive!!
+## https://cognitiveindex.shinyapps.io/index_app/
+## 
+## 19aug2022 - 1
+## Now live with a choice between single entry or file upload, and download option for results in both cases.
+## Wishlist:
+## - Still missing is a better labelling, however this works for now.
+##
+## Sources: 
+## - How about uploading dataset? https://shiny.rstudio.com/articles/upload.html
+## - And then download: https://shiny.rstudio.com/articles/download.html
+## 
+## Now moved to my PhysicalActivityandStrokeOutcome-repository.
+## 
+## 19aug2022 - 2
+## Now table headers are updated. Done for now!
+## 
+## 
--- a/apps/Group
+++ b/apps/Group
@ -0,0 +1,39 @@
+## -----------------------------------------------------------------------------
+## Group assignment app
+## -----------------------------------------------------------------------------
+## 
+## Special cases to consider
+## - duplicate scores - DON'T CARE
+## - missing scores - DONE
+## - Pre-assignment of special cases - SOLVED
+## - Make sure to remove assigned subjects from all subjects when pre-assigning - DONE
+## - Set class to output list and have plot function only accept correct class (not necessary for Shiny)
+## - Use knitr::kable() to show sample data, alternatively use gt() - DONE
+## - Handle [NA, 0, ""] - DONE
+##
+## I believe we are ready for a shiny app!
+
+
+## -- START WITH THIS -- ##
+old_wd<-getwd()
+
+setwd(paste0(old_wd,"/apps/Assignment"))
+
+setwd(old_wd)
+
+## Run app
+
+shiny::runApp(appDir = here::here("apps/Assignment"),launch.browser = TRUE)
+
+## App deployment
+
+require(rsconnect)
+
+keys<-suppressWarnings(read.csv("/Users/au301842/shinyapp_token.csv",colClasses = "character"))
+
+rsconnect::setAccountInfo(name='cognitiveindex', 
+                          token=keys$key[1], secret=keys$key[2])
+
+deployApp(appDir = "/Users/au301842/PAaSO/apps/Assignment")
+
+## Raw sketch, doesn't load correctly...
--- a/apps/HWE
+++ b/apps/HWE
@ -0,0 +1,22 @@
+## -----------------------------------------------------------------------------
+## HWE Calc test app deployment
+## -----------------------------------------------------------------------------
+## 
+## This app was written as proof of concept for my Research year program, 
+## as no online calculators were found to calculate the 
+## Hardy-Weinberg-equilibrium of allele distributions.
+## 
+## Source: https://raw.githubusercontent.com/agdamsbo/daDoctoR/master/R/hwe_geno.R
+## 
+## /AG Damsbo 
+## 
+
+old_wd<-getwd()
+
+setwd(paste0(old_wd,"/apps/HWE Calc"))
+shiny::runApp()
+
+source(paste0(old_wd,"/apps/app_deploy.R"))
+
+setwd(old_wd)
+
--- a/Calc/rsconnect/shinyapps.io/cognitiveindex/hwe_calc.dcf
+++ b/Calc/rsconnect/shinyapps.io/cognitiveindex/hwe_calc.dcf
@ -0,0 +1,11 @@
+name: hwe_calc
+title:
+username:
+account: cognitiveindex
+server: shinyapps.io
+hostUrl: https://api.shinyapps.io/v1
+appId: 6803322
+bundleId: 6213208
+url: https://cognitiveindex.shinyapps.io/hwe_calc/
+when: 1660807491.6397
+lastSyncTime: 1660807491.63971
--- a/Calc/server.R
+++ b/Calc/server.R
@ -0,0 +1,69 @@
+server <- function(input, output, session) {
+  
+  cale <- reactive({
+    as.numeric(input$ale)
+  })
+  
+  dat<-reactive({
+    df<-data.frame(lbls=c("MM","MN","NN","MO","NO","OO"),
+                   value=rbind(input$mm,input$mn,input$nn,input$mo,input$no,input$oo),
+                   stringsAsFactors = FALSE)
+    print(df)
+    df
+  })
+  
+  cmm <- reactive({
+    as.numeric(input$mm)
+  })
+  
+  cmn <- reactive({
+    as.numeric(input$mn)
+  })
+  
+  cnn <- reactive({
+    as.numeric(input$nn)
+  })
+  
+  cmo <- reactive({
+    as.numeric(input$mo)
+  })
+  
+  cno <- reactive({
+    as.numeric(input$no)
+  })
+  
+  coo <- reactive({
+    as.numeric(input$oo)
+  })
+  
+  hwe_p <- function() ({ hwe_geno(cmm(),cmn(),cnn(),cmo(),cno(),coo(),alleles=cale()) })
+  
+  output$allele.tbl <- renderTable({ hwe_p()$allele.dist })
+  
+  output$obs.tbl <- renderTable({ hwe_p()$observed.dist })
+  
+  output$exp.tbl <- renderTable({ hwe_p()$expected.dist })
+  
+  output$chi.val <- renderTable({ hwe_p()$chi.value })
+  
+  output$p.val <- renderTable({ hwe_p()$p.value })
+  
+  output$allele.dist <- renderText({"Allele distribution"})
+  
+  output$obs.dist <- renderText({"Observed distribution"})
+  
+  output$exp.dist <- renderText({"Expected distribution"})
+  
+  output$chi <- renderText({"Chi square value"})
+  
+  output$p <- renderText({"P value"})
+  
+  output$geno.pie.plt<- renderPlot({
+    ggplot(dat(), aes(x="", y=value, fill=lbls))+
+      geom_bar(width = 1, stat = "identity")+ 
+      coord_polar("y", start=0)+ 
+      scale_fill_brewer(palette="Dark2")
+  })
+  
+  output$geno.pie.ttl <- renderText({"Genotype distribution"})
+}
--- a/Calc/ui.R
+++ b/Calc/ui.R
@ -0,0 +1,85 @@
+source("https://raw.githubusercontent.com/agdamsbo/daDoctoR/master/R/hwe_geno.R")
+
+library(shiny)
+library(ggplot2)
+
+ui <- fluidPage(
+  
+  # Application title
+  titlePanel("Chi square test of HWE for bi- or triallelic systems"),
+  
+  sidebarLayout(
+    sidebarPanel(
+      
+      # Input: Numeric entry for number of alleles ----
+      radioButtons(inputId = "ale",
+                   label = "Number of alleles:",
+                   inline = FALSE,
+                   choiceNames=c("Two alleles (M, N)",
+                                 "Three alleles (M, N, O)"),
+                   choiceValues=c(2,3)),
+      
+      h4("Observed genotype distribution"),
+      
+      numericInput(inputId = "mm",
+                   label = "MM:",
+                   value=NA),
+      
+      numericInput(inputId = "mn",
+                   label = "MN:",
+                   value=NA),
+      
+      numericInput(inputId = "nn",
+                   label = "NN:",
+                   value=NA),
+      conditionalPanel(condition = "input.ale==3",
+                       
+                       numericInput(inputId = "mo",
+                                    label = "MO:",
+                                    value=NA),
+                       
+                       numericInput(inputId = "no",
+                                    label = "NO:",
+                                    value=NA),
+                       
+                       numericInput(inputId = "oo",
+                                    label = "OO:",
+                                    value=NA))
+      
+    ),
+    
+    mainPanel(
+      tabsetPanel(
+        tabPanel("Summary",
+                 h3(textOutput("obs.dist", container = span)),
+                 htmlOutput("obs.tbl", container = span),
+                 
+                 h3(textOutput("exp.dist", container = span)),
+                 htmlOutput("exp.tbl", container = span),
+                 
+                 h3(textOutput("allele.dist", container = span)),
+                 htmlOutput("allele.tbl", container = span),
+                 
+                 value=1),
+        
+        tabPanel("Calculations",
+                 
+                 h3(textOutput("chi", container = span)),
+                 htmlOutput("chi.val", container = span),
+                 
+                 h3(textOutput("p", container = span)),
+                 htmlOutput("p.val", container = span),
+                 
+                 value=2),
+        
+        
+        
+        tabPanel("Plots",
+                 h3(textOutput("geno.pie.ttl", container = span)),
+                 plotOutput("geno.pie.plt"),
+                 
+                 value=3),
+        selected= 2, type = "tabs")
+    )
+  )
+)
--- a/app/rsconnect/shinyapps.io/cognitiveindex/index_app.dcf
+++ b/app/rsconnect/shinyapps.io/cognitiveindex/index_app.dcf
@ -0,0 +1,9 @@
+name: index_app
+title:
+username:
+account: cognitiveindex
+server: shinyapps.io
+hostUrl: https://api.shinyapps.io/v1
+appId: 6803928
+bundleId: 8182645
+url: https://cognitiveindex.shinyapps.io/index_app/
--- a/app/sample
+++ b/app/sample
@ -0,0 +1,24 @@
+# Samlpe data from data base
+
+source("https://raw.githubusercontent.com/agdamsbo/ENIGMAtrial_R/main/src/redcap_api_export_short.R")
+
+df<-redcap_api_export_short(id= c(40:45),
+                            instruments= "rbans",
+                            event= "3_months_arm_1") %>%
+  select(c("record_id",ends_with(c("_version","_age","_rs")))) %>%
+  na.omit()|>
+  rbind(redcap_api_export_short(id= c(10:15),
+                                instruments= "rbans",
+                                event= "12_months_arm_1") %>%
+          select(c("record_id",ends_with(c("_version","_age","_rs")))) %>%
+          na.omit())
+
+colnames(df)<-c("record_id","ab","age","imm","vis","ver","att","del")
+
+## New index numbers
+df$record_id<-1:nrow(df)
+
+## Age is changed for obscurity
+df$age<-sample(-2:2,nrow(df),TRUE)+df$age
+
+write.csv(df, "sample.csv", row.names = FALSE)
--- a/app/sample.csv
+++ b/app/sample.csv
@ -0,0 +1,13 @@
+"record_id","ab","age","imm","vis","ver","att","del"
+1,1,67,26,31,24,42,38
+2,1,69,34,31,27,40,34
+3,1,63,43,35,29,46,38
+4,1,66,45,37,30,54,40
+5,1,66,44,34,33,54,44
+6,1,83,39,34,23,37,31
+7,2,71,49,37,24,52,42
+8,2,81,33,30,39,47,42
+9,2,61,50,38,36,52,56
+10,2,88,32,20,26,13,30
+11,2,73,36,28,22,34,33
+12,2,89,22,30,21,29,30
--- a/app/server.R
+++ b/app/server.R
@ -0,0 +1,104 @@
+server <- function(input, output, session) {
+  library(dplyr)
+  library(ggplot2)
+  library(tidyr)
+  source("https://raw.githubusercontent.com/agdamsbo/ENIGMAtrial_R/main/src/plot_index.R")
+  source("https://raw.githubusercontent.com/agdamsbo/ENIGMAtrial_R/main/src/index_from_raw.R")
+
+  dat<-reactive({
+    
+    df<-data.frame(record_id="1",
+                   ab=input$version,
+                   age=input$age,
+                   imm=input$rs1,
+                   vis=input$rs2,
+                   ver=input$rs3,
+                   att=input$rs4,
+                   del=input$rs5,
+                   stringsAsFactors = FALSE)
+    return(df)
+  })
+
+  dat_u<-reactive({
+  # input$file1 will be NULL initially. After the user selects
+  # and uploads a file, head of that data file by default,
+  # or all rows if selected, will be shown.
+  
+  
+  req(input$file1)
+  
+  df <- read.csv(input$file1$datapath,
+                 header = input$header,
+                 sep = input$sep,
+                 quote = input$quote)
+  
+  return(df)
+  })
+  
+  dat_f<-reactive({
+    
+    if (input$type==1){
+      return(dat())}
+    if (input$type==2){
+      return(head(dat_u(),10))}
+  })
+  
+  index_p <- reactive({ df<-index_from_raw(ds=dat_f(),
+                                          indx=read.csv("https://raw.githubusercontent.com/agdamsbo/ENIGMAtrial_R/main/data/index.csv"),
+                                          version = dat_f()$ab,
+                                          age = dat_f()$age,
+                                          raw_columns=c("imm","vis","ver","att","del")) 
+    
+    colnames(df)<-c("id",
+                    "a_is",
+                    "b_is",
+                    "c_is",
+                    "d_is",
+                    "e_is",
+                    "i_is",
+                    "a_ci",
+                    "b_ci",
+                    "c_ci",
+                    "d_ci",
+                    "e_ci",
+                    "i_ci",
+                    "a_per",
+                    "b_per",
+                    "c_per",
+                    "d_per",
+                    "e_per",
+                    "i_per")
+    return(df)
+    })
+
+  
+  output$ndx.tbl <- renderTable({ 
+    index_p()|>
+      select("id",contains("_is"))
+    })
+  
+  output$per.tbl <- renderTable({
+    index_p()|>
+      select("id",contains("_per"))
+  })
+  
+  
+  output$ndx.plt<-renderPlot({
+
+    plot_index(index_p(),sub_plot = "_is")
+  })
+
+  output$per.plt<-renderPlot({
+    plot_index(index_p(),sub_plot = "_per")
+  })
+  
+  # Downloadable csv of selected dataset ----
+  output$downloadData <- downloadHandler(
+    filename = "index_lookup.csv",
+    
+    content = function(file) {
+      write.csv(index_p(), file, row.names = FALSE)
+    }
+  )
+  
+}
--- a/app/trouble
+++ b/app/trouble
@ -0,0 +1,18 @@
+df<-data.frame(record_id="1",
+           imm=35,
+           vis=35,
+           ver=35,
+           att=35,
+           del=35,
+           stringsAsFactors = FALSE)
+
+source("https://raw.githubusercontent.com/agdamsbo/ENIGMAtrial_R/main/src/index_from_raw.R")
+
+df_c<-index_from_raw(ds=df,
+               indx=read.csv("https://raw.githubusercontent.com/agdamsbo/ENIGMAtrial_R/main/data/index.csv"),
+               version = "1",
+               age = 60,
+               raw_columns=c("imm","vis","ver","att","del"),
+               mani=TRUE)
+
+plot_index(ds=df_c,id="id",sub_plot = "_is")
--- a/apps/Index
+++ b/apps/Index
@ -0,0 +1,152 @@
+library(shiny)
+library(ggplot2)
+
+ui <- fluidPage(
+  
+  ## -----------------------------------------------------------------------------
+  ## Application title
+  ## ----------------------------------------------------------------------------- 
+
+  titlePanel("Calculating cognitive index scores in multidimensional testing.",
+             windowTitle = "Cognitive test index calculator"),
+  h5("Please note this calculator is only meant as a proof of concept for educational purposes, 
+     and the author will take no responsibility for the results of the calculator. 
+     Uploaded data is not kept, but please, do not upload any sensitive data."),
+  
+  ## -----------------------------------------------------------------------------
+  ## Side panel
+  ## ----------------------------------------------------------------------------- 
+  
+  sidebarPanel(
+      h4("Test resultsData format"),
+      
+      radioButtons(inputId = "type",
+                   label = "Data type",
+                   inline = FALSE,
+                   choiceNames=c("Single entry",
+                                 "File upload (10 records)"),
+                   choiceValues=c(1,2)),
+      
+      # Horizontal line ----
+      tags$hr(),
+      
+      ## -----------------------------------------------------------------------------
+      ## Single entry
+      ## -----------------------------------------------------------------------------      
+      
+      conditionalPanel(condition = "input.type==1",
+      numericInput(inputId = "age",
+                   label = "Age",
+                   value=60),
+      
+      radioButtons(inputId = "version",
+                   label = "Test version (A/B)",
+                   inline = FALSE,
+                   choiceNames=c("A",
+                                 "B"),
+                   choiceValues=c(1,2)),
+      
+      numericInput(inputId = "rs1",
+                   label = "Immediate memory",
+                   value=35),
+      numericInput(inputId = "rs2",
+                   label = "Visuospatial functions",
+                   value=35),
+      numericInput(inputId = "rs3",
+                   label = "Verbal functions",
+                   value=30),
+      numericInput(inputId = "rs4",
+                   label = "Attention",
+                   value=35),
+      numericInput(inputId = "rs5",
+                   label = "Delayed memory",
+                   value=40)
+      ),
+      
+      ## -----------------------------------------------------------------------------
+      ## File upload
+      ## ----------------------------------------------------------------------------- 
+      
+      conditionalPanel(condition = "input.type==2",
+      
+                       # Input: Select a file ----
+                       
+                       fileInput("file1", "Choose CSV File",
+                                 multiple = FALSE,
+                                 accept = c("text/csv",
+                                            "text/comma-separated-values,text/plain",
+                                            ".csv")),
+                       h6("Columns: record_id, ab, age, imm, vis, ver, att, del."),
+                       
+                       # Horizontal line ----
+                       tags$hr(),
+                       
+                       # Input: Checkbox if file has header ----
+                       checkboxInput("header", "Header", TRUE),
+                       
+                       # Input: Select separator ----
+                       radioButtons("sep", "Separator",
+                                    choices = c(Comma = ",",
+                                                Semicolon = ";",
+                                                Tab = "\t"),
+                                    selected = ","),
+                       
+                       # Input: Select quotes ----
+                       radioButtons("quote", "Quote",
+                                    choices = c(None = "",
+                                                "Double Quote" = '"',
+                                                "Single Quote" = "'"),
+                                    selected = '"'),
+                       
+      ),                 
+      
+      
+      ## -----------------------------------------------------------------------------
+      ## Download output
+      ## ----------------------------------------------------------------------------- 
+      
+      # Horizontal line ----
+      tags$hr(),
+      
+      h4("Download results"),
+      
+      # Button
+      downloadButton("downloadData", "Download")
+      
+      
+      ),
+    
+    mainPanel(
+      tabsetPanel(
+        
+        ## -----------------------------------------------------------------------------
+        ## Summary tab
+        ## ----------------------------------------------------------------------------- 
+        
+        tabPanel("Summary",
+                 h3("Index Scores"),
+
+                 htmlOutput("ndx.tbl", container = span),
+                 
+                 h3("Percentiles"),
+                 
+                 htmlOutput("per.tbl", container = span)
+    ),
+    
+    ## -----------------------------------------------------------------------------
+    ## Plots tab
+    ## ----------------------------------------------------------------------------- 
+    
+    tabPanel("Plots",
+             h3("Index Scores"),
+
+             plotOutput("ndx.plt"),
+
+             h3("Percentiles"),
+
+             plotOutput("per.plt")
+    )
+    
+    )
+    )
+)
--- a/apps/app_deploy.R
+++ b/apps/app_deploy.R
@ -0,0 +1,16 @@
+## Cognitive Index app deployment
+
+require(rsconnect)
+
+# keys <- suppressWarnings(read.csv("/Users/au301842/shinyapp_token.csv", colClasses = "character"))
+# 
+# keyring::key_get(service = "rsconnect_cognitiveindex_token")
+# keyring::key_get(service = "rsconnect_cognitiveindex_secret")
+
+rsconnect::setAccountInfo(
+  name = "cognitiveindex",
+  token = keyring::key_get(service = "rsconnect_cognitiveindex_token"), 
+  secret = keyring::key_get(service = "rsconnect_cognitiveindex_secret")
+)
+
+rsconnect::deployApp(appDir = here::here("app"))
--- a/apps/shinyDAG-1.0.0/.gitignore
+++ b/apps/shinyDAG-1.0.0/.gitignore
@ -0,0 +1,79 @@
+# ---- Project files ----
+shiny_bookmarks/
+www/errors/*
+
+# ---- Default .gitignore From grkmisc ----
+.Rproj.user
+.Rhistory
+.RData
+.DS_Store
+
+# Directories that start with _
+_*/
+
+## https://github.com/github/gitignore/blob/master/R.gitignore
+# History files
+.Rhistory
+.Rapp.history
+
+# Session Data files
+.RData
+
+# Example code in package build process
+*-Ex.R
+
+# Output files from R CMD build
+/*.tar.gz
+
+# Output files from R CMD check
+/*.Rcheck/
+
+# RStudio files
+.Rproj.user/
+
+# produced vignettes
+vignettes/*.html
+vignettes/*.pdf
+
+# OAuth2 token, see https://github.com/hadley/httr/releases/tag/v0.3
+.httr-oauth
+
+# knitr and R markdown default cache directories
+/*_cache/
+/cache/
+
+# Temporary files created by R markdown
+*.utf8.md
+*.knit.md
+
+# Shiny token, see https://shiny.rstudio.com/articles/shinyapps.html
+rsconnect/
+
+## https://github.com/github/gitignore/blob/master/Global/macOS.gitignore
+# General
+.DS_Store
+.AppleDouble
+.LSOverride
+
+# Icon must end with two \r
+Icon
+
+
+# Thumbnails
+._*
+
+# Files that might appear in the root of a volume
+.DocumentRevisions-V100
+.fseventsd
+.Spotlight-V100
+.TemporaryItems
+.Trashes
+.VolumeIcon.icns
+.com.apple.timemachine.donotpresent
+
+# Directories potentially created on remote AFP share
+.AppleDB
+.AppleDesktop
+Network Trash Folder
+Temporary Items
+.apdisk
--- a/apps/shinyDAG-1.0.0/.travis.yml
+++ b/apps/shinyDAG-1.0.0/.travis.yml
@ -0,0 +1,27 @@
+sudo: required
+services:
+  - docker
+
+env:
+  global:
+    - DOCKER_USER="grrrck"
+    - DOCKER_ORG="gerkelab"
+    - secure: "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"
+    - COMMIT=${TRAVIS_COMMIT::8}
+    - REPO="shinydag"
+
+script:
+  - docker build -f Dockerfile -t $DOCKER_ORG/$REPO:$COMMIT .
+
+after_success:
+  - docker login -u $DOCKER_USER -p $DOCKER_PASS
+  - if [[ $TRAVIS_PULL_REQUEST == "false" ]] && [[ $TRAVIS_BRANCH == "master" ]]; then
+    docker tag $DOCKER_ORG/$REPO:$COMMIT $DOCKER_ORG/$REPO:latest;
+    docker tag $DOCKER_ORG/$REPO:$COMMIT $DOCKER_ORG/$REPO:$TRAVIS_BUILD_NUMBER;
+    docker push $DOCKER_ORG/$REPO;
+    fi
+  - if [[ $TRAVIS_PULL_REQUEST == "false" ]] && [[ $TRAVIS_BRANCH == "dev" ]]; then
+    docker tag $DOCKER_ORG/$REPO:$COMMIT $DOCKER_ORG/$REPO:dev;
+    docker tag $DOCKER_ORG/$REPO:$COMMIT $DOCKER_ORG/$REPO:$TRAVIS_BUILD_NUMBER;
+    docker push $DOCKER_ORG/$REPO;
+    fi
--- a/apps/shinyDAG-1.0.0/Dockerfile
+++ b/apps/shinyDAG-1.0.0/Dockerfile
@ -0,0 +1,64 @@
+FROM rocker/shiny-verse:3.5.3
+
+LABEL maintainer="Travis Gerke (Travis.Gerke@moffitt.org)"
+
+# Install system dependencies for required packages
+RUN apt-get update -qq && apt-get -y --no-install-recommends install \
+  libssl-dev \
+  libxml2-dev \
+  libmagick++-dev \
+  libv8-3.14-dev \
+  libglu1-mesa-dev \
+  freeglut3-dev \
+  mesa-common-dev \
+  libudunits2-dev \
+  libpoppler-cpp-dev \
+  libwebp-dev \
+  && apt-get clean \
+  && rm -rf /var/lib/apt/lists/ \
+  && rm -rf /tmp/downloaded_packages/ /tmp/*.rds
+  
+RUN install2.r --error \
+  shinyAce \
+  shinydashboard \
+  shinyWidgets \
+  DiagrammeR \
+  ggdag \
+  igraph \
+  pdftools \
+  shinyBS \
+  && rm -rf /tmp/downloaded_packages/ /tmp/*.rds
+  
+RUN Rscript -e "devtools::install_github('metrumresearchgroup/texPreview', ref = 'e954322')" \
+  && rm -rf /tmp/downloaded_packages/ /tmp/*.rds
+
+# Install TinyTeX
+RUN install2.r --error tinytex \
+  && wget -qO- \ 
+     "https://github.com/yihui/tinytex/raw/master/tools/install-unx.sh" | \ 
+     sh -s - --admin --no-path \
+  && mv ~/.TinyTeX /opt/TinyTeX \
+  && /opt/TinyTeX/bin/*/tlmgr path add \ 
+  && tlmgr install metafont mfware inconsolata tex ae parskip listings \ 
+  && tlmgr install standalone varwidth xcolor colortbl multirow psnfss setspace pgf \
+  && tlmgr path add \ 
+  && Rscript -e "tinytex::r_texmf()" \ 
+  && chown -R root:staff /opt/TinyTeX \ 
+  && chmod -R a+w /opt/TinyTeX \ 
+  && chmod -R a+wx /opt/TinyTeX/bin \ 
+  && echo "PATH=${PATH}" >> /usr/local/lib/R/etc/Renviron \
+  && rm -rf /tmp/downloaded_packages/ /tmp/*.rds
+  
+RUN install2.r --error shinyjs \
+  && rm -rf /tmp/downloaded_packages/ /tmp/*.rds
+
+RUN install2.r --error plotly shinycssloaders \
+  && rm -rf /tmp/downloaded_packages/ /tmp/*.rds
+
+RUN installGithub.r gadenbuie/shinyThings@4e8becb2972aa2f7f1960da6e5fe6ad39aeceda0 \
+  && rm -rf /tmp/downloaded_packages/ /tmp/*.rds
+
+ARG SHINY_APP_IDLE_TIMEOUT=600
+RUN sed -i "s/directory_index on;/app_idle_timeout ${SHINY_APP_IDLE_TIMEOUT};/g" /etc/shiny-server/shiny-server.conf
+COPY . /srv/shiny-server/shinyDAG
+RUN chown -R shiny:shiny /srv/shiny-server/
--- a/apps/shinyDAG-1.0.0/Figures/AddNodeEdge.gif
+++ b/apps/shinyDAG-1.0.0/Figures/AddNodeEdge.gif
--- a/apps/shinyDAG-1.0.0/Figures/editEdge.gif
+++ b/apps/shinyDAG-1.0.0/Figures/editEdge.gif
--- a/apps/shinyDAG-1.0.0/Figures/example1.png
+++ b/apps/shinyDAG-1.0.0/Figures/example1.png
--- a/apps/shinyDAG-1.0.0/Figures/example1_hernan.png
+++ b/apps/shinyDAG-1.0.0/Figures/example1_hernan.png
--- a/apps/shinyDAG-1.0.0/Figures/paths.png
+++ b/apps/shinyDAG-1.0.0/Figures/paths.png
--- a/apps/shinyDAG-1.0.0/Figures/paths2.png
+++ b/apps/shinyDAG-1.0.0/Figures/paths2.png
--- a/apps/shinyDAG-1.0.0/LICENSE
+++ b/apps/shinyDAG-1.0.0/LICENSE
@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2018 Jordan Creed and Travis Gerke
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.
--- a/apps/shinyDAG-1.0.0/R/aes_ui.R
+++ b/apps/shinyDAG-1.0.0/R/aes_ui.R
@ -0,0 +1,183 @@
+
+# * ui_edge_controls() builds an individual UI control element. These elements
+#   are re-rendered whenever the tab is opened, so this function finds the
+#   current value of the input and uses that instead of the value declared
+#   in the definition in ui_edge_controls_row(). This function also isolates
+#   the edge control UI from other changes in nodes, etc, because they happen
+#   on different screens.
+ui_controls <- function(hash, inputFn, prefix_input, label, ..., input = NULL) {
+  stopifnot(!is.null(input))
+  current_value_arg_name <- intersect(names(list(...)), c("selected", "value"))
+  if (!length(current_value_arg_name)) {
+    stop("Must specifiy `selected` or `value` when specifying edge UI controls")
+  }
+  input_name <- paste(prefix_input, hash, sep = "__")
+  input_label <- label
+
+  if (input_name %in% names(isolate(input))) {
+    # Make sure current value doesn't change
+    dots <- list(...)
+    dots[current_value_arg_name] <- paste(isolate(input[[input_name]]))
+    dots$inputId <- input_name
+    dots$label <- HTML(input_label)
+    do.call(inputFn, dots)
+  } else {
+    # Create new input
+    inputFn(input_name, HTML(input_label), ...)
+  }
+}
+
+get_hashed_input_with_prefix <- function(input, prefix, hash_sep = "__") {
+  prefix <- glue::glue("^({prefix}){hash_sep}")
+
+  tibble(
+    inputId = grep(prefix, names(input), value = TRUE)
+  ) %>%
+    filter(!grepl("-selectized$", inputId)) %>%
+    # get current value of input
+    mutate(value = lapply(inputId, function(x) input[[x]])) %>%
+    tidyr::separate(inputId, into = c("var", "hash"), sep = hash_sep) %>%
+    tidyr::spread(var, value) %>%
+    mutate_if(is.list, ~ purrr::map(.x, ~ if (is.null(.x)) NA else .x)) %>%
+    tidyr::unnest() %>%
+    split(.$hash)
+}
+
+# The input for angles (here for easy refactoring or future changes)
+selectDegree <- function(inputId, label = "Degree", min = -180, max = 180, by = 15, value = 0, ...) {
+  sliderInput(inputId, label = label, min = min, max = max, value = value, step = by)
+}
+
+
+# Edge Aesthetic UI -------------------------------------------------------
+
+# These helper functions build up the Edge UI elements.
+#
+# * ui_edge_controls_row() creates the entire row of UI elements for a given
+#   edge. This function is where the UI inputs are initially defined.
+
+ui_edge_controls_row <- function(hash, from_name, to_name, ..., input = NULL) {
+  stopifnot(!is.null(input))
+  
+  extra <- list(...)
+
+  col_4 <- function(x) {
+    tags$div(class = "col-sm-6 col-md-3", style = "min-height: 80px", x)
+  }
+  title_row <- function(x) tags$div(class = "col-xs-12", tags$h3(x))
+  edge_label <- paste0(from_name, "&nbsp;&#8594; ", to_name)
+
+  tagList(
+    fluidRow(
+      title_row(HTML(edge_label))
+    ),
+    fluidRow(
+      # Edge Curve Angle
+      col_4(ui_controls(
+        hash,
+        inputFn = selectDegree,
+        prefix_input = "angle",
+        label = "Angle",
+        value = extra[["angle"]] %||% 0,
+        width = "95%",
+        input = input
+      )),
+      # Edge Color
+      col_4(ui_controls(
+        hash,
+        inputFn = xcolorPicker,
+        prefix_input = "color",
+        label = "Edge",
+        selected = extra[["color"]] %||% "Black",
+        width = "95%",
+        input = input
+      )),
+      # Curve Angle
+      col_4(ui_controls(
+        hash,
+        inputFn = selectInput,
+        prefix_input = "lty",
+        label = "Line Type",
+        choices = c("solid", "dashed"),
+        selected = extra[["lty"]] %||% "solid",
+        width = "95%",
+        input = input
+      )),
+      # Curve Angle
+      col_4(ui_controls(
+        hash,
+        inputFn = selectInput,
+        prefix_input = "lineT",
+        label = "Line Thickness",
+        choices = c("ultra thin", "very thin", "thin", "semithick", "thick", "very thick", "ultra thick"),
+        selected = extra[["lineT"]] %||% "thin",
+        width = "95%",
+        input = input
+      ))
+    )
+  )
+}
+
+
+# Node Aesthetic UI -------------------------------------------------------
+
+ui_node_controls_row <- function(hash, name, adjusted, name_latex, ..., input = NULL) {
+  stopifnot(!is.null(input))
+  
+  extra <- list(...)
+
+  col_4 <- function(x) {
+    tags$div(class = "col-sm-6 col-md-3", style = "min-height: 80px", x)
+  }
+  title_row <- function(x) tags$div(class = "col-xs-12", tags$h3(x))
+
+  tagList(
+    fluidRow(
+      title_row(HTML(name))
+    ),
+    fluidRow(
+      # LaTeX version of node label
+      col_4(ui_controls(
+        hash,
+        inputFn = textInput,
+        prefix_input = "name_latex",
+        label = "LaTeX Label",
+        value = name_latex,
+        width = "95%",
+        input = input
+      )),
+      # Text Color
+      col_4(ui_controls(
+        hash,
+        inputFn = xcolorPicker,
+        prefix_input = "color_text",
+        label = "Text",
+        selected = extra[["color_text"]] %||% "Black",
+        width = "95%",
+        input = input
+      )),
+      # Fill Color
+      col_4(ui_controls(
+        hash,
+        inputFn = xcolorPicker,
+        prefix_input = "color_fill",
+        label = "Fill",
+        selected = extra[["color_fill"]] %||% "White",
+        width = "95%",
+        input = input
+      )),
+      # Box Color (if shown)
+      if (adjusted) {
+        col_4(ui_controls(
+          hash,
+          inputFn = xcolorPicker,
+          prefix_input = "color_draw",
+          label = "Border",
+          selected = extra[["color_draw"]] %||% "Black",
+          width = "95%",
+          input = input
+        ))
+      }
+    )
+  )
+}
--- a/apps/shinyDAG-1.0.0/R/columns.R
+++ b/apps/shinyDAG-1.0.0/R/columns.R
@ -0,0 +1,28 @@
+class_3_col <- "col-md-4 col-md-offset-0 col-sm-8 col-sm-offset-2 col-xs-12"
+
+
+# Component Builders ------------------------------------------------------
+
+two_column_flips_on_mobile <- function(left, right, override_width_classes = TRUE) {
+  
+  left_col_class <- "col-sm-12 col-md-pull-6 col-md-6 col-lg-5 col-lg-pull-7"
+  right_col_class <- "col-sm-12 col-md-push-6 col-md-6 col-lg-7 col-lg-push-5"
+  
+  if (!override_width_classes) {
+    right <- tags$div(class = right_col_class, right)
+    left  <- tags$div(class = left_col_class,  left)
+  } else {
+    strip_col_class <- function(x) gsub("col-(xs|sm|md|lg)-\\d{1,2}\\s*", "", x)
+    left$attrib$class  <- strip_col_class(left$attrib$class)
+    right$attrib$class <- strip_col_class(right$attrib$class)
+    
+    left$attrib$class  <- paste(left$attrib$class,  left_col_class)
+    right$attrib$class <- paste(right$attrib$class, right_col_class)
+  }
+  
+  fluidRow(right, left)
+}
+
+col_4 <- function(x) {
+  tags$div(class = "col-sm-6 col-md-3", style = "min-height: 80px", x)
+}
--- a/apps/shinyDAG-1.0.0/R/edge.R
+++ b/apps/shinyDAG-1.0.0/R/edge.R
@ -0,0 +1,114 @@
+# rve$edges is a named list, e.g. for hash(A) -> hash(B):
+# rve$edges[edge_key(hash(A), hash(B))] = list(from = hash(A), to = hash(B))
+
+# ---- Edge Helper Functions ----
+edge_key <- function(x, y) digest::digest(c(x, y))
+
+edge_frame <- function(edges, nodes, ...) {
+  dots <- rlang::enexprs(...)
+  
+  dag_edges <- edges_in_dag(edges, nodes)
+  
+  if (!length(dag_edges)) return(tibble())
+  
+  ensure_exists <- function(x, ...) {
+    cols <- list(...)
+    stopifnot(!is.null(names(cols)), all(nzchar(names(cols))))
+    for (col in names(cols)) {
+      x[[col]] <- x[[col]] %||% cols[[col]]
+    }
+    x %>% tidyr::replace_na(cols)
+  }
+  
+  edges %>%
+    bind_rows(.id = "hash") %>% 
+    filter(hash %in% edges_in_dag(edges, nodes)) %>% 
+    tidyr::nest(-from) %>% 
+    left_join(
+      nodes %>% node_frame() %>% select(from = hash, from_name = name),
+      by = "from"
+    ) %>% 
+    tidyr::unnest() %>% 
+    tidyr::nest(-to) %>% 
+    left_join(
+      nodes %>% node_frame() %>% select(to = hash, to_name = name),
+      by = "to"
+    ) %>% 
+    tidyr::unnest() %>% 
+    select(hash, names(edges[[1]]), everything()) %>% 
+    ensure_exists(angle = 0L, color = "black", lty = "solid", lineT = "thin") %>% 
+    mutate(!!!dots)
+}
+
+edges_in_dag <- function(edges, nodes) {
+  if (!length(nodes) || !length(edges)) return(character())
+  all_edges <- bind_rows(edges) %>%
+    mutate(hash = names(edges)) %>%
+    tidyr::gather(position, node_hash, from:to)
+  
+  edges_not_in_graph <- all_edges %>%
+    filter(!node_hash %in% nodes_in_dag(nodes))
+  
+  setdiff(all_edges$hash, edges_not_in_graph$hash)
+}
+
+edge_edges <- function(edges, nodes, ...) {
+  do.call(edge, as.list(edge_frame(edges, nodes, ...)))
+}
+
+edge_exists <- function(edges, from_hash = NULL, to_hash = NULL) {
+  if (purrr::some(list(from_hash, to_hash), is.null)) return(FALSE)
+  
+  edges %>% 
+    purrr::keep(~ .$from %in% from_hash) %>% 
+    purrr::keep(~ .$to %in% to_hash) %>% 
+    length() %>% 
+    `>`(0)
+}
+
+edge_points <- function(edges, nodes, push_by = 0) {
+  dag_edges <- edges_in_dag(edges, nodes)
+  
+  if (!length(dag_edges)) return(tibble())
+  
+  edge_frame(edges, nodes) %>% 
+    tidyr::nest(-from) %>% 
+    left_join(
+      nodes %>% node_frame() %>% select(from = hash, from.x = x, from.y = y),
+      by = "from"
+    ) %>% 
+    tidyr::unnest() %>% 
+    tidyr::nest(-to) %>% 
+    left_join(
+      nodes %>% node_frame() %>% select(to = hash, to.x = x, to.y = y),
+      by = "to"
+    ) %>% 
+    tidyr::unnest() %>% 
+    select(hash, names(edges[[1]]), everything()) %>% 
+    mutate(
+      d_x = to.x - from.x,
+      d_y = to.y - from.y,
+      from.x = from.x + push_by * d_x,
+      from.y = from.y + push_by * d_y,
+      to.x = to.x - push_by * d_x,
+      to.y = to.y - push_by * d_y,
+      color = if_else(color == "", "Black", color)
+    ) %>% 
+    select(-d_x, -d_y)
+}
+
+edge_toggle <- function(edges, from_hash, to_hash) {
+  existing <- 
+    edges %>% 
+    purrr::keep(~ .$from == from_hash) %>% 
+    purrr::keep(~ .$to == to_hash)
+  
+  if (length(existing)) {
+    for (edge_key in names(existing)) {
+      edges[[edge_key]] <- NULL
+    }
+  } else {
+    edges[[edge_key(from_hash, to_hash)]] <- list(from = from_hash, to = to_hash)
+  }
+  edges
+}
--- a/apps/shinyDAG-1.0.0/R/inputs.R
+++ b/apps/shinyDAG-1.0.0/R/inputs.R
@ -0,0 +1,41 @@
+# A fancy selectizeInput for angles
+selectDegree <- function(
+  inputId,
+  label = "Degree",
+  min = -180 + by,
+  max = 180,
+  by = 45,
+  value = 0,
+  ...
+) {
+  if (sign(min + (max - min)) != sign(by)) {
+    by <- -by
+  }
+  choices <- seq(min, max, by)
+  
+  selectizeInput(inputId, label = label, choices, selected = value, multiple = FALSE, ..., )
+}
+
+
+# A button group that toggles state and optionally allows one button to be active at a time
+buttonGroup <- function(inputId, options, btn_class = "btn-default", multiple = FALSE, aria_label = NULL) {
+  btn_class <- paste("btn", paste(btn_class, collapse = " "))
+  button_list <- purrr::imap(options, button_in_group, class = btn_class)
+  selected <- shiny::restoreInput(inputId, default = "")
+  tagList(
+    singleton(tags$head(tags$script(src = "shinythingsButtonGroup.js"))),
+    tags$div(
+      class = "shinythings-btn-group btn-group",
+      id = inputId,
+      `data-input-id` = inputId,
+      `data-active` = selected,
+      `data-multiple` = as.integer(multiple),
+      role = "group",
+      button_list
+    )
+  )
+}
+
+button_in_group <- function(input_id, text, class = "btn btn-default") {
+  tags$button(id = input_id, class = class, text)
+}
--- a/apps/shinyDAG-1.0.0/R/module/clickpad.R
+++ b/apps/shinyDAG-1.0.0/R/module/clickpad.R
@ -0,0 +1,310 @@
+clickpad_UI <- function(id, ...) {
+  library(plotly)
+  ns <- NS(id)
+  tagList(
+    plotlyOutput(ns("plot"), ...)
+  )
+}
+
+clickpad_debug <- function(id, relayout = TRUE, doubleclick = TRUE, selected = FALSE, clickannotation = TRUE) {
+  ns <- NS(id)
+  col_width <- 12 / sum(relayout, doubleclick, selected, clickannotation)
+  tagList(
+    fluidRow(
+      style = "overflow-y: scroll; max-height: 200px;",
+      if (relayout) column(
+        col_width, 
+        tags$p(tags$code("plotly_relayout")),
+        verbatimTextOutput(ns("v_relayout"))
+      ),
+      if (doubleclick) column(
+        col_width,
+        tags$p(tags$code("plotly_doubleclick")),
+        verbatimTextOutput(ns("v_doubleclick"))
+      ),
+      if (selected) column(
+        col_width,
+        tags$p(tags$code("plotly_selected")),
+        verbatimTextOutput(ns("v_selected"))
+      ),
+      if (clickannotation) column(
+        col_width,
+        tags$p(tags$code("plotly_clickannotation")),
+        verbatimTextOutput(ns("v_clickannotation"))
+      )
+    )
+  )
+}
+
+clickpad <- function(
+  input, output, session, 
+  nodes, edges, 
+  plotly_source = "clickpad"
+) {
+  library(plotly)
+  ns <- session$ns
+  
+  node_primary <- reactive({ node_parent(nodes()) })
+  node_secondary <- reactive({ node_child(nodes()) })
+  node_is_adjusted <- reactive({ node_adjusted(nodes()) })
+  node_exposure <- reactive({ names(node_with_attribute(nodes(), "exposure")) })
+  node_outcome <- reactive({ names(node_with_attribute(nodes(), "outcome")) })
+  
+  output$v_relayout <- renderPrint({ 
+    str(event_data("plotly_relayout", priority = "event", source = plotly_source))
+  })
+  
+  output$v_doubleclick <- renderPrint({ 
+    str(event_data("plotly_doubleclick", priority = "event", source = plotly_source))
+  })
+  
+  output$v_selected <- renderPrint({ 
+    str(event_data("plotly_clickannotation", priority = "event", source = plotly_source))
+  })
+  
+  output$v_clickannotation <- renderPrint({ 
+    str(event_data("plotly_clickannotation", priority = "event", source = plotly_source))
+  })
+  
+  arrow_path <- function(from.x, from.y, to.x, to.y, dist = 0.2, ...) {
+    # angle of the line between `from` and `to`
+    theta  <- atan2(to.y - from.y, to.x - from.x)
+    
+    # push line starting/ending points away from node by a fixed distance
+    path_points = list(
+      x0 = from.x + dist * cos(theta), 
+      y0 = from.y + dist * sin(theta),
+      x1 = to.x   - dist * cos(theta), 
+      y1 = to.y   - dist * sin(theta)
+    )
+    
+    # Find points for corners of arrow head (third point is `to`)
+    arrow_anchor_x = path_points$x1 - dist * cos(theta)
+    arrow_anchor_y = path_points$y1 - dist * sin(theta)
+    ad <- 0.1 * dist / tan(1/6 * pi)
+    
+    path_points$a1_x = arrow_anchor_x + ad * cos(theta + 1/2 * pi)
+    path_points$a1_y = arrow_anchor_y + ad * sin(theta + 1/2 * pi)
+    path_points$a2_x = arrow_anchor_x - ad * cos(theta + 1/2 * pi)
+    path_points$a2_y = arrow_anchor_y - ad * sin(theta + 1/2 * pi)
+    
+    # Draw arrow head in SVG path notation
+    as.character(glue::glue_data(
+      path_points,
+      "M{x0},{y0} L{x1},{y1} L{a1_x},{a1_y} L{a2_x},{a2_y} L{x1},{y1}"
+    ))
+  }
+  
+  arrows <- reactive({
+    if (is.null(edges()) || length(edges()) == 0) return(NULL)
+    if (is.null(nodes()) || length(nodes()) == 0) return(NULL)
+    
+    ep <- edge_points(edges(), nodes())
+    if (!nrow(ep)) return(NULL)
+    
+    ep %>% 
+      purrr::pmap_chr(arrow_path, dist = 0.2) %>% 
+      purrr::map(~ list(
+        type = "path",
+        line = list(color = "#000", width = 1), 
+        fillcolor = "#000",
+        path = .x,
+        opacity = 0.75
+      ))
+  })
+  
+  create_node_annotations <- function(x, y, name, hash, ...) {
+    set_color <- function(
+      default, not_in_dag = NULL, 
+      primary = NULL, secondary = NULL, 
+      exposure = NULL, outcome = NULL, adjusted = NULL,
+      apply_order = c("primary", "not_in_dag", "adjusted", "exposure", "outcome", "secondary")
+    ) {
+      applicable_states <- c(
+        "primary" = !is.null(node_primary()) && hash %in% node_primary(),
+        "secondary" = !is.null(node_secondary()) && hash %in% node_secondary(),
+        "adjusted" = !is.null(node_is_adjusted()) && hash %in% node_is_adjusted(),
+        "exposure" = !is.null(node_exposure()) && hash %in% node_exposure(),
+        "outcome" = !is.null(node_outcome()) && hash %in% node_outcome(),
+        "not_in_dag" = x < 0
+      )
+      
+      applicable_states <- applicable_states[applicable_states]
+      if (!length(applicable_states)) return(default)
+      
+      applicable_states <- applicable_states[apply_order]
+      applicable_states <- applicable_states[!is.na(applicable_states)]
+      if (!length(applicable_states)) return(default)
+      
+      color <- switch(
+        names(applicable_states)[1],
+        primary = primary,
+        secondary = secondary,
+        adjusted = adjusted,
+        outcome = outcome,
+        exposure = exposure,
+        not_in_dag = not_in_dag,
+        default
+      )
+      
+      color %||% default
+    }
+    
+    background_color <- set_color(
+      default = "rgba(255, 255, 255, 0.5)", 
+      not_in_dag = "#FDFDFD", 
+      primary = "rgba(246, 227, 209, 0.75)"
+    )
+    font_color <- set_color(
+      default = "#000000", 
+      not_in_dag = "#666666", 
+      primary = "#D3751C", 
+      exposure = "#418c7a", 
+      outcome = "#ba2d0b",
+      apply_order = c("not_in_dag", "exposure", "outcome", "primary")
+    )
+    border_color <- set_color(
+      default = "#EDEDED", 
+      not_in_dag = "#AAAAAA", 
+      primary = list(NULL), 
+      adjusted = "#1c2d3f",
+      apply_order = c("not_in_dag", "adjusted", "primary")
+    )
+      
+    list(text = name, 
+         node_hash = hash, 
+         x = x, 
+         y = y, 
+         font = list(size = 24, color = font_color),
+         showarrow = FALSE, 
+         align = "center",
+         captureevents = TRUE,
+         textposition = "middle center",
+         bordercolor = border_color,
+         bgcolor = background_color,
+         borderpad = 4)
+  }
+  
+  annotations <- reactive({
+    if (is.null(nodes()) || length(nodes()) == 0) return(NULL)
+    node_frame(nodes(), full = TRUE) %>% 
+      purrr::pmap(create_node_annotations)
+  })
+  
+  left_margin <- list(
+    type = "rect",
+    line = list(color = "#AAAAAA", width = 1),
+    fillcolor = "#EEEEEE",
+    x0 = -100,
+    y0 = -100,
+    x1 = 0,
+    y1 = 100
+  )
+  
+  output$plot <- renderPlotly({
+    debug_line("rendering clickpad")
+    redraw_plot()
+    
+    ax <- list(
+      title = "",
+      zeroline = FALSE,
+      showline = FALSE,
+      showticklabels = FALSE,
+      showgrid = TRUE,
+      range = list(-1.5, 12.5)
+    )
+    ay <- ax
+    y_min <- purrr::map_dbl(nodes(), "y") %>% min()
+    y_max <- purrr::map_dbl(nodes(), "y") %>% max()
+    ay$range <- list(min(0.5, y_min), max(7.5, y_max))
+    
+    p <- plot_ly(type = "scatter", source = plotly_source)
+    
+    p %>% 
+      layout(
+        annotations = annotations(), 
+        shapes = c(list(left_margin), arrows()),
+        xaxis = ax,
+        yaxis = ay
+      ) %>% 
+      config(
+        edits = list(
+          annotationPosition = TRUE
+        ),
+        showAxisDragHandles = FALSE
+        # displayModeBar = FALSE
+      ) %>% 
+      plotly::event_register("plotly_click") %>% 
+      plotly::event_register("plotly_doubleclick") %>% 
+      plotly::event_register("plotly_selected") %>% 
+      plotly::event_register("plotly_clickannotation") %>% 
+      htmlwidgets::onRender("
+        function(el) { 
+          el.on('plotly_hover', function(d) { console.log('Hover: ', d) });
+          el.on('plotly_click', function(d) { console.log('Click: ', d) });
+          el.on('plotly_selected', function(d) { console.log('Select: ', d) });
+        }
+      ")
+  })
+  
+  redraw_plot <- reactiveVal(Sys.time())
+  
+  new_coords_lag <- list(hash = NA_character_, x = NA_real_, y = NA_real_)
+  
+  new_locations <- reactive({
+    req(annotations())
+    ## https://stackoverflow.com/questions/54990350/extract-xyz-coordinates-from-draggable-shape-in-plotly-ternary-r-shiny
+    
+    event <- event_data("plotly_relayout", source = plotly_source)
+    if (!length(event)) return()
+    
+    annot_event <- event[grepl("^annotations\\[\\d+\\]\\.[xy]$", names(event))]
+    annot_index <- sub(".+\\[(\\d+)\\].+", "\\1", names(annot_event)[1]) %>% as.integer()
+    
+    if (is.na(annot_index) || !is.integer(annot_index)) return()
+    
+    if (length(annotations()) <= annot_index) {
+      stop("An error occurred, unable to match plotly update to correct node")
+    }
+    
+    node_hash <- annotations()[[annot_index + 1]]$node_hash
+    # cli::cat_line("event_name: ", names(event)[1])
+    # cli::cat_line("annot_index: ", annot_index)
+    # cli::cat_line("node_hash: ", node_hash)
+    
+    req(!is.null(node_hash))
+    
+    new_x <- annot_event[grepl("\\.x", names(annot_event))] %>% unlist() %>% unname()
+    new_x <- if (new_x > 0) round(new_x, 0) else new_x
+    
+    new_y <- annot_event[grepl("\\.y", names(annot_event))] %>% unlist() %>% unname()
+    new_y <- if (new_x > 0) round(new_y, 0) else new_y
+    
+    i_nodes <- isolate(nodes())
+    current_pos <- i_nodes[[node_hash]][c("x", "y")] %>% unlist() %>% unname()
+    
+    new_coords <- list(
+      hash = node_hash,
+      x = new_x,
+      y = new_y
+    )
+
+    if (identical(c(new_coords$x, new_coords$y), current_pos)) {
+      # No change in current node position
+      return()
+    }
+    
+    if (identical(new_coords, new_coords_lag)) {
+      # The plotly_redraw may not have been a result of annotation position change
+      return()
+    }
+    
+    new_coords_lag <<- new_coords
+    
+    # cli::cat_line("new_x: ", new_x)
+    # cli::cat_line("new_y: ", new_y)
+    new_coords
+  })
+  
+  return(reactive(new_locations()))
+}
--- a/apps/shinyDAG-1.0.0/R/module/dagPreview.R
+++ b/apps/shinyDAG-1.0.0/R/module/dagPreview.R
@ -0,0 +1,288 @@
+
+# UI Function -------------------------------------------------------------
+
+dagPreviewUI <- function(id, include_graph_downloads = TRUE, start_hidden = FALSE) {
+  ns <- shiny::NS(id)
+  
+  class_3_col <- "col-md-4 col-md-offset-0 col-sm-8 col-sm-offset-2 col-xs-12"
+  
+  download_choices <- c(
+    "PDF" = "pdf",
+    "PNG" = "png",
+    "LaTeX TikZ" = "tikz"
+  )
+  
+  if (include_graph_downloads) {
+    download_choices <- c(
+      download_choices,
+      "dagitty (R: RDS)" = "dag_dagitty",
+      "ggdag (R: RDS)" = "dag_tidy"
+    )
+  }
+  
+  tagList(
+    fluidRow(
+      column(
+        width = 12, 
+        align = "center", 
+        shinyjs::hidden(tags$div(
+          id = ns("tikzOut-help"),
+          class="alert alert-danger",
+          role="alert",
+          HTML(
+            "<p>An error occurred while compiling the preview.",
+            "Are there syntax errors in your labels?</p>",
+            "<p>Note that using characters that are",
+            '<a href="https://en.wikibooks.org/wiki/LaTeX/Special_Characters" target="_blank">reserved', 
+            'characters in LaTeX</a> syntax may cause issues. For example,',
+            "single <code>$</code> need to be escaped: <code>\\$</code>.</p>"
+          )
+        )),
+        tags$div(
+          class = "dag-preview-tikz",
+          shinycssloaders::withSpinner(uiOutput(ns("tikzOut")), color = "#C4C4C4", proxy.height = "400px")
+        )
+      )
+    ),
+    fluidRow(
+      tags$div(
+        class = class_3_col,
+        tags$div(
+          id = ns("showPreviewContainer"),
+          prettySwitch(ns("showPreview"), "Preview DAG", status = "primary", fill = TRUE, value = !start_hidden)
+        )
+      ),
+      tags$div(
+        class = class_3_col,
+        selectInput(
+          inputId = ns("downloadType"),
+          label = "Type of download",
+          choices = download_choices
+        ),
+        uiOutput(ns("downloadType_helptext"))
+      ),
+      tags$div(
+        class = paste(class_3_col, "dagpreview-download-ui"),
+        div(
+          class = "btn-group",
+          role = "group",
+          id = ns("download-buttons"),
+          downloadButton(ns("downloadButton"))
+        )
+      )
+    )
+  )
+}
+
+
+# Server Module -----------------------------------------------------------
+
+# This module takes tikz code and creates DAG preview content and returns TRUE
+# or FALSE value to track whether the preview is visible.
+dagPreview <- function(
+  input, output, session, 
+  session_dir, 
+  tikz_code, 
+  dag_dagitty = reactive(NULL), 
+  dag_tidy = reactive(NULL),
+  has_edges = reactive(FALSE)
+) {
+  ns <- session$ns
+  SESSION_TEMPDIR <- file.path(session_dir, sub("-$", "", ns("")))
+  
+  tikz_cache_dir <- reactiveVal(NULL)
+  
+  # Render tikz preview ----
+  observe({
+    req(input$showPreview)
+    
+    tikz_lines <- tikz_code()
+    req(gsub("\\s", "", tikz_lines) != "")
+    debug_input(tikz_lines, ns("tikz_code"))
+    
+    useLib <- "\\usetikzlibrary{matrix,arrows,decorations.pathmorphing}"
+    
+    pkgs <- paste(buildUsepackage(pkg = list("tikz"), uselibrary = useLib), collapse = "\n")
+    
+    tex_dir <- 
+      tex_cached_preview(
+        session_dir = SESSION_TEMPDIR,
+        obj = tikz_lines,
+        stem = "DAGimage",
+        imgFormat = "png",
+        returnType = "shiny",
+        density = tex_opts$get("density"),
+        keep_pdf = TRUE,
+        usrPackages = pkgs,
+        margin = tex_opts$get("margin"),
+        cleanup = tex_opts$get("cleanup")
+      )
+    tikz_cache_dir(tex_dir)
+  }, priority = -100)
+  
+  # Create tikz preview UI ----
+  output$tikzOut <- renderUI({
+    req(input$showPreview)
+    
+    shiny::validate(
+      shiny::need(
+        tryCatch({tikz_code(); TRUE}, error = function(e) FALSE) ||
+          tryCatch(gsub("\\s", "", tikz_code()), error = function(e) "") != "",
+        paste(
+          "Nothing to see here... yet. Please use the Sketch tab to create", 
+          "and layout a DAG."
+        )
+      )
+    )
+    
+    if (is.null(tikz_cache_dir())) return()
+    if (!length(tikz_cache_dir())) {
+      shinyjs::show("tikzOut-help")
+      return()
+    } else {
+      shinyjs::hide("tikzOut-help")
+    }
+    
+    image_path <- file.path(tikz_cache_dir(), "DAGimage.png")
+    if (!file.exists(image_path)) {
+      debug_line("Image does not exist: ", image_path)
+      return()
+    }
+    
+    image_tmp <- tempfile("dag_image_", SESSION_TEMPDIR, ".png")
+    file.copy(image_path, image_tmp)
+    debug_line("Serving image: ", image_tmp)
+    
+    tags$img(
+      src = sub("www/", "", image_tmp, fixed = TRUE),
+      contentType = "image/png",
+      style = "max-width: 100%; max-height: 600px; -o-object-fit: contain;",
+      alt = "DAG"
+    )
+  })
+  
+  output$downloadType_helptext <- renderUI({
+    is_tikz_download <- input$downloadType %in% c("pdf", "png", "tikz")
+    if (is_tikz_download && !input$showPreview) {
+      shinyjs::disable("downloadButton")
+      return(helpText("Please preview DAG to enable downloads"))
+    }
+    
+    if (!is_tikz_download && !has_edges()) {
+      shinyjs::disable("downloadButton")
+      return(helpText("Please add at least one edge to the DAG"))
+    }
+    
+    if (!length(tikz_cache_dir())) {
+      shinyjs::disable("downloadButton")
+      return()
+    }
+    
+    shinyjs::enable("downloadButton")
+  })
+  
+  output$downloadButton <- downloadHandler(
+    filename = function() {
+      paste0(
+        "DAG.", 
+        switch(
+          input$downloadType,
+          "dagitty" =,
+          "ggdag" = "rds",
+          "tikz" = "tex",
+          "png" = "png",
+          "pdf" = "pdf"
+        )
+      )
+    },
+    content = function(file) {
+      if (input$downloadType == "pdf") {
+        
+        file.copy(file.path(tikz_cache_dir(), "DAGimageDoc.pdf"), file)
+        
+      } else if (input$downloadType == "png") {
+        
+        file.copy(file.path(tikz_cache_dir(), "DAGimage.png"), file)
+        
+      } else if (input$downloadType == "tikz") {
+        
+        merge_tex_files(
+          file.path(tikz_cache_dir(), "DAGimageDoc.tex"),
+          file.path(tikz_cache_dir(), "DAGimage.tex"),
+          file
+        )
+        
+      } else if (input$downloadType == "dag_dagitty") {
+        
+        if (is.null(dag_dagitty())) return(NULL)
+        
+        saveRDS(dag_dagitty(), file = file)
+        
+      } else if (input$downloadType == "dag_tidy") {
+        
+        if (is.null(dag_tidy())) return(NULL)
+        
+        saveRDS(dag_tidy(), file = file)
+      }
+    },
+    contentType = NA
+  )
+  
+  return(reactive(input$showPreview))
+}
+
+
+# Helper Functions --------------------------------------------------------
+
+tex_cached_preview <- function(session_dir, ...) {
+  # Takes arguments for texPreview() except for fileDir
+  # hashes inputs and then writes preview into session_dir/args_hash
+  # Skips rendering if the cache already exists
+  # Returns directory containing the preview documents
+  
+  args <- list(...)
+  args_hash <- digest::digest(args)
+  
+  session_token <- basename(dirname(session_dir))
+  error_file <- paste0(session_token, "_", args_hash, ".tex")
+  
+  cache_dir <- file.path(session_dir, args_hash)
+  error_dir <- file.path("www", "errors")
+  
+  if (dir.exists(cache_dir)) {
+    return(cache_dir)
+  } else {
+    if (file.exists(file.path(error_dir, error_file))) {
+      # we already know that this tikz code won't work
+      warning("Bad tikz is still bad: ", error_file)
+      return(character())
+    }
+  }
+  
+  dir.create(cache_dir, recursive = TRUE)
+  args$fileDir <- cache_dir
+  tryCatch({
+    do.call("texPreview", args)
+    cache_dir
+  }, error = function(e) {
+    # write bad tex code to disk
+    dir.create(error_dir, showWarnings = FALSE)
+    cat(
+      args$obj, 
+      sep = "\n", 
+      file = file.path(error_dir, error_file)
+    )
+    unlink(cache_dir, recursive = TRUE)
+    character()
+  })
+}
+
+# Merge tikz TeX source into main TeX file
+merge_tex_files <- function(main_file, input_file, out_file) {
+  x <- readLines(main_file)
+  y <- readLines(input_file)
+  which_line <- grep("input{", x, fixed = TRUE)
+  which_line <- intersect(which_line, grep(basename(input_file), x))
+  x[which_line] <- paste(y, collapse = "\n")
+  writeLines(x, out_file)
+}
--- a/apps/shinyDAG-1.0.0/R/module/examples.R
+++ b/apps/shinyDAG-1.0.0/R/module/examples.R
@ -0,0 +1,133 @@
+add_slug <- function(ex) {
+  ex %>% 
+    purrr::map(~ {
+      .x$slug <- gsub("[.]rds$", "", .x$file, ignore.case = TRUE)
+      .x
+    })
+}
+
+keep_ex_with_file <- function(ex) {
+  ex %>% 
+    purrr::keep(~ file.exists(.$file))
+}
+
+nullify_missing <- function(ex, field = "image") {
+  ex %>% 
+    purrr::modify_depth(
+      .depth = 1,
+      ~ purrr::modify_at(., field, ~ {
+        if (!file.exists(.x)) list(NULL) else .x
+      })
+    )
+}
+
+full_path <- function(ex, field, path = file.path("www", "examples")) {
+  ex %>% 
+    purrr::modify_depth(
+      .depth = 1,
+      ~ purrr::modify_at(., field, ~ file.path(path, .x))
+    )
+}
+
+rel_path <- function(ex, field, path = file.path("www/")) {
+  ex %>% 
+    purrr::modify_depth(
+      .depth = 1,
+      ~ purrr::modify_at(., field, ~ if (!is.null(.x)) sub(path, "", .x, fixed = TRUE) else list(NULL))
+    )
+}
+
+load_example_values <- function(ex) {
+  purrr::map(ex, ~ {
+    values <- readRDS(.x$file)
+    .x$values <- list()
+    .x$values$nodes <- values$rvn$nodes
+    .x$values$edges <- values$rve$edges
+    .x
+  })
+}
+
+load_examples <- function(path = file.path("www", "examples")) {
+  ex_yaml <- file.path(path, "examples.yml")
+  if (!file.exists(ex_yaml)) {
+    stop("Unable to locate ", ex_yaml)
+  }
+  
+  ex <- yaml::read_yaml(ex_yaml)
+  
+  ex %>% 
+    add_slug() %>% 
+    full_path("image", path) %>% 
+    full_path("file", path) %>% 
+    keep_ex_with_file() %>% 
+    nullify_missing("image") %>% 
+    rel_path("image") %>% 
+    load_example_values()
+}
+
+
+EXAMPLES <- load_examples()
+
+examples_UI <- function(id) {
+  ns <- NS(id)
+  
+  make_examples_ui <- function(name, description, slug, image = NULL, ...) {
+    tagList(
+      tags$h3(name),
+      if (!is.null(image)) tags$div(
+        class = "example-image", 
+        tags$img(src = image)
+      ),
+      tags$p(
+        HTML(description)
+      ),
+      actionButton(ns(slug), "Load Example")
+    )
+  }
+  
+  tagList(
+    EXAMPLES %>% 
+      purrr::map(`[`, c("name", "description", "slug", "image")) %>% 
+      purrr::map(~ purrr::pmap(.x, make_examples_ui))
+  )
+}
+
+examples <- function(input, output, session) {
+  input_ids <- EXAMPLES %>% purrr::map_chr("slug")
+  values <- EXAMPLES %>% purrr::map("values")
+  names(values) <- input_ids
+  
+  lagged_value <- setNames(rep(0L, length(input_ids)), input_ids)
+  
+  example_value <- reactiveVal(NULL)
+
+  observe({
+    current_btn_vals <- purrr::map_int(input_ids, ~ input[[.x]])
+    req(any(current_btn_vals > 0L))
+    # cli::cat_line("lagged: ", lagged_value)
+    # cli::cat_line("current: ", current_btn_vals)
+    
+    idx <- which(current_btn_vals != lagged_value)
+    lagged_value <<- current_btn_vals
+    
+    if (!length(idx)) {
+      example_value(NULL)
+      return(NULL)
+    }
+    
+    changed_input <- input_ids[idx]
+    
+    example_value(values[[changed_input]])
+  })
+  
+  return(reactive(example_value()))
+}
+
+
+# ui <- fluidPage(
+#   examples_UI("example")
+# )
+# server <- function(input, output, session){
+#   callModule(examples, 'example')
+# }
+# shinyApp(ui, server)
--- a/apps/shinyDAG-1.0.0/R/node.R
+++ b/apps/shinyDAG-1.0.0/R/node.R
@ -0,0 +1,289 @@
+# ---- Node Helper Functions ----
+node_new <- function(nodes, hash, name, gap_y = 0.75, min_y = 1) {
+  # new nodes are added into the clickpad area but with x = -0.75
+  # need to check if there are other nodes in the holding space and adjust y
+  taken_y <- nodes %>% purrr::keep(~ !is.na(.$y)) %>% purrr::map_dbl(`[[`, "y")
+  new_y <- find_new_y(taken_y, gap_y, min_y)
+  nodes[[hash]] <- list(name = name, x = -0.75, y = new_y)
+  nodes
+}
+
+find_new_y <- function(y, gap_y = 0.75, min_y = 0.5) {
+  if (!length(y)) return(min_y)
+  if (min(y) >= (min_y + gap_y)) return(min_y)
+  if (length(y) == 1) return(y + gap_y)
+  
+  y <- sort(y)
+  
+  gap_size <- c(lead(y) - y)[-length(y)]
+  if (any(gap_size >= 2 * gap_y)) {
+    first_gap <- which(gap_size > 2 * gap_y)[1]
+    return(y[first_gap] + gap_y)
+  }
+  
+  max(y) + gap_y
+}
+
+node_name_valid <- function(nodes, name, warn = FALSE) {
+  if (!nzchar(name)) {
+    warnNotification("Please specify a name for the node")
+    return(FALSE)
+  }
+  name_in_nodes <- vapply(nodes, function(n) name == n$name, FALSE)
+  if (any(name_in_nodes)) {
+    if (warn) warnNotification('"', name, '" is already the name of a node')
+    FALSE
+  } else {
+    TRUE
+  }
+}
+
+node_names <- function(nodes, all = FALSE) {
+  if (!length(nodes)) {
+    return(character())
+  }
+  x <- invertNames(sapply(nodes, function(x) x$name))
+  if (all) {
+    return(x)
+  }
+  in_dag <- sapply(nodes, function(n) n$x >= 0)
+  x[in_dag]
+}
+
+node_name_from_hash <- function(nodes, hash) {
+  invertNames(node_names(nodes))[hash]
+}
+
+node_update <- function(nodes, hash, name = NULL, x = NULL, y = NULL, name_latex = NULL) {
+  # in general update a property if arg is not null, default to current value
+  nodes[[hash]]$name <- name %||% nodes[[hash]]$name
+  nodes[[hash]]$x <- x %||% nodes[[hash]]$x
+  nodes[[hash]]$y <- y %||% nodes[[hash]]$y
+  # for name_latex precedence is arg > name (arg) > existing > name (existing)
+  nodes[[hash]]$name_latex <- name_latex %||% (
+    (name %??% name) %>% escape_quotes() %>% escape_latex()
+  ) %||% nodes[[hash]]$name_latex %||% (
+    (nodes[[hash]]$name %??% nodes[[hash]]$name) %>% escape_quotes() %>% escape_latex()
+  )
+  nodes
+}
+
+node_set_attribute <- function(nodes, hash, attribs) {
+  for (node in names(nodes)) {
+    for (attrib in attribs) {
+      nodes[[node]][[attrib]] <- node %in% hash
+    }
+  }
+  nodes
+}
+
+node_unset_attribute <- function(nodes, hashes, attribs) {
+  for (hash in hashes) {
+    for (attrib in attribs) {
+      nodes[[hash]][[attrib]] <- FALSE
+    }
+  }
+  nodes
+}
+
+node_with_attribute <- function(nodes, attrib) {
+  if (length(nodes) == 0) return(NULL)
+  n <- nodes %>% 
+    purrr::map(attrib) %>% 
+    purrr::keep(isTRUE)
+  if (length(n)) n
+}
+
+node_parent <- function(nodes) {
+  names(node_with_attribute(nodes, "parent"))
+}
+
+node_child <- function(nodes) {
+  names(node_with_attribute(nodes, "child"))
+}
+
+node_adjusted <- function(nodes) {
+  names(node_with_attribute(nodes, "adjusted"))
+}
+
+node_delete <- function(nodes, hash) {
+  .nodes <- nodes[setdiff(names(nodes), hash)]
+  if (length(.nodes)) .nodes else list()
+}
+
+node_frame <- function(nodes, full = FALSE) {
+  if (!length(nodes)) {
+    return(tibble())
+  }
+  x <- bind_rows(nodes) %>%
+    mutate(hash = names(nodes)) %>%
+    select(hash, everything()) %>% 
+    mutate(visible = !is.na(x), in_dag = x > 0) %>% 
+    node_frame_complete()
+  if (full) {
+    return(x)
+  }
+  filter(x, in_dag)
+}
+
+node_frame_complete <- function(nodes) {
+  nodes$adjusted   <- nodes[["adjusted"]]   %||% FALSE
+  nodes$color_draw <- nodes[["color_draw"]] %||% "Black"
+  nodes$color_fill <- nodes[["color_fill"]] %||% "White"
+  nodes$color_text <- nodes[["color_text"]] %||% "Black"
+  nodes
+}
+
+node_vertices <- function(nodes) {
+  v_df <- node_frame(nodes)
+  vertices(
+    name = v_df$name,
+    x = v_df$x,
+    y = v_df$y,
+    hash = v_df$hash
+  )
+}
+
+node_nearest <- function(nodes, coordinfo, threshold = 0.5) {
+  nodes %>%
+    node_frame() %>%
+    mutate(dist = (x - coordinfo$x)^2 + (y - coordinfo$y)^2) %>%
+    arrange(dist) %>%
+    filter(dist <= threshold) %>%
+    slice(1) %>%
+    select(-dist)
+}
+
+nodes_in_dag <- function(nodes, include_staged = FALSE) {
+  n <- nodes %>%
+    purrr::keep(~ !is.na(.$x))
+  
+  if (!include_staged) {
+    n <- purrr::keep(n, ~ .$x > 0)
+  }
+  names(n)
+}
+
+node_btn_id <- function(node_hash) paste0("node_toggle_", node_hash)
+node_btn_get_hash <- function(node_btn_id) sub("node_toggle_", "", node_btn_id, fixed = TRUE)
+
+node_tikz_style <- function(hash, adjusted, color_draw, color_fill, color_text, ...) {
+  # B/.style={fill=DarkRed, text=White}
+  if (!adjusted && color_fill == "White" && color_text == "Black") {
+    return(NA_character_)
+  }
+  style <- 
+    list(
+      draw = if (adjusted) color_draw, 
+      fill = color_fill, 
+      text = color_text
+    ) %>% 
+    purrr::compact() %>% 
+    purrr::imap_chr(~ glue::glue("{.y}={.x}")) %>% 
+    paste(collapse = ", ")
+  
+  glue::glue("{hash}/.style={{{style}}}")
+}
+
+node_frame_add_style <- function(nodes) {
+  if (!"name_latex" %in% names(nodes)) nodes$name_latex <- ""
+  nodes %>% 
+    mutate(
+      tikz_style = purrr::pmap_chr(nodes, node_tikz_style),
+      name_latex = case_when(
+        is.na(name_latex) | name_latex == "" ~ escape_latex(name),
+        TRUE ~ name_latex
+      ),
+      tikz_node = case_when(
+        !is.na(tikz_style) ~ paste(glue::glue("|[{hash}]| {name_latex}")),
+        TRUE ~ name_latex
+      )
+    )
+}
+
+escape_quotes <- function(x) {
+  x %??% gsub("(['\"])", "\\\\\\1", x)
+}
+
+escape_latex <- function(x, force = FALSE) {
+  if (is.null(x)) return(NULL)
+  if (!force && grepl("$", x, fixed = TRUE)) {
+    # has at least one dollar sign so we'll try to parse out the math
+    x_math <- chunk_math(x)
+    is_math <- attr(x_math, "is_math")
+    if (is.null(is_math) || !any(is_math)) {
+      # no math, just escape the original string
+      return(escape_latex(x, force = TRUE))
+    }
+    x_math[!is_math] <- x_math[!is_math] %>% 
+      purrr::map_chr(escape_latex, force = TRUE)
+    
+    return(paste0(x_math, collapse = ""))
+  }
+  
+  ## escape: # $ % ^ & _ { } 
+  ## replace: ~ -> \~{}
+  ## replace: \ -> \textbackslash
+  ## replace: < > -> \textless \textgreater
+  x <- gsub("\\", "\\textbackslash ", x, fixed = TRUE)
+  x <- gsub("<", "\\textless ", x, fixed = TRUE)
+  x <- gsub(">", "\\textgreater ", x, fixed = TRUE)
+  x <- gsub("([#$%^&_{}])", "\\\\\\1", x)
+  x <- gsub("~", "\\~{}", x, fixed = TRUE)
+  x
+}
+
+chunk_math <- function(x) {
+  x_s <- strsplit(x, character())[[1]]
+  
+  idx <- which(grepl("$", x_s, fixed = TRUE))
+  if (!length(idx)) {
+    return(x)
+  }
+  # remove \\$ pairs from indexes
+  idx_has_escape <- which(grepl("\\", x_s[idx[idx > 1L] - 1L], fixed = TRUE))
+  if (length(idx_has_escape)) {
+    idx <- idx[-(idx_has_escape + as.integer(any(idx == 1)))]
+  }
+  
+  # only include $ that touch at least one alphanum character
+  x_around_dollar <- purrr::map_chr(idx, ~ {
+    substr(x, max(0, .x - 1, na.rm = TRUE), min(nchar(x), .x + 1))
+  })
+  idx_no_adjacent_alpha <- which(!grepl("[[:alnum:]+=*{}.-]", x_around_dollar))
+  if (length(idx_no_adjacent_alpha)) {
+    idx <- idx[-idx_no_adjacent_alpha]
+  }
+  if (!length(idx)) {
+    return(x)
+  }
+  
+  # finally, find the math chunks
+  chunks <- c()
+  is_math <- c()
+  i <- 1L
+  while (i < length(idx)) {
+    # idx[i - 1] ... idx[i]-1 -> not math
+    # idx[i]...idx[i+1] -> math
+    # skip ahead to idx[i + 2]
+    idx_not_math <- max(idx[i-1], 0, na.rm = TRUE)
+    chunks <- c(
+      chunks,
+      if (idx_not_math != idx[i] - 1L) substr(x, idx_not_math, idx[i] - 1L),
+      substr(x, idx[i], idx[i + 1]),
+      if (is.na(idx[i + 2]) & !idx[i + 1] == nchar(x)) {
+        substr(x, idx[i + 1] + 1, nchar(x))
+      }
+    )
+    is_math <- c(
+      is_math,
+      if (idx_not_math != idx[i] - 1L) FALSE,
+      TRUE,
+      if (is.na(idx[i + 2]) & !idx[i + 1] == nchar(x)) FALSE
+    )
+    i <- i + 2L
+  }
+  
+  attributes(chunks)$is_math <- is_math
+  chunks
+}
--- a/apps/shinyDAG-1.0.0/R/tests/test-escape_latex.R
+++ b/apps/shinyDAG-1.0.0/R/tests/test-escape_latex.R
@ -0,0 +1,37 @@
+source("../node.R")
+
+latex_text <- list(
+  list(t = "$m^2$",           e = "$m^2$"),
+  list(t = "a $m^2$",         e = "a $m^2$"),
+  list(t = "$m^2$ b",         e = "$m^2$ b"),
+  list(t = "a $m^2$ b",       e = "a $m^2$ b"),
+  list(t = "a $e=$$m^2$ b",   e = "a $e=$$m^2$ b"),
+  list(t = "a $$ math",       e = "a \\$\\$ math"),
+  list(t = "\\textbackslash", e = "\\textbackslash textbackslash"),
+  list(t = "# of",            e = "\\# of"),
+  list(t = "$ amount",        e = "\\$ amount"),
+  list(t = "my $$ is",        e = "my \\$\\$ is"),
+  list(t = "$m $$ m$",        e = "$m $$ m$"),
+  list(t = "$$ is $mc^2$",    e = "\\$\\$ is $mc^2$"),
+  list(t = "a > b",           e = "a \\textgreater  b"), #<< extra space before b
+  list(t = "a < b",           e = "a \\textless  b"), #<< same
+  list(t = "a % b",           e = "a \\% b"),
+  list(t = "a_b",             e = "a\\_b"),
+  list(t = "a & b",           e = "a \\& b"),
+  list(t = "a & b \\ c",      e = "a \\& b \\textbackslash  c"), #<< + space
+  list(t = "{a}",             e = "\\{a\\}"),
+  list(t = "a ~ b",           e = "a \\~{} b")
+)
+
+passed_test <- purrr::map_lgl(latex_text, function(x) {
+  identical(escape_latex(x$t), x$e)
+})
+
+if (all(passed_test)) {
+  cat('\nAll (', sum(passed_test), ') tests passed!', sep = '')
+} else {
+  cat('\nThere were', sum(!passed_test), "failures...")
+  purrr::walk(latex_text[!passed_test], function(x) {
+    cat("\n'", x$t, "' returned '", escape_latex(x$t), "' not '", x$e, "'", sep = "")
+  })
+}
--- a/apps/shinyDAG-1.0.0/R/xcolorPicker.R
+++ b/apps/shinyDAG-1.0.0/R/xcolorPicker.R
@ -0,0 +1,81 @@
+# xcolors list ----
+
+if (!file.exists(file.path("data", "xcolors.csv"))) {
+  if (!dir.exists('data')) {
+    stop("Not sure where I am")
+  }
+  message("Getting xcolors color list")
+  read_gz <- function(x) readLines(gzcon(url(x)))
+  
+  xcolors <- 
+    list(
+      # x11 = "http://www.ukern.de/tex/xcolor/tex/x11nam.def.gz",
+      svg = "http://www.ukern.de/tex/xcolor/tex/svgnam.def.gz"
+    ) %>% 
+    purrr::map(read_gz) %>% 
+    purrr::flatten_chr() %>% 
+    stringr::str_subset("^(%%|\\\\| )", negate = TRUE) %>% 
+    stringr::str_remove("(;%|\\})$") %>% 
+    readr::read_csv(col_names = c("color", "r", "g", "b")) %>% 
+    arrange(color) %>% 
+    readr::write_csv(file.path("data", "xcolors.csv"))
+} else {
+  xcolors <- 
+    file.path("data/xcolors.csv") %>% 
+    read.csv(stringsAsFactors = FALSE)
+}
+
+# Color Functions ----
+
+choose_dark_or_light <- function(x, black = "#000000", white = "#FFFFFF") {
+  # x = color_hex
+  color_rgb <- col2rgb(x)[, 1]
+  # from https://stackoverflow.com/a/3943023/2022615
+  color_rgb <- color_rgb / 255
+  color_rgb[color_rgb <= 0.03928] <- color_rgb[color_rgb <= 0.03928]/12.92
+  color_rgb[color_rgb > 0.03928] <- ((color_rgb[color_rgb > 0.03928] + 0.055)/1.055)^2.4
+  lum <- t(c(0.2126, 0.7152, 0.0722)) %*% color_rgb
+  if (lum[1, 1] > 0.179) eval(black) else eval(white)
+}
+
+xcolor_style <- function(hex, text, ...) {
+  glue::glue('background-color:{hex};color:{text}')
+}
+
+# Prep Color List ----
+
+xcolors <- 
+  xcolors %>% 
+  mutate(
+    hex = rgb(r, g, b, maxColorValue = 1),
+    text = purrr::map_chr(hex, choose_dark_or_light)
+  ) %>% 
+  select(color, hex, text)
+
+
+xcolors_list <- xcolors$color
+names(xcolors_list) <- purrr::pmap_chr(xcolors, xcolor_style)
+
+xcolor_label <- function(value) {
+  xcolors %>% filter(color == value) %>% purrr::pmap_chr(xcolor_style)
+}
+
+# xcolorPicker() ----
+
+xcolorPicker <- function(inputId, label = NULL, selected = NULL, ...) {
+  selectizeInput(
+    inputId,
+    label = label,
+    choices = c("", xcolors_list),
+    multiple = FALSE,
+    selected = selected,
+    options = list(
+      searchField = "value",
+      render = I(
+        '{
+          item: (item, escape) => `<div>${escape(item.value)}</div>`,
+          option: (item, escape) => `<div style="${item.label};line-height: 2.5em">${escape(item.value)}</div>`
+        }'
+      ))
+  )
+}
--- a/apps/shinyDAG-1.0.0/README.md
+++ b/apps/shinyDAG-1.0.0/README.md
@ -0,0 +1,59 @@
+# shinyDAG
+
+shinyDAG is a web application that uses R and LaTeX to create publication-quality images of directed acyclic graphs (DAGs). Additionally, the application leverages complementary R packages to evaluate correlational structures and identify appropriate adjustment sets for estimating causal effects<sup>1-4</sup>. The web-based application can be accessed at [https://apps.gerkelab.com/shinyDAG/](https://apps.gerkelab.com/shinyDAG/).
+
+## Key operations
+
+### Adding nodes and edges
+
+![Alt Text](Figures/AddNodeEdge.gif)
+
+### Editing DAG aesthetics
+
+![Alt Text](Figures/editEdge.gif)
+
+## Examplary usage
+
+The following DAG was reproduced from "A structural approach to selection bias"<sup>5</sup> (Figure 6A) using the shinyDAG web app.
+
+![alt text](Figures/example1.png "Hernan Example")
+
+For comparison, the DAG from the original article is shown below.
+
+![alt text](Figures/example1_hernan.png "Hernan Original")
+
+The DAG represents a study on the effects of antiretroviral therapy (E) on AIDS risk (D), where immunosuppression (U) is unmeasured. L represents presence of symptoms (such as fever, weight loss, and diarrhea) and C represents censoring. A spurious path exists between E and D due to selection bias. We can see this in shinyDAG by ensuring that we've selected E as the exposure, D as the outcome, adjusted for C, and then toggling the "Examine DAG elements" button in the bottom left corner. The spurious open path is displayed as D <- U -> L -> C <- E.
+
+![alt text](Figures/paths.png "shinyDAG path output")
+
+One possible resolution for this bias is to adjust for L. After toggling L in the "Select nodes to adjust" section, we see that all spurious E to D paths are now closed.
+
+![alt text](Figures/paths2.png "shinyDAG final path output")
+
+## Other features
+
+In addition PDF and PNG exports, users can download R objects in `ggdag` or `daggity` formats, as well as the source LaTeX code. The "Edit LaTeX" pane permits in-app modification of the LaTeX code with a preview window; however, users should be aware that the information in "Examine DAG elements" is not responsive to changes in the Edit LaTeX pane.
+
+shinyDAG should work in most modern web browsers, however, we have observed optimal performance in Chrome. The most notable difference across OS/browsers is likely to be in display handling for the PDF preview in the main panel: various user or browser-specific settings will determine the default zoom level.
+
+## Citing shinyDAG
+
+shinyDAG was developed by Jordan Creed, Garrick Aden-Buie and Travis Gerke.
+
+Concept DOI: 10.5281/zenodo.1288712
+
+v0.1.0 DOI: 10.5281/zenodo.1296477
+
+v0.0.0 DOI: 10.5281/zenodo.1288713
+
+## References
+
+1. Richard Iannone (NA). DiagrammeR: Graph/Network Visualization. R package version 1.0.0.
+  [https://github.com/rich-iannone/DiagrammeR](https://github.com/rich-iannone/DiagrammeR).
+1. Johannes Textor and Benito van der Zander (2016). dagitty: Graphical Analysis of Structural Causal
+  Models. R package version 0.2-2. [https://CRAN.R-project.org/package=dagitty](https://CRAN.R-project.org/package=dagitty).
+1. Malcolm Barrett (2018). ggdag: Analyze and Create Elegant Directed Acyclic Graphs. R package
+  version 0.1.0. [https://CRAN.R-project.org/package=ggdag](https://CRAN.R-project.org/package=ggdag).
+1. Csardi G, Nepusz T: The igraph software package for complex network research, InterJournal,
+  Complex Systems 1695. 2006. [http://igraph.org](http://igraph.org).
+1. Hernan MA, Hernandez-Díaz S, Robins JM. A structural approach to selection bias. Epidemiology 2004;15:615-625.
--- a/apps/shinyDAG-1.0.0/VERSION
+++ b/apps/shinyDAG-1.0.0/VERSION
@ -0,0 +1 @@
+1.0.0
--- a/apps/shinyDAG-1.0.0/data/xcolors.csv
+++ b/apps/shinyDAG-1.0.0/data/xcolors.csv
@ -0,0 +1,152 @@
+color,r,g,b
+AliceBlue,0.94,0.972,1
+AntiqueWhite,0.98,0.92,0.844
+Aqua,0,1,1
+Aquamarine,0.498,1,0.83
+Azure,0.94,1,1
+Beige,0.96,0.96,0.864
+Bisque,1,0.894,0.77
+Black,0,0,0
+BlanchedAlmond,1,0.92,0.804
+Blue,0,0,1
+BlueViolet,0.54,0.17,0.888
+Brown,0.648,0.165,0.165
+BurlyWood,0.87,0.72,0.53
+CadetBlue,0.372,0.62,0.628
+Chartreuse,0.498,1,0
+Chocolate,0.824,0.41,0.116
+Coral,1,0.498,0.312
+CornflowerBlue,0.392,0.585,0.93
+Cornsilk,1,0.972,0.864
+Crimson,0.864,0.08,0.235
+Cyan,0,1,1
+DarkBlue,0,0,0.545
+DarkCyan,0,0.545,0.545
+DarkGoldenrod,0.72,0.525,0.044
+DarkGray,0.664,0.664,0.664
+DarkGreen,0,0.392,0
+DarkGrey,0.664,0.664,0.664
+DarkKhaki,0.74,0.716,0.42
+DarkMagenta,0.545,0,0.545
+DarkOliveGreen,0.332,0.42,0.185
+DarkOrange,1,0.55,0
+DarkOrchid,0.6,0.196,0.8
+DarkRed,0.545,0,0
+DarkSalmon,0.912,0.59,0.48
+DarkSeaGreen,0.56,0.736,0.56
+DarkSlateBlue,0.284,0.24,0.545
+DarkSlateGray,0.185,0.31,0.31
+DarkSlateGrey,0.185,0.31,0.31
+DarkTurquoise,0,0.808,0.82
+DarkViolet,0.58,0,0.828
+DeepPink,1,0.08,0.576
+DeepSkyBlue,0,0.75,1
+DimGray,0.41,0.41,0.41
+DimGrey,0.41,0.41,0.41
+DodgerBlue,0.116,0.565,1
+FireBrick,0.698,0.132,0.132
+FloralWhite,1,0.98,0.94
+ForestGreen,0.132,0.545,0.132
+Fuchsia,1,0,1
+Gainsboro,0.864,0.864,0.864
+GhostWhite,0.972,0.972,1
+Gold,1,0.844,0
+Goldenrod,0.855,0.648,0.125
+Gray,0.5,0.5,0.5
+Green,0,0.5,0
+GreenYellow,0.68,1,0.185
+Grey,0.5,0.5,0.5
+Honeydew,0.94,1,0.94
+HotPink,1,0.41,0.705
+IndianRed,0.804,0.36,0.36
+Indigo,0.294,0,0.51
+Ivory,1,1,0.94
+Khaki,0.94,0.9,0.55
+Lavender,0.9,0.9,0.98
+LavenderBlush,1,0.94,0.96
+LawnGreen,0.488,0.99,0
+LemonChiffon,1,0.98,0.804
+LightBlue,0.68,0.848,0.9
+LightCoral,0.94,0.5,0.5
+LightCyan,0.88,1,1
+LightGoldenrod,0.933,0.867,0.51
+LightGoldenrodYellow,0.98,0.98,0.824
+LightGray,0.828,0.828,0.828
+LightGreen,0.565,0.932,0.565
+LightGrey,0.828,0.828,0.828
+LightPink,1,0.712,0.756
+LightSalmon,1,0.628,0.48
+LightSeaGreen,0.125,0.698,0.668
+LightSkyBlue,0.53,0.808,0.98
+LightSlateBlue,0.518,0.44,1
+LightSlateGray,0.468,0.532,0.6
+LightSlateGrey,0.468,0.532,0.6
+LightSteelBlue,0.69,0.77,0.87
+LightYellow,1,1,0.88
+Lime,0,1,0
+LimeGreen,0.196,0.804,0.196
+Linen,0.98,0.94,0.9
+Magenta,1,0,1
+Maroon,0.5,0,0
+MediumAquamarine,0.4,0.804,0.668
+MediumBlue,0,0,0.804
+MediumOrchid,0.73,0.332,0.828
+MediumPurple,0.576,0.44,0.86
+MediumSeaGreen,0.235,0.7,0.444
+MediumSlateBlue,0.484,0.408,0.932
+MediumSpringGreen,0,0.98,0.604
+MediumTurquoise,0.284,0.82,0.8
+MediumVioletRed,0.78,0.084,0.52
+MidnightBlue,0.098,0.098,0.44
+MintCream,0.96,1,0.98
+MistyRose,1,0.894,0.884
+Moccasin,1,0.894,0.71
+NavajoWhite,1,0.87,0.68
+Navy,0,0,0.5
+NavyBlue,0,0,0.5
+OldLace,0.992,0.96,0.9
+Olive,0.5,0.5,0
+OliveDrab,0.42,0.556,0.136
+Orange,1,0.648,0
+OrangeRed,1,0.27,0
+Orchid,0.855,0.44,0.84
+PaleGoldenrod,0.932,0.91,0.668
+PaleGreen,0.596,0.985,0.596
+PaleTurquoise,0.688,0.932,0.932
+PaleVioletRed,0.86,0.44,0.576
+PapayaWhip,1,0.936,0.835
+PeachPuff,1,0.855,0.725
+Peru,0.804,0.52,0.248
+Pink,1,0.752,0.796
+Plum,0.868,0.628,0.868
+PowderBlue,0.69,0.88,0.9
+Purple,0.5,0,0.5
+Red,1,0,0
+RosyBrown,0.736,0.56,0.56
+RoyalBlue,0.255,0.41,0.884
+SaddleBrown,0.545,0.27,0.075
+Salmon,0.98,0.5,0.448
+SandyBrown,0.956,0.644,0.376
+SeaGreen,0.18,0.545,0.34
+Seashell,1,0.96,0.932
+Sienna,0.628,0.32,0.176
+Silver,0.752,0.752,0.752
+SkyBlue,0.53,0.808,0.92
+SlateBlue,0.415,0.352,0.804
+SlateGray,0.44,0.5,0.565
+SlateGrey,0.44,0.5,0.565
+Snow,1,0.98,0.98
+SpringGreen,0,1,0.498
+SteelBlue,0.275,0.51,0.705
+Tan,0.824,0.705,0.55
+Teal,0,0.5,0.5
+Thistle,0.848,0.75,0.848
+Tomato,1,0.39,0.28
+Turquoise,0.25,0.88,0.815
+Violet,0.932,0.51,0.932
+VioletRed,0.816,0.125,0.565
+Wheat,0.96,0.87,0.7
+White,1,1,1
+WhiteSmoke,0.96,0.96,0.96
+Yellow,1,1,0
+YellowGreen,0.604,0.804,0.196
--- a/apps/shinyDAG-1.0.0/dev/Dockerfile
+++ b/apps/shinyDAG-1.0.0/dev/Dockerfile
@ -0,0 +1,95 @@
+# shiny-verse:3.6.0
+FROM rocker/verse:3.5.3
+
+RUN apt-get update -qq && apt-get -y --no-install-recommends install \
+  libxml2-dev \
+  libcairo2-dev \
+  libsqlite3-dev \
+  libmariadbd-dev \
+  libmariadb-client-lgpl-dev \
+  libpq-dev \
+  libssl-dev \
+  libcurl4-openssl-dev \
+  libssh2-1-dev \
+  unixodbc-dev \
+  && install2.r --error \
+    --deps TRUE \
+    tidyverse \
+    dplyr \
+    devtools \
+    formatR \
+    remotes \
+    selectr \
+    caTools \
+    BiocManager
+
+LABEL maintainer="Travis Gerke (Travis.Gerke@moffitt.org)"
+
+# Install system dependencies for required packages
+RUN apt-get update -qq && apt-get -y --no-install-recommends install \
+  libssl-dev \
+  libxml2-dev \
+  libmagick++-dev \
+  libv8-3.14-dev \
+  libglu1-mesa-dev \
+  freeglut3-dev \
+  mesa-common-dev \
+  libudunits2-dev \
+  libpoppler-cpp-dev \
+  libwebp-dev \
+  && apt-get clean \
+  && rm -rf /var/lib/apt/lists/ \
+  && rm -rf /tmp/downloaded_packages/ /tmp/*.rds
+  
+RUN install2.r --error --deps TRUE \
+  shinyAce \
+  shinydashboard \
+  shinyWidgets \
+  DiagrammeR \
+  ggdag \
+  igraph \
+  pdftools \
+  shinyBS \
+  && rm -rf /tmp/downloaded_packages/ /tmp/*.rds
+  
+RUN Rscript -e "devtools::install_github('metrumresearchgroup/texPreview', ref = 'e954322')" \
+  && rm -rf /tmp/downloaded_packages/ /tmp/*.rds
+
+# Install TinyTeX
+RUN install2.r --error tinytex \
+  && export CTAN_REPO="http://mirror.las.iastate.edu/tex-archive/systems/texlive/tlnet" \
+  && wget -qO- \ 
+     "https://github.com/yihui/tinytex/raw/master/tools/install-unx.sh" | \ 
+     sh -s - --admin --no-path \
+  && mv ~/.TinyTeX /opt/TinyTeX \
+  && /opt/TinyTeX/bin/*/tlmgr path add \ 
+  && tlmgr update --self \
+  && tlmgr install metafont mfware inconsolata tex ae parskip listings \ 
+  && tlmgr install standalone varwidth xcolor colortbl multirow psnfss setspace pgf \
+  && tlmgr path add \ 
+  && Rscript -e "tinytex::r_texmf()" \ 
+  && chown -R root:staff /opt/TinyTeX \ 
+  && chmod -R a+w /opt/TinyTeX \ 
+  && chmod -R a+wx /opt/TinyTeX/bin \ 
+  && echo "PATH=${PATH}" >> /usr/local/lib/R/etc/Renviron \
+  && rm -rf /tmp/downloaded_packages/ /tmp/*.rds
+  
+RUN install2.r --error --deps TRUE shinyjs \
+  && rm -rf /tmp/downloaded_packages/ /tmp/*.rds
+
+RUN install2.r --error plotly \
+  && rm -rf /tmp/downloaded_packages/ /tmp/*.rds
+  
+RUN install2.r --error shinycssloaders \
+  && rm -rf /tmp/downloaded_packages/ /tmp/*.rds
+
+ARG TRIGGER_UPDATE=unknown
+RUN installGithub.r gadenbuie/grkstyle r-lib/styler 
+
+RUN installGithub.r gadenbuie/shinyThings@undo \
+  && rm -rf /tmp/downloaded_packages/ /tmp/*.rds
+
+#ARG SHINY_APP_IDLE_TIMEOUT=600
+#RUN sed -i "s/directory_index on;/app_idle_timeout ${SHINY_APP_IDLE_TIMEOUT};/g" /etc/shiny-server/shiny-server.conf
+#COPY . /srv/shiny-server/shinyDAG
+#RUN chown -R shiny:shiny /srv/shiny-server/
--- a/apps/shinyDAG-1.0.0/dev/README.md
+++ b/apps/shinyDAG-1.0.0/dev/README.md
@ -0,0 +1,36 @@
+## Building and developing shinyDAG
+
+### shinyDAG dev environment
+
+I use the Dockerfile in this folder to create a fully-featured RStudio docker container that is *pretty close* to the final shinyDAG environment.
+Note that it's not perfect and if you install packages into this container, you'll need to also update the main shinyDAG docker file [here](../Dockerfile).
+
+To create the dev environment:
+
+```bash
+# make sure you're in the ./dev folder
+cd dev
+
+# make the dev image
+docker build -t shinydag-dev .
+
+# move back to shinyDAG proper and start up the dev image
+cd ..
+docker run --rm -p 8787:8787 -v $(pwd):/home/rstudio/shinydag -e PASSWORD="password" shinydag-dev
+```
+
+(Note that you should probably change the password above, but if you're only running locally it's not a big deal.)
+
+Then navigate to <localhost:8787> and login using the password you entered.
+
+### Create shinyDAG image
+
+```bash
+docker build -t gerkelab/shinydag:dev .
+
+# To send up to docker hub
+docker push
+```
+
+The `:dev` indicates that this image is tagged `dev`, but this can be anything you want.
+If you don't add a tag, it's assumed to be `:latest` which is kind of like git's `master` but for docker containers.
--- a/apps/shinyDAG-1.0.0/global.R
+++ b/apps/shinyDAG-1.0.0/global.R
@ -0,0 +1,83 @@
+library(shiny)
+library(shinydashboard)
+library(DiagrammeR)
+library(dagitty)
+library(igraph)
+library(texPreview)
+library(shinyAce)
+library(shinyBS)
+library(dplyr)
+library(ggdag)
+library(shinyWidgets)
+library(shinyjs)
+library(shinycssloaders)
+library(shinyThings)
+source("R/node.R")
+source("R/edge.R")
+source("R/columns.R")
+source("R/module/clickpad.R")
+source("R/module/dagPreview.R")
+source("R/module/examples.R")
+source("R/xcolorPicker.R")
+source("R/aes_ui.R")
+# Additional libraries: tidyr, digest, rlang
+
+enableBookmarking(store = "server")
+
+tex_opts$set(list(
+  density = 1200,
+  margin = list(left = 0, top = 0, right = 0, bottom = 0),
+  cleanup = c("aux", "log")
+))
+
+
+
+# Functions ---------------------------------------------------------------
+
+DEBUG <- getOption("shinydag.debug", FALSE)
+debug_input <- function(x, x_name = NULL) {
+  if (!isTRUE(DEBUG)) return()
+
+  if (is.null(x)) {
+    cat(if (!is.null(x_name)) paste0(x_name, ":"), "NULL", "\n")
+  } else if (inherits(x, "igraph")) {
+    cat(capture.output(print(x)), "", sep = "\n")
+  } else if (length(x) == 1 && !is.list(x)) {
+    cat(if (!is.null(x_name)) paste0(x_name, ":"), if (length(names(x))) names(x), "-", x, "\n")
+  } else if (is.list(x) && length(x) == 0) {
+    cat(if (!is.null(x_name)) paste0(x_name, ":"), "list()", "\n")
+  } else {
+    if (!inherits(x, "data.frame")) x <- tibble::enframe(x)
+    cat(if (!is.null(x_name)) paste0(x_name, ":"), knitr::kable(x), "", sep = "\n")
+  }
+}
+debug_line <- function(...) {
+  if (!isTRUE(DEBUG)) return()
+  cli::cat_line(...)
+}
+
+
+buildUsepackage <- if (length(find("build_usepackage"))) texPreview::build_usepackage else texPreview::buildUsepackage
+
+# use y if x is.null
+`%||%` <- function(x, y) if (is.null(x)) y else x
+# use y if x is not null(ish) (otherwise NULL)
+`%??%` <- function(x, y) if (!is.null(x) && x != "") y
+
+warnNotification <- function(...) showNotification(
+  paste0(...), duration = 5, closeButton = TRUE, type = "warning"
+)
+
+invertNames <- function(x) setNames(names(x), unname(x))
+
+# String utilities ----
+
+str_and <- function(...) {
+  x <- c(...)
+  last <- if (length(x) > 2) ", and " else " and "
+  glue::glue_collapse(x, sep = ", ", last = last)
+}
+
+str_plural <- function(x, word, plural = paste0(word, "s")) {
+  if (length(x) > 1) plural else word
+}
--- a/apps/shinyDAG-1.0.0/server.R
+++ b/apps/shinyDAG-1.0.0/server.R
@ -0,0 +1,895 @@
+
+# Server ------------------------------------------------------------------
+server <- function(input, output, session) {
+  # ---- Global - Session Temp Directory ----
+  SESSION_TEMPDIR <- file.path("www", session$token)
+  dir.create(SESSION_TEMPDIR, showWarnings = FALSE)
+  onStop(function() {
+    message("Removing session tempdir: ", SESSION_TEMPDIR)
+    unlink(SESSION_TEMPDIR, recursive = TRUE)
+  })
+  message("Using session tempdir: ", SESSION_TEMPDIR)
+  
+  # ---- Global - Bookmarking ----
+  onBookmark(function(state) {
+    state$values$rvn <- list()
+    state$values$rvn$nodes <- rvn$nodes
+    state$values$rve <- list()
+    state$values$rve$edges <- rve$edges
+    state$values$query_string <- session$clientData$url_search
+    
+    # Store outcome/exposure/adjust node selections
+    state$values$sel <- list(
+      exposureNode = input$exposureNode,
+      outcomeNode = input$outcomeNode,
+      adjustNode = input$adjustNode
+    )
+  })
+  
+  onBookmarked(function(url) {
+    message("bookmark: ", url)
+    showBookmarkUrlModal(url)
+    updateQueryString(url)
+  })
+  
+  onRestore(function(state) {
+    showModal(modalDialog(
+      title = NULL,
+      easyClose = FALSE,
+      footer = NULL,
+      tags$p(class = "text-center", "Loading your shinyDag workspace, please wait."),
+      tags$div(class = "gerkelab-spinner")
+    ))
+    
+    # clear selected node and text input to try to prevent existing values from
+    # changing the name of the node that gets selected on restore
+    rvn$nodes <- node_unset_attribute(rvn$nodes, names(rvn$nodes), "parent")
+    updateTextInput(session, "node_list_node_name", value = "")
+    
+    if (isTRUE(getOption("shinydag.debug", FALSE))) {
+      names(state$values) %>%
+        purrr::set_names() %>%
+        purrr::map(~ state$values[[.]]) %>%
+        purrr::compact() %>%
+        purrr::iwalk(~ debug_input(.x, paste0("state$values$", .y)))
+    }
+    rvn$nodes <- state$values$rvn$nodes
+    rve$edges <- state$values$rve$edges
+  })
+  
+  onRestored(function(state) {
+    removeModal()
+    updateSelectInput(session, "exposureNode", selected = state$values$sel$exposureNode)
+    updateSelectInput(session, "outcomeNode", selected = state$values$sel$outcomeNode)
+    updateSelectizeInput(session, "adjustNode", selected = state$values$sel$adjustNode)
+  })
+  
+  # ---- Global - Reactive Values ----
+  rve <- reactiveValues(edges = list())
+  rvn <- reactiveValues(nodes = list())
+
+  # rve$edges is a named list, e.g. for hash(A) -> hash(B):
+  # rve$edges[edge_key(hash(A), hash(B))] = list(from = hash(A), to = hash(B))
+  
+  # rvn$nodes is a named list where name is a hash
+  # rvn$nodes$abcdefg = list(name, x, y)
+  
+  # ---- Sketch - Reactive Values Undo/Redo ----
+  rv_undo_state <- shinyThings::undoHistory(
+    id = "undo_rv", 
+    value = reactive({
+      req(length(rvn$nodes) > 0)
+      
+      node_params <- c("name", "x", "y", "parent", "exposure", "outcome", "adjusted")
+      nodes <- rvn$nodes %>% 
+        purrr::map(`[`, node_params) %>% 
+        purrr::map(purrr::compact)
+      
+      edge_params <- c("from", "to")
+      edges <- rve$edges %>% 
+        purrr::map(`[`, edge_params) %>% 
+        purrr::map(purrr::compact)
+      
+      list(
+        nodes = nodes,
+        edges = edges
+      )
+    })
+  )
+  
+  observe({
+    req(!is.null(rv_undo_state()))
+    
+    rv_state <- rv_undo_state()
+    debug_input(rv_state$nodes, "undo/redo - new nodes")
+    debug_input(rv_state$edges, "undo/redo - new edges")
+    rvn$nodes <- rv_state$nodes
+    rve$edges <- rv_state$edges
+  }, priority = 1000)
+
+  # ---- Sketch - Node Controls ----
+  node_btn_id <- function(node_hash) paste0("node_toggle_", node_hash)
+  node_btn_get_hash <- function(node_btn_id) sub("node_toggle_", "", node_btn_id, fixed = TRUE)
+  
+  node_list_buttons_redraw <- reactiveVal(Sys.time())
+  node_list_node_is_new <- reactiveVal(FALSE)
+  node_list_selected_child <- reactive({ node_child(rvn$nodes) }) # TODO: remove
+  node_list_selected_node <- reactiveVal(NULL)
+  observe({
+    I("update selected node?")
+    # this feels hacky but on the one hand we want to be able to update the 
+    # selected parent node just by updating rvn$nodes, and on the other we don't
+    # want to propagate a reactive change if the value stays the same. So this
+    # observer is kind of like a debouncer for node_list_selected_node()
+    current_selected_node <- isolate(node_list_selected_node())
+    new_selected_node <- node_parent(rvn$nodes)
+    if (!identical(current_selected_node, new_selected_node)) {
+      node_list_selected_node(new_selected_node)
+    }
+  })
+  
+  # debug selected nodes
+  observe({
+    debug_input(node_list_selected_node(), "node_list_selected_node")
+    debug_input(node_list_selected_child(), "node_list_selected_child")
+  })
+  
+  # Handle add node button, creates new node and sets focus
+  observeEvent(input$node_list_node_add, {
+    new_node_hash <- digest::digest(Sys.time())
+    rvn$nodes <- node_new(rvn$nodes, new_node_hash, "new node") %>% 
+      node_set_attribute(new_node_hash, "parent")
+    node_list_buttons_redraw(Sys.time())
+    node_list_node_is_new(TRUE)
+  })
+  
+  # Show, hide or update node name text input
+  observe({
+    I("show/hide/update node name text box")
+    if (is.null(node_list_selected_node())) {
+      shinyjs::hide("node_list_node_name_container")
+      return()
+    } 
+    
+    s_node_selected <- node_list_selected_node()
+    
+    # Selected node already exists, update UI
+    shinyjs::show("node_list_node_name_container")
+    shinyjs::runjs("set_input_focus('node_list_node_name')")
+    s_node_name <- node_name_from_hash(isolate(rvn$nodes), s_node_selected)
+    if (isolate(node_list_node_is_new())) {
+      node_list_node_is_new(FALSE)
+      updateTextInput(session, "node_list_node_name", value = "", placeholder = "Enter Node Name")
+    } else {
+      updateTextInput(
+        session, 
+        "node_list_node_name", 
+        value = unname(s_node_name)
+      )
+    }
+  }, priority = 1000)
+  
+  # Handle node name text input
+  node_name_text_input <- reactive({
+    input$node_list_node_name
+  })
+  
+  observe({
+    I("update node name")
+    node_name_debounced <- debounce(node_name_text_input, 750)
+    node_name <- node_name_debounced()
+    debug_input(node_name, "node_list_node_name (debounced)")
+    s_node <- isolate(node_list_selected_node())
+    req(s_node, node_name != "")
+    rvn$nodes <- node_update(isolate(rvn$nodes), s_node, node_name)
+  }, priority = 2000)
+  
+  # Show editing buttons when appropriate
+  observe({
+    I("toggle edit buttons")
+    if (is.null(node_list_selected_node()) || !length(rvn$nodes)) {
+      # no node selected, can only add a new node
+      shinyjs::hide("node_list_node_delete")
+    } else {
+      # can now delete any selected node
+      shinyjs::show("node_list_node_delete")
+    }
+  })
+  
+  # Action: delete node
+  observeEvent(input$node_list_node_delete, {
+    # Remove node
+    node_to_delete <- node_list_selected_node()
+    rvn$nodes[[node_to_delete]] <- NULL
+    
+    # Remove any edges
+    edges_with_node <- rve$edges %>% 
+      purrr::keep(~ node_to_delete %in% c(.$from, .$to)) %>% 
+      names()
+    
+    if (length(edges_with_node)) rve$edges[edges_with_node] <- NULL
+    
+    shinyjs::hide("node_list_node_name_container")
+    shinyjs::hide("node_list_node_delete")
+  })
+  
+  # ---- Sketch - Help Text ----
+  output$node_list_helptext <- renderUI({
+    s_node <- node_list_selected_node()
+    no_nodes <- length(rvn$nodes) == 0
+    not_enough_nodes <- length(rvn$nodes) < 2
+    no_node_selected <- !no_nodes && is.null(s_node)
+    no_dag_nodes <- !no_nodes && length(nodes_in_dag(rvn$nodes)) == 0
+    not_enough_dag_nodes <- !no_dag_nodes && length(nodes_in_dag(rvn$nodes)) < 2
+    node_in_dag <- !no_dag_nodes && s_node %in% nodes_in_dag(rvn$nodes)
+    
+    if (no_nodes) {
+      helpText(
+        "Use the", icon("plus"), "button above to add a node",
+        "to your shinyDAG workspace"
+      )
+    } else if (not_enough_nodes) {
+      helpText("Add another node to your shinyDAG workspace")
+    } else if (no_dag_nodes) {
+      helpText("Drag a node from the staging area into the DAG or click its label to edit")
+    } else if (not_enough_dag_nodes) {
+      helpText("Drag another node from the staging area into the DAG")
+    } else if (input$clickpad_click_action == "parent") {
+      helpText("Click on a node label to activate as causal node or to edit its label")
+    } else if (input$clickpad_click_action == "child") {
+      helpText(
+        "Click on a node label to draw or remove a causal arrow from", 
+        tags$strong(node_name_from_hash(rvn$nodes, node_list_selected_node())),
+        "or click",
+        tags$strong(node_name_from_hash(rvn$nodes, node_list_selected_node())),
+        "again to deselect"
+      )
+    }
+  })
+  
+  # ---- Sketch - Edge Help Text ----
+  req_nodes <- function() {
+    if (!length(rvn$nodes)) {
+      cat("\n No Nodes!")
+      edge_helptext("Please add a node to the DAG first.")
+      FALSE
+    } else TRUE
+  }
+  
+  edge_helptext <- function(inner, tag = "div", class = "help-block text-danger alert-edge") {
+    edge_helptext_trigger(Sys.time())
+    edge_helptext_feedback(list(class = class, inner = inner, tag = tag))
+  }
+  
+  edge_normal_help_html <- list(
+    inner = "Double-click on a node to set parent node. Single-click to set child node.",
+    class = "help-block",
+    tag = "p"
+  )
+  edge_helptext_trigger <- reactiveVal(Sys.time())
+  edge_helptext_feedback <- reactiveVal(NULL)
+  
+  output$edge_list_helptext <- renderUI({
+    debug_input(isolate(edge_helptext_feedback()), "edge_helptext_feedback")
+    
+    edge_helptext_trigger()
+    
+    if (!is.null(isolate(edge_helptext_feedback()))) {
+      invalidateLater(4800)
+    } 
+    
+    html <- isolate(edge_helptext_feedback()) %||% edge_normal_help_html
+    edge_helptext_feedback(NULL)
+    tag(html$tag, list(class = html$class, html$inner))
+  })
+  
+  # ---- Sketch - Clickpad ----
+  plotly_source_id <- paste0("clickpad_", session$token)
+  clickpad_new_locations <- callModule(
+    clickpad, "clickpad", 
+    nodes = reactive(rvn$nodes),
+    edges = reactive(rve$edges),
+    plotly_source = plotly_source_id
+  )
+  
+  observe({
+    req(clickpad_new_locations())
+    
+    new <- clickpad_new_locations()
+    debug_input(new, "clickpad_new_locations()")
+    
+    rvn$nodes <- node_update(rvn$nodes, new$hash, x = unname(new$x), y = unname(new$y))
+  })
+  
+  # ---- Sketch - Clickpad - Click Events ----
+  observe({
+    I("clickpad click event handler")
+    clicked_annotation <- event_data(
+      "plotly_clickannotation", source = plotly_source_id, priority = "event"
+    )
+    req(clicked_annotation[["_input"]]$node_hash)
+    
+    click_action = isolate(input$clickpad_click_action)
+    clicked_hash = clicked_annotation[["_input"]]$node_hash
+    
+    nodes <- isolate(rvn$nodes)
+    
+    s_node_parent <- node_parent(nodes)
+    s_node_child <- node_child(nodes)
+    
+    if (click_action == "parent") {
+      # toggle clicked node as parent node
+      update_button <- nodes[[clicked_hash]]$x >= 0 &&
+        nodes %>% purrr::map_dbl("x") %>% { sum(. >= 0) > 1 }
+      
+      if (is.null(s_node_parent)) {
+        nodes <- node_set_attribute(nodes, clicked_hash, "parent")
+      } else if (clicked_hash == s_node_parent) {
+        update_button <- FALSE
+        nodes <- node_unset_attribute(nodes, clicked_hash, c("parent", "child"))
+      } else {
+        nodes <- node_set_attribute(nodes, clicked_hash, "parent")
+        nodes <- node_unset_attribute(nodes, clicked_hash, "child")
+      }
+      if (update_button) updateRadioSwitchButtons("clickpad_click_action", "child")
+      
+    } else if (click_action == "child") {
+      # toggle clicked node as child node
+      has_edge <- edge_exists(isolate(rve$edges), s_node_parent, s_node_child %||% clicked_hash)
+      has_reverse_edge <- edge_exists(isolate(rve$edges), s_node_child %||% clicked_hash, s_node_parent)
+      
+      if (!is.null(s_node_parent) && s_node_parent == clicked_hash) {
+        # Can't add edges to self
+        rvn$nodes <- node_unset_attribute(nodes, names(nodes), c("parent", "child"))
+        updateRadioSwitchButtons("clickpad_click_action", "parent")
+        return()
+      } else if (has_edge) {
+        # Clicked on child node that already has edge, will be removing edge
+        nodes <- node_unset_attribute(nodes, clicked_hash, "child")
+      } else if (nodes[[clicked_hash]]$x < 0) {
+        showNotification(
+          "Edges can only be drawn between nodes that are in the DAG area.",
+          duration = 5,
+          type = "error"
+        )
+        return()
+      } else {
+        nodes <- node_set_attribute(nodes, clicked_hash, "child")
+      }
+      
+      # Remove reverse edge if it exists
+      rv_edges <- isolate(rve$edges)
+      if (has_reverse_edge) {
+        rv_edges <- edge_toggle(rv_edges, clicked_hash, s_node_parent)
+      }
+      rve$edges <- edge_toggle(rv_edges, s_node_parent, clicked_hash)
+    }
+    rvn$nodes <- nodes
+  })
+  
+  # ---- Sketch - Clickpad - Click Type Buttons ----
+  observe({
+    I("clickpad click action reset to select?")
+    reset_clickpad_action <- function() {
+      updateRadioSwitchButtons("clickpad_click_action", "parent")
+      invisible()
+    }
+    
+    if (length(rvn$nodes) < 2) return(reset_clickpad_action())
+    
+    dag_has_two_nodes <- rvn$nodes %>% purrr::map_dbl("x") %>% { sum(. >= 0) > 1 }
+    if (!dag_has_two_nodes) return(reset_clickpad_action())
+    
+    if (!is.null(node_list_selected_node())) {
+      if (rvn$nodes[[node_list_selected_node()]]$x < 0) {
+        reset_clickpad_action()
+      }
+    }
+  })
+  
+  # Don't allow clickpad edge adding unless node conditions are met
+  observeEvent(input$clickpad_click_action, {
+    req(input$clickpad_click_action == "child")
+    valid <- FALSE
+    if (length(rvn$nodes) < 2) {
+      showNotification("Please add at least 2 nodes to your DAG workspace first.", duration = 5)
+    } else if (rvn$nodes %>% purrr::keep(~ .$x >= 0) %>% length() < 2) {
+      showNotification("Please drag at least 2 nodes into the DAG area first.", duration = 5)
+    } else if (is.null(node_list_selected_node())) {
+      showNotification("A parent node must be selected first", duration = 5)
+    } else if (!length(nodes_in_dag(rvn$nodes))) {
+      showNotification(
+        "Please add a node to the DAG by dragging it out of the staging area.", 
+        duration = 5
+      )
+    } else {
+      valid <- TRUE
+    }
+    if (!valid) updateRadioSwitchButtons("clickpad_click_action", "parent")
+  })
+  
+  # ---- Sketch - Node Options ----
+  update_node_options <- function(
+    nodes,
+    inputId,
+    updateFn,
+    none_choice = TRUE,
+    ...
+  ) {
+    available_choices <- c("None" = "", node_names(nodes))
+    if (!none_choice) available_choices <- available_choices[-1]
+    s_choice <- intersect(isolate(input[[inputId]]), available_choices)
+    if (!length(s_choice) && none_choice) s_choice <- ""
+    
+    updateFn(
+      session,
+      inputId,
+      choices = available_choices,
+      selected = s_choice,
+      ...
+    )
+  }
+  
+  observe({
+    update_node_options(
+      rvn$nodes %>% purrr::keep(~ .$x >= 0), 
+      "adjustNode", 
+      updateSelectizeInput
+    )
+    update_node_options(
+      rvn$nodes %>% purrr::keep(~ .$x >= 0), 
+      "exposureNode", 
+      updateSelectInput
+    )
+    update_node_options(
+      rvn$nodes %>% purrr::keep(~ .$x >= 0), 
+      "outcomeNode", 
+      updateSelectInput
+    )
+  })
+  
+  observeEvent(input$exposureNode, {
+    nodes <- isolate(rvn$nodes)
+    if (input$exposureNode == "") {
+      rvn$nodes <- node_unset_attribute(nodes, names(nodes), "exposure")
+    } else if (input$exposureNode == input$outcomeNode) {
+      updateSelectInput(session, "outcomeNode", selected = "")
+      rvn$nodes <- node_unset_attribute(nodes, names(nodes), "outcome")
+    } else {
+      rvn$nodes <- node_set_attribute(nodes, input$exposureNode, "exposure")
+    }
+  })
+  
+  observeEvent(input$outcomeNode, {
+    nodes <- isolate(rvn$nodes)
+    if (input$outcomeNode == "") {
+      rvn$nodes <- node_unset_attribute(nodes, names(nodes), "outcome")
+    } else if (input$outcomeNode == input$exposureNode) {
+      updateSelectInput(session, "exposureNode", selected = "")
+      rvn$nodes <- node_unset_attribute(nodes, names(nodes), "exposure")
+    } else {
+      rvn$nodes <- node_set_attribute(nodes, input$outcomeNode, "outcome")
+    }
+  })
+  
+  observeEvent(input$adjustNode, {
+    nodes <- isolate(rvn$nodes)
+    if (is.null(input$adjustNode)) return()
+    s_adjust <- input$adjustNode
+    rvn$nodes <- if (length(s_adjust) == 1 && s_adjust == "") {
+      node_unset_attribute(nodes, names(node), "adjusted")
+    } else {
+      node_set_attribute(nodes, s_adjust, "adjusted")
+    }
+  })
+  
+  output$adjustText <- renderText({
+    if (is.null(input$exposureNode) & is.null(input$outcomeNode)) {
+      paste0("Minimal sufficient adjustment sets")
+    } else {
+      paste0(
+        "Minimal sufficient adjustment set(s) to estimate the effect of ",
+        input$exposureNode,
+        " on ",
+        input$outcomeNode
+      )
+    }
+  })
+  
+  # ---- DAG - Functions ----
+  make_dagitty <- function(nodes, edges, exposure = NULL, outcome = NULL, adjusted = NULL) {
+    dagitty_edges <- edge_frame(edges, nodes) %>% 
+      glue::glue_data('"{from_name}" -> "{to_name}"') %>% 
+      paste(collapse = "; ")
+    
+    dagitty_code <- glue::glue("dag {{ {dagitty_edges} }}")
+    debug_input(dagitty_code, "dagitty_code")
+    
+    gdag <- dagitty(dagitty_code)
+    
+    if (isTruthy(exposure)) exposures(gdag) <- node_name_from_hash(nodes, exposure)
+    if (isTruthy(outcome))  outcomes(gdag) <- node_name_from_hash(nodes, outcome)
+    if (isTruthy(adjusted)) adjustedNodes(gdag) <- node_name_from_hash(nodes, adjusted)
+    
+    gdag
+  }
+  
+  dagitty_open_paths <- function(nodes, edges, exposure, outcome, adjusted) {
+    node_names <- invertNames(node_names(nodes))
+    gd <- make_dagitty(
+      edges = edges, nodes = nodes,
+      exposure = exposure, outcome = outcome, adjusted = adjusted
+    )
+    
+    exp_outcome_paths <- paths(
+      gd,
+      Z = adjusted %??% unname(node_names[adjusted])
+    )
+    
+    exp_outcome_paths$paths[as.logical(exp_outcome_paths$open)]
+  }
+  
+  dagitty_format_paths <- function(paths) {
+    HTML(paste0(
+      "<pre><code>",
+      paste(trimws(paths), collapse = "\n"),
+      "\n</code></pre>"
+    ))
+  }
+  
+  # ---- Sketch - DAG - Open Exp/Outcome Paths ----
+  dagitty_open_exp_outcome_paths <- reactive({
+    req(
+      length(nodes_in_dag(rvn$nodes)),
+      length(edges_in_dag(rve$edges, rvn$nodes))
+    )
+    
+    # need both exposure and outcome node
+    requires_nodes <- c("Exposure" = input$exposureNode, "Outcome" = input$outcomeNode)
+    missing_nodes <- names(requires_nodes[grepl("^$", requires_nodes)])
+    validate(
+      need(
+        length(missing_nodes) == 0,
+        glue::glue("Please choose {str_and(missing_nodes)} {str_plural(missing_nodes, 'node')}")
+      )
+    )
+    
+    purrr::safely(dagitty_open_paths)(
+      nodes = rvn$nodes, edges = rve$edges, exposure = input$exposureNode, 
+      outcome = input$outcomeNode, adjusted = input$adjustNode
+    )
+  })
+  
+  
+  output$openExpOutcomePaths <- renderUI({
+    validate(need(length(edges_in_dag(rve$edges, rvn$nodes)) > 0, "Please add at least one edge"))
+    
+    open_paths <- dagitty_open_exp_outcome_paths()
+    
+    validate(need(
+      is.null(open_paths$error),
+      paste(
+        "There was an error building your graph. It may not be fully or",
+        "correctly specified. If you have special characters in your node",
+        "change the node name to something short and representative. You can",
+        "set more detailed node labels in the \"Tweak\" panel."
+      )
+    ), errorClass = " text-danger")
+    
+    open_paths <- open_paths$result
+    
+    if (length(open_paths)) {
+      tagList(
+        h5("Open associations between exposure and outcome"),
+        dagitty_format_paths(open_paths)
+      )
+    } else {
+      tagList(
+        helpText("No open associations between exposure and outcome.")
+      )
+    }
+  })
+  
+  # ---- Tweak - Edge Aesthetics ----
+
+  # Create the edge aesthetics control UI, only updated when tab is activated
+  output$edge_aes_ui <- renderUI({
+    req(input$shinydag_page == "tweak")
+    req(length(isolate(rve$edges)) > 0)
+    rv_edge_frame <- edge_frame(isolate(rve$edges), isolate(rvn$nodes)) %>% 
+      arrange(from_name, to_name)
+    
+    tagList(
+      purrr:::pmap(rv_edge_frame, ui_edge_controls_row, input = input)
+    )
+  })
+  
+  # Watch edge UI inputs and update rve$edges when inputs change
+  observe({
+    I("update edge aesthetics")
+    req(length(rve$edges) > 0, grepl("^angle__", names(input)))
+    rv_edges <- isolate(rve$edges)
+    
+    edge_ui <- get_hashed_input_with_prefix(
+      input,
+      prefix = "angle|color|lty|lineT",
+      hash_sep = "__"
+    )
+    
+    for (edge in edge_ui) {
+      if (!edge$hash %in% names(rv_edges)) next
+      this_edge <- edge[setdiff(names(edge), "hash")]
+      for (prop in names(this_edge)) {
+        if (is.na(this_edge[[prop]])) next
+        rv_edges[[edge$hash]][[prop]] <- this_edge[[prop]]
+      }
+    }
+    debug_input(bind_rows(rv_edges, .id = "hash"), "rve$edges after aes update")
+    rve$edges <- rv_edges
+  }, priority = -50)
+  
+  # ---- Tweak - Node Aesthetics ----
+  
+  # Create the node aesthetics control UI, only updated when tab is activated
+  output$node_aes_ui <- renderUI({
+    req(input$shinydag_page == "tweak")
+    req(length(isolate(rvn$nodes)) > 0)
+    rv_node_frame <- node_frame(isolate(rvn$nodes))
+    
+    tagList(
+      purrr:::pmap(rv_node_frame, ui_node_controls_row, input = input)
+    )
+  })
+  
+  # Watch edge UI inputs and update rve$edges when inputs change
+  observe({
+    I("update node aesthetics")
+    req(length(rvn$nodes) > 0, grepl("^color_fill_", names(input)))
+    rv_nodes <- isolate(rvn$nodes)
+    
+    node_ui <- get_hashed_input_with_prefix(
+      input,
+      prefix = "name_latex|(color_(draw|fill|text))",
+      hash_sep = "__"
+    )
+    
+    for (node in node_ui) {
+      if (!node$hash %in% names(rv_nodes)) next
+      this_node <- node[setdiff(names(node), "hash")]
+      for (prop in names(this_node)) {
+        if (is.na(this_node[[prop]])) next
+        rv_nodes[[node$hash]][[prop]] <- this_node[[prop]]
+      }
+    }
+    debug_input(bind_rows(rv_nodes, .id = "hash"), "rvn$nodes after aes update")
+    rvn$nodes <- rv_nodes
+  }, priority = -50)
+  
+  
+  # ---- Global - TikZ Code ----
+  edge_points_rv <- reactive({
+    req(length(rve$edges) > 0)
+    ep <- edge_points(rve$edges, rvn$nodes)
+    req(nrow(ep) > 0)
+    ep
+  })
+  
+  dag_node_lines <- function(nodeFrame) {
+    dag_bounds <- 
+      nodeFrame %>% 
+      filter(!is.na(name)) %>% 
+      summarize_at(vars(x, y), list(min = min, max = max))
+    
+    nodeFrame <- nodeFrame %>% 
+      filter(
+        between(x, dag_bounds$x_min, dag_bounds$x_max) &&
+        between(y, dag_bounds$y_min, dag_bounds$y_max)
+      )
+    
+    nodeFrame[is.na(nodeFrame$tikz_node), "tikz_node"] <- "~"
+    
+    nodeLines <- vector("character", 0)
+    for (i in unique(nodeFrame$y)) {
+      createLines <- paste0(
+        paste(nodeFrame[nodeFrame$y == i, ]$tikz_node, collapse = " & "), 
+        "  \\\\\n"
+      )
+      nodeLines <- c(nodeLines, createLines)
+    }
+    nodeLines <- rev(nodeLines)
+    
+    paste0(
+      "\\matrix(m)[matrix of nodes, row sep=2.6em, column sep=2.8em,", 
+      "text height=1.5ex, text depth=0.25ex]\n", 
+      "{\n  ", paste(nodeLines, collapse = "  "), "};"
+    )
+  }
+  
+  tikz_node_points <- reactive({
+    req(length(rvn$nodes))
+    update_tikz_because_global_opts()
+    node_df <- node_frame(rvn$nodes)
+    req(nrow(node_df) > 0)
+    node_df %>% node_frame_add_style()
+  })
+  
+  tikz_code_from_app <- reactive({
+    d_tikz_node_points <- debounce(tikz_node_points, 1000)
+    nodePts <- d_tikz_node_points()
+    req(nrow(nodePts) > 0)
+    
+    has_style <- any(!is.na(nodePts$tikz_style))
+    tikz_style_defs <- nodePts$tikz_style[!is.na(nodePts$tikz_style)]
+    
+    styleZ <- paste(
+      "\\tikzset{", 
+      paste0("  every node/.style={ }", if (has_style) "," else "\n}"),
+      if (has_style) paste(" ", tikz_style_defs, collapse = ",\n"),
+      if (has_style) "}",
+      sep = "\n"
+    )
+    startZ <- "\\begin{tikzpicture}[>=latex]"
+    endZ <- "\\end{tikzpicture}"
+    pathZ <- "\\path[->,font=\\scriptsize,>=angle 90]"
+    
+    d_x <- min(nodePts$x) - 1L
+    d_y <- min(nodePts$y) - 1L
+  
+    nodePts$x <- nodePts$x - d_x
+    nodePts$y <- nodePts$y - d_y
+    
+    y_max <- max(nodePts$y)
+    
+    nodeLines <- nodePts %>% 
+      tidyr::complete(
+        x = seq(min(nodePts$x), max(nodePts$x)), 
+        y = seq(min(nodePts$y), max(nodePts$y))
+      ) %>% 
+      dag_node_lines()
+    
+    edgeLines <- character()
+    
+    if (length(edges_in_dag(rve$edges, isolate(rvn$nodes)))) {
+      # edge_points_rv() is a reactive that gathers values from aesthetics UI
+      # but it can be noisy, so we're debouncing to delay TeX rendering until values are constant
+      edgePts <- debounce(edge_points_rv, 5000)()
+      
+      tikz_point <- function(x, y, d_x, d_y, y_max) {
+        glue::glue("(m-{y_max - (y - d_y) + 1}-{x - d_x})")
+      }
+      
+      edgePts <- edgePts %>%
+        mutate(
+          parent = tikz_point(from.x, from.y, d_x, d_y, y_max),
+          child = tikz_point(to.x, to.y, d_x, d_y, y_max),
+          edgeLine = glue::glue(
+            "{parent} edge [>={input$arrowShape}, bend left = {edgePts$angle}, ",
+            "color = {edgePts$color},{edgePts$lineT},{edgePts$lty}] node[auto] {{$~$}} {child}"
+          )
+        )
+      
+      debug_input(select(edgePts, hash, matches("^(from|to)_name"), parent, child, edgeLine), "edgeLines")
+      edgeLines <- edgePts$edgeLine
+    }
+    
+    edgeLines <- paste0(pathZ, paste(edgeLines, collapse = ""), ";")
+    
+    paste(c(styleZ, startZ, nodeLines, edgeLines, endZ), collapse = "\n")
+  })
+  
+  make_graph <- function(nodes, edges) {
+    g <- make_empty_graph()
+    if (nrow(node_frame(nodes))) {
+      g <- g + node_vertices(nodes)
+    }
+    if (length(edges)) {
+      # Add edges
+      g <- g + edge_edges(edges, nodes)
+    }
+    g
+  }
+  
+  # ---- Tweak - Global Options ----
+  update_tikz_because_global_opts <- reactiveVal(FALSE)
+  
+  observe({
+    I("update tex_opts")
+    `%|%` <- function(x, y) {
+      x <- x %||% y
+      if (is.na(x)) y else x
+    }
+    tex_opts$set(list(
+      density = 1200,
+      margin = list(
+        left = input$tex_opts_margin_left %|% 0,
+        top = input$tex_opts_margin_bottom %|% 0, # bug?
+        right = input$tex_opts_margin_right %|% 0,
+        bottom = input$tex_opts_margin_top %|% 0
+      ),
+      cleanup = c("aux", "log")
+    ))
+    update_tikz_because_global_opts(!isolate(update_tikz_because_global_opts()))
+  })
+
+  # ---- Tweak - dagitty DAG ----
+  dag_dagitty <- reactive({
+    req(
+      tweak_preview_visible(),
+      length(nodes_in_dag(rvn$nodes)), 
+      length(edges_in_dag(rve$edges)),
+      input$exposureNode, input$outcomeNode, input$adjustNode
+    )
+    make_dagitty(rvn$nodes, rve$edges, input$exposureNode, input$outcomeNode, input$adjustNode)
+  })
+  
+  dag_tidy <- reactive({
+    req(
+      tweak_preview_visible(),
+      length(nodes_in_dag(rvn$nodes)), 
+      length(edges_in_dag(rve$edges)),
+      input$exposureNode, input$outcomeNode, input$adjustNode
+    )
+    make_dagitty(rvn$nodes, rve$edges, input$exposureNode, input$outcomeNode, input$adjustNode) %>% 
+      tidy_dagitty()
+  })
+  
+  # ---- Tweak - Preview ----
+  tweak_preview_visible <- callModule(
+    module = dagPreview,
+    id = "tweak_preview",
+    session_dir = SESSION_TEMPDIR,
+    tikz_code = reactive({
+      req(input$shinydag_page == "tweak")
+      tikz_code_from_app()
+    }),
+    dag_dagitty,
+    dag_tidy,
+    has_edges = reactive(nrow(edge_frame(rve$edges, rvn$nodes)))
+  )
+  
+  # ---- LaTeX - Editor ----
+  output$texEdit <- renderUI({
+    tikz_lines <- tikz_code_from_app()
+    
+    if (is.null(tikz_lines)) {
+      tikz_lines <- "\\\\begin{tikzpicture}[>=latex]\n\\\\end{tikzpicture}"
+    } else {
+      # double escape backslashes
+      tikz_lines <- gsub("\\", "\\\\", tikz_lines, fixed = TRUE)
+    }
+    aceEditor(
+      "manual_tikz", 
+      mode = "latex", 
+      value = paste(tikz_lines, collapse = "\n"), 
+      theme = "chrome",
+      wordWrap = TRUE, 
+      highlightActiveLine = TRUE
+    )
+  })
+  
+  latex_preview_visible <- callModule(
+    module = dagPreview,
+    id = "latex_preview",
+    session_dir = SESSION_TEMPDIR,
+    reactive({
+      req(input$shinydag_page == "latex")
+      input$manual_tikz
+    })
+  )
+  
+  # ---- About - Examples ----
+  example_value <- callModule(examples, "example")
+  
+  observe({
+    req(example_value())
+    
+    ex_val <- example_value()
+    rvn$nodes <- ex_val$nodes
+    rve$edges <- ex_val$edges
+    
+    Sys.sleep(0.25)
+    shinydashboard::updateTabItems(session, "shinydag_page", "sketch")
+    
+  })
+
+}
--- a/apps/shinyDAG-1.0.0/shinydag.Rproj
+++ b/apps/shinyDAG-1.0.0/shinydag.Rproj
@ -0,0 +1,13 @@
+Version: 1.0
+
+RestoreWorkspace: No
+SaveWorkspace: No
+AlwaysSaveHistory: Default
+
+EnableCodeIndexing: Yes
+UseSpacesForTab: Yes
+NumSpacesForTab: 2
+Encoding: UTF-8
+
+RnwWeave: Sweave
+LaTeX: pdfLaTeX
--- a/apps/shinyDAG-1.0.0/ui.R
+++ b/apps/shinyDAG-1.0.0/ui.R
@ -0,0 +1,357 @@
+
+# Components --------------------------------------------------------------
+
+components <- list(toolbar = list())
+
+# Components - Clickpad ----
+components$toolbar$clickpad_action <- tags$div(
+  radioSwitchButtons(
+    "clickpad_click_action",
+    HTML(paste(icon("mouse-pointer"), "Click a node to...")),
+    choices = c("Select" = "parent", "Draw/Remove Edge" = "child"),
+    selected = "parent",
+    selected_background = "#D3751C"
+  )
+)
+
+# Components - Node List ----
+components$toolbar$node_list_actions <- tags$div(
+  class = "btn-toolbar",
+  role = "toolbar",
+  tags$form(
+    class = "form-inline",
+    tags$div(
+      class = "form-group",
+      tags$div(
+        class = "btn-group",
+        role = "group",
+        actionButton(
+          input = "node_list_node_add", 
+          label = "Add New Node", 
+          icon = icon("plus"),
+          alt = "Add New Node to Workspace",
+          `data-toggle` = "tooltip",
+          `data-placement` = "bottom",
+          title = "Add New Node to Workspace"
+        ),
+        shinyjs::hidden(
+          actionButton(
+            "node_list_node_delete", "Delete Node", icon("trash"),
+            alt = "Delete Node",
+            `data-toggle` = "tooltip",
+            `data-placement` = "bottom",
+            title = "Delete Node")
+        )
+      )
+    )
+  )
+)
+
+components$toolbar$node_list_name <- tags$div(
+  style = "padding-top: 15px; min-height: 90px;",
+  shinyjs::hidden(
+    tags$div(
+      id = "node_list_node_name_container",
+      class = "col-xs-12",
+      textInput("node_list_node_name", "Node Name", width = "100%")
+    )
+  )
+)
+
+# Components - About ----
+components$about <- list()
+
+components$about$gerkelab <- tagList(
+  h3("Development Team"),
+  tags$ul(
+    tags$li("Jordan Creed"),
+    tags$li(tags$a(href = "https://www.garrickadebuie.com", "Garrick Aden-Buie")),
+    tags$li(tags$a(href = "https://travisgerke.com", "Travis Gerke"))
+  ),
+  p(
+    "For more information about our lab and other projects please check",
+    "out our website at",
+    tags$a(href = "http://gerkelab.com", "gerkelab.com")
+  ),
+  p(
+    "All code and detailed instructions for usage is available on GitHub at",
+    tags$a(
+      href = "https://github.com/GerkeLab/shinyDAG",
+      "GerkeLab/shinyDag"
+    )
+  ),
+  p(
+    "If you have any questions or comments, we would love to hear them.",
+    "You can email us at",
+    tags$a(href = "mailto:travis.gerke@moffitt.org", "travis.gerke@moffitt.org"),
+    "or",
+    HTML(paste0(
+      tags$a(href = "mailto:jordan.h.creed@moffitt.org", "jordan.h.creed@moffitt.org"),
+      "."
+    )),
+    "Or feel free to",
+    tags$a(
+      href = "https://github.com/GerkeLab/shinyDAG/issues",
+      "open an issue"
+    ),
+    "in our GitHub repository."
+  )
+)
+
+# components$about$usage <- tagList(
+#   tags$h3("Using shinyDAG"),
+#   tags$p(
+#     "For more details on using shinyDAG please check out our",
+#     tags$a(
+#       href = "https://github.com/GerkeLab/shinyDAG/blob/master/README.md",
+#       "README."
+#     ))
+# )
+
+# Components - Build ----
+components$build <- box(
+  title = "Build",
+  id = "build-box",
+  width = 12,
+  fluidRow(
+    id = "shinydag-toolbar",
+    tags$div(
+      class = "col-xs-12 col-md-5 shinydag-toolbar-actions",
+      tags$div(
+        class = "col-xs-12 col-sm-6 col-md-12",
+        id = "shinydag-toolbar-node-list-action",
+        components$toolbar$node_list_action
+      ),
+      tags$div(
+        class = "col-xs-12 col-sm-6 col-md-12",
+        style = "padding: 10px",
+        id = "shinydag-toolbar-clickpad-action",
+        components$toolbar$clickpad_action
+      )
+    ),
+    tags$div(
+      class = "col-xs-12 col-md-7",
+      components$toolbar$node_list_name
+    )
+  ),
+  fluidRow(
+    column(
+      width = 12,
+      tags$div(
+        class = "pull-left",
+        uiOutput("node_list_helptext")
+      ),
+      shinyThings::undoHistoryUI(
+        id = "undo_rv", 
+        class = "pull-right",
+        back_text = "Undo",
+        fwd_text = "Redo"
+      )
+    )
+  ),
+  fluidRow(
+    column(
+      width = 12,
+      clickpad_UI("clickpad", height = "600px", width = "100%")
+    )
+  ),
+  if (getOption("shinydag.debug", FALSE)) fluidRow(
+    column(width = 12, shinyThings::undoHistoryUI_debug("undo_rv"))
+  ),
+  fluidRow(
+    tags$div(
+      class = class_3_col,
+      selectInput("exposureNode", "Exposure", choices = c("None" = ""), width = "100%")
+    ),
+    tags$div(
+      class = class_3_col,
+      selectInput("outcomeNode", "Outcome", choices = c("None" = ""), width = "100%")
+    ),
+    tags$div(
+      class = class_3_col,
+      selectizeInput("adjustNode", "Adjust for...", choices = c("None" = ""), width = "100%", multiple = TRUE)
+    )
+  ),
+  fluidRow(
+    tags$div(
+      class = "col-sm-12",
+      uiOutput("openExpOutcomePaths")
+    )
+  )
+)
+
+# Components - LaTeX ----
+components$latex <- tagList(
+  tags$p(
+    "Use this tab to manually edit the TikZ generated by shinyDAG."
+  ),
+  helpText(
+    "Note that changes made to the TikZ code below will not affect",
+    "the DAG settings in the app. Changes made to the DAG elsewhere",
+    "in shinyDAG will overwrite any changes made to the manually",
+    "edited TikZ code below."
+  ),
+  uiOutput("texEdit")
+)
+
+# Components - Tweak ----
+components$tweak <- tabBox(
+  title = "Edit DAG",
+  id = "tab_control",
+  # ---- Tab: Edit Aesthetics
+  tabPanel(
+    "Edges",
+    value = "edit_edge_aesthetics",
+    selectInput(
+      "arrowShape",
+      "Select arrow head",
+      choices = c(
+        "stealth",
+        "stealth'",
+        "diamond",
+        "triangle 90",
+        "hooks",
+        "triangle 45",
+        "triangle 60",
+        "hooks reversed",
+        "*"
+      ),
+      selected = "stealth"
+    ),
+    uiOutput("edge_aes_ui")
+  ),
+  tabPanel(
+    "Nodes",
+    value = "edit_node_aesthetics",
+    uiOutput("node_aes_ui")
+  ),
+  tabPanel(
+    "Page",
+    value = "edit_page_aesthetics",
+    tags$h3("Margins"),
+    fluidRow(
+      col_4(
+        numericInput("tex_opts_margin_top", "Top", value = 0L, min = 0L, max = 500L, step = 1L)
+      ),
+      col_4(
+        numericInput("tex_opts_margin_right", "Right", value = 0L, min = 0L, max = 500L, step = 1L)
+      ),
+      col_4(
+        numericInput("tex_opts_margin_bottom", "Bottom", value = 0L, min = 0L, max = 500L, step = 1L)
+      ),
+      col_4(
+        numericInput("tex_opts_margin_left", "Left", value = 0L, min = 0L, max = 500L, step = 1L)
+      )
+    )
+  )
+)
+
+# UI - shinyDAG -----------------------------------------------------------
+
+function(request) {
+  dashboardPage(
+    title = "shinyDAG",
+    skin = "black",
+    dashboardHeader(
+      title = "shinyDAG",
+      tags$li(
+        class = "dropdown",
+        actionLink(
+          inputId = "._bookmark_", 
+          label = "Bookmark",
+          icon = icon("link", lib = "glyphicon"),
+          title = "Bookmark shinyDAG's state and get a URL for sharing.",
+          `data-toggle` = "tooltip",
+          `data-placement` = "bottom"
+        )
+      ),
+      tags$li(
+        class = "dropdown",
+        tags$a(
+          href = "https://github.com/gerkelab/shinyDAG/",
+          title = "shinyDAG on GitHub",
+          target = "_blank",
+          icon("github")
+        )
+      ),
+      tags$li(
+        class = "dropdown",
+        tags$a(
+          href = "https://gerkelab.com/project/shinyDAG/",
+          title = "GerkeLab Project Page",
+          target = "_blank",
+          icon("flask")
+        )
+      )
+    ),
+    dashboardSidebar(
+      sidebarMenu(
+        id = "shinydag_page",
+        menuItem("Sketch", tabName = "sketch", icon = icon("share-alt")),
+        menuItem("Tweak", tabName = "tweak", icon = icon("sliders")),
+        menuItem("LaTeX", tabName = "latex", icon = icon("file-text-o")),
+        menuItem("About", tabName = "about", icon = icon("info"))
+      )
+    ),
+    dashboardBody(
+      shinyjs::useShinyjs(),
+      tags$script(src = "shinydag.js", async = TRUE),
+      includeCSS("www/AdminLTE.gerkelab.min.css"),
+      includeCSS("www/_all-skins.gerkelab.min.css"),
+      includeCSS("www/shinydag.css"),
+      chooseSliderSkin("Flat", "#418c7a"),
+      tags$a(
+        href = "https://gerkelab.com", 
+        target = "_blank", 
+        tags$div(class = "gerkelab-logo")
+      ),
+      tabItems(
+        tabItem(
+          tabName = "sketch",
+          components$build
+        ),
+        tabItem(
+          tabName = "tweak",
+          two_column_flips_on_mobile(
+            components$tweak,
+            box(
+              title = "Preview DAG",
+              dagPreviewUI("tweak_preview", include_graph_downloads = TRUE)
+            )
+          )
+        ),
+        tabItem(
+          tabName = "latex",
+          two_column_flips_on_mobile(
+            box(
+              title = "Edit LaTeX",
+              components$latex
+            ),
+            box(
+              title = "Preview LaTeX",
+              dagPreviewUI("latex_preview", include_graph_downloads = FALSE)
+            )
+          )
+        ),
+        tabItem(
+          tabName = "about",
+          box(
+            title = "Examples",
+            width = "12 col-md-6",
+            examples_UI("example")
+          ),
+          box(
+            title = "About shinyDAG",
+            width = "12 col-md-6",
+            components$about$gerkelab
+          )#,
+          # box(
+          #   title = "About shinyDAG",
+          #   width = "12 col-md-6",
+          #   components$about$usage
+          # )
+        )
+      )
+    )
+  )
+}
--- a/apps/shinyDAG-1.0.0/www/AdminLTE.gerkelab.min.css
+++ b/apps/shinyDAG-1.0.0/www/AdminLTE.gerkelab.min.css
--- a/apps/shinyDAG-1.0.0/www/GerkeLab.png
+++ b/apps/shinyDAG-1.0.0/www/GerkeLab.png
--- a/apps/shinyDAG-1.0.0/www/_all-skins.gerkelab.min.css
+++ b/apps/shinyDAG-1.0.0/www/_all-skins.gerkelab.min.css
--- a/apps/shinyDAG-1.0.0/www/examples/README.md
+++ b/apps/shinyDAG-1.0.0/www/examples/README.md
@ -0,0 +1,31 @@
+## Creating Examples
+
+To create a new example, run ShinyDAG locally using the shinydag dev docker file.
+
+Set up your example and then save it as a bookmark.
+
+Note the URL created by shiny for the bookmark, it should end with
+
+```
+?_state_id_=9d49cb0ba72b00f2
+```
+
+Navigate to the `shiny_bookmarks` folder and find the folder with the bookmark token, e.g. `9d49cb0ba72b00f2`.
+
+Copy `values.rds` to `www/examples` and give the file a descriptive name.
+These names are used for the shiny inputs, so keep the characters sane (and no spaces).
+
+Also, save the DAG image into `www/examples` with the same name (not required but a good idea).
+
+Finally, add the description text to `www/examples/examples.yml`.
+Here's an example template that you can copy.
+Note that if you can use HTML in the `description`, but it needs to be valid or it will cause problems on the page.
+
+```yaml
+- name: Classic Confounding
+  description: >
+    This is a description of classic confounding. Descriptions may include
+    <strong>HTML</strong>.
+  file: classic-confounding.rds
+  image: classic-confounding.png
+```
--- a/apps/shinyDAG-1.0.0/www/examples/classic-confounding.png
+++ b/apps/shinyDAG-1.0.0/www/examples/classic-confounding.png
--- a/apps/shinyDAG-1.0.0/www/examples/classic-confounding.rds
+++ b/apps/shinyDAG-1.0.0/www/examples/classic-confounding.rds
--- a/apps/shinyDAG-1.0.0/www/examples/differential-loss-to-follow-up.png
+++ b/apps/shinyDAG-1.0.0/www/examples/differential-loss-to-follow-up.png
--- a/apps/shinyDAG-1.0.0/www/examples/differential-loss-to-follow-up.rds
+++ b/apps/shinyDAG-1.0.0/www/examples/differential-loss-to-follow-up.rds
--- a/apps/shinyDAG-1.0.0/www/examples/examples.yml
+++ b/apps/shinyDAG-1.0.0/www/examples/examples.yml
@ -0,0 +1,23 @@
+- name: Classic Confounding
+  description: >
+    This depicts <em>classic confounding</em>, where a confounder C is a common cause of exposure (E) and outcome (Y).
+  file: classic-confounding.rds
+  image: classic-confounding.png
+  
+- name: Differential Loss to Follow-Up
+  description: >
+    This depicts <em>differential loss to follow up</em>, where patients may be censored (C) depending on their value of L.
+  file: differential-loss-to-follow-up.rds
+  image: differential-loss-to-follow-up.png
+
+- name: Mediator with Confounding
+  description: >
+    This shows a <em>mediator with confounding</em>, where the variable M mediates the effect of E on Y, which is confounded by the variable C.
+  file: mediator-with-confounding.rds
+  image: mediator-with-confounding.png
+  
+- name: Selection Bias
+  description: >
+    This depicts classic <em>selection bias</em>, where C denotes criteria under which the data are observed which, in turn, is a downstream consequence of exposure (E) and outcome (D).
+  file: selection-bias.rds
+  image: selection-bias.png
--- a/apps/shinyDAG-1.0.0/www/examples/mediator-with-confounding.png
+++ b/apps/shinyDAG-1.0.0/www/examples/mediator-with-confounding.png
--- a/apps/shinyDAG-1.0.0/www/examples/mediator-with-confounding.rds
+++ b/apps/shinyDAG-1.0.0/www/examples/mediator-with-confounding.rds
--- a/apps/shinyDAG-1.0.0/www/examples/selection-bias.png
+++ b/apps/shinyDAG-1.0.0/www/examples/selection-bias.png
--- a/apps/shinyDAG-1.0.0/www/examples/selection-bias.rds
+++ b/apps/shinyDAG-1.0.0/www/examples/selection-bias.rds
--- a/apps/shinyDAG-1.0.0/www/shinydag.css
+++ b/apps/shinyDAG-1.0.0/www/shinydag.css
@ -0,0 +1,264 @@
+@import url('https://fonts.googleapis.com/css?family=Lato:300,400,400i,700,700i');
+
+@media (min-width: 768px) and (max-width: 991px) {
+  #shinydag-toolbar-node-list-action {
+    padding-top: 32px;
+  }
+}
+
+/* ---- GerkeLab Admin LTE Theme Tweaks ---- */
+body, h1, h2, h3, h4, h5, h6, .h1, .h2, .h3, .h4, .h5, .h6, .main-header .logo {
+  font-family: Lato, sans-serif;
+}
+
+.main-header > .logo {
+  color: #989898 !important;
+  text-decoration: none;
+  font-weight: bold;
+}
+
+.main-header {
+  position: fixed;
+  width: 100%;
+  box-shadow: 0 3px 3px rgba(0,0,0,0.1) !important;
+  -webkit-box-shadow: 0 3px 3px rgba(0,0,0,0.1) !important;
+}
+
+.wrapper, .content-wrapper {
+  min-height: 100vh !important;
+  height: 100% !important;
+  background-color: #f0f0f0 !important;
+}
+
+@media (max-width:767px) {
+  .content-wrapper {
+    padding-top: 100px;
+  }
+}
+@media (min-width:768px) {
+  .content-wrapper {
+    padding-top: 50px;
+  }
+}
+
+.skin-black .main-header .navbar .navbar-custom-menu .navbar-nav > li > a,
+.skin-black .main-header .navbar .navbar-right > li > a {
+  border-left: none;
+}
+
+.gerkelab-logo {
+  background: url("GerkeLab.png");
+  background-size: contain;
+  width: 100px;
+  height: 100px;
+  position: absolute;
+  bottom: 25px;
+  left: 65px;
+  filter: drop-shadow(0 3px 4px rgba(0,0,0,0.2));
+  transition: z-index 0s, left 0.25s ease-in-out, filter 0.25s ease-in-out, opacity 1s ease-in-out;
+  z-index: 1000;
+  opacity: 1;
+}
+
+.sidebar-collapse .gerkelab-logo {
+  transition: z-index 0s 0.5s, left 0.25s ease-in-out, filter 0.25s ease-in-out;
+  z-index: 0;
+  left: 2%;
+  bottom: 25px;
+}
+
+.sidebar-collapse .gerkelab-logo:hover {
+  filter: drop-shadow(0 0 1px rgba(0,0,0,0.2));
+}
+
+@media (max-width: 767px) {
+  .gerkelab-logo {
+    z-index: 0;
+    opacity: 0;
+  }
+}
+
+.disable-buttons {
+  pointer-events: none;
+}
+
+.disabled {
+  pointer-events: none;
+}
+
+#shiny-tab-sketch .box {
+  margin-bottom: 100px;
+}
+
+.dag-preview-tikz {
+  min-height: 400px;
+}
+
+.example-image {
+  text-align: center;
+}
+
+.example-image img {
+  width: 80%;
+  max-width: 500px;
+}
+
+/* ---- ShinyDAG specific tweaks ---- */
+
+#edge_aes_ui label {
+  color: #777;
+  font-weight: normal;
+}
+
+#showPreviewContainer {
+  padding-top: 32px;
+}
+
+.dagpreview-download-ui {
+  padding-top: 25px;
+}
+
+#node_delete {
+  margin-top: 20px;
+  color: #FFF
+}
+
+#edge_btn {
+  margin-top: 25px;
+  color: #FFF
+}
+
+#ui_edge_swap_btn {
+  margin-top: 25px;
+}
+
+@media (min-width: 768px) {
+  #node_delete {
+    margin-left: -25px;
+  }
+}
+
+.edge-selector-hint {
+  font-size: 28px;
+  line-height: 14px;
+  padding-left: 4px;
+  vertical-align: top;
+}
+
+.help-block {
+  padding-top: 0;
+  font-style: italic;
+}
+
+.help-block.text-warning {
+  color: #db8b0b;
+  background-color: #db8b0b20;
+}
+
+.help-block.text-danger {
+  color: #d33724;
+  background-color: #d3372420;
+}
+
+#edge_list_helptext .help-block, #node_list_helptext .help-block {
+  padding: 0.5em;
+  border-radius: 3px;
+}
+
+.btn-text {
+  padding-left: 5px;
+}
+
+@media (min-width: 992px) and (max-width: 1825px) {
+  .btn-text {
+    display: none;
+  }
+}
+
+.gerkelab-spinner {
+    margin: auto;
+    width: 100px;
+    height: 100px;
+    background: url("GerkeLab.png");
+    background-size: cover;
+    -webkit-animation-name: spin;
+    -webkit-animation-duration: 4000ms;
+    -webkit-animation-iteration-count: infinite;
+    -webkit-animation-timing-function: linear;
+    -moz-animation-name: spin;
+    -moz-animation-duration: 4000ms;
+    -moz-animation-iteration-count: infinite;
+    -moz-animation-timing-function: linear;
+    -ms-animation-name: spin;
+    -ms-animation-duration: 4000ms;
+    -ms-animation-iteration-count: infinite;
+    -ms-animation-timing-function: linear;
+    
+    animation-name: spin;
+    animation-duration: 4000ms;
+    animation-iteration-count: infinite;
+    animation-timing-function: linear;
+}
+@-ms-keyframes spin {
+    from { -ms-transform: rotate(0deg); }
+    to { -ms-transform: rotate(-360deg); }
+}
+@-moz-keyframes spin {
+    from { -moz-transform: rotate(0deg); }
+    to { -moz-transform: rotate(-360deg); }
+}
+@-webkit-keyframes spin {
+    from { -webkit-transform: rotate(0deg); }
+    to { -webkit-transform: rotate(-360deg); }
+}
+@keyframes spin {
+    from {
+        transform:rotate(0deg);
+    }
+    to {
+        transform:rotate(-360deg);
+    }
+}
+
+.alert-edge {
+  animation: fadeout 5s;
+  -moz-animation: fadeout 5s;
+  -webkit-animation: fadeout 5s;
+  -o-animation: fadeout 5s;
+}
+
+@keyframes fadeout {
+    0% {
+        opacity: 1;
+    }
+    75% {
+        opacity: 1;
+    }
+    100% {
+        opacity: 0;
+    }
+}
+
+@-moz-keyframes fadeout {
+    0% {
+        opacity: 1;
+    }
+    75% {
+        opacity: 1;
+    }
+    100% {
+        opacity: 0;
+    }
+}
+
+@-webkit-keyframes fadeout {
+    0% {
+        opacity: 1;
+    }
+    75% {
+        opacity: 1;
+    }
+    100% {
+        opacity: 0;
+    }
+}
--- a/apps/shinyDAG-1.0.0/www/shinydag.js
+++ b/apps/shinyDAG-1.0.0/www/shinydag.js
@ -0,0 +1,78 @@
+const set_input_focus = (id) => {
+  const el = document.getElementById(id);
+  if (el) {
+    el.focus();
+  }
+};
+
+const wrap_btn_text_in_span = (id, text) => {
+  var $el = $("#" + id);
+  $el.html([$el.children()[0], "<span class='btn-text'>" + text + "</span>"]);
+};
+
+$( document ).ready(function() {
+  setTimeout(function() {wrap_btn_text_in_span("downloadButton", "Download")}, 1000);
+  setTimeout(function() {wrap_btn_text_in_span("\\._bookmark_", "Bookmark")}, 1000);
+});
+
+// Block name change updates while Shiny is re-rendering to avoid wonkiness
+var text_input_timeout;
+$(document).on("shiny:busy", (e) => { 
+  text_input_timeout = setTimeout(() => {
+    $("#node_list_node_name").prop("disabled", true);
+  }, 500);
+});
+$(document).on("shiny:idle", (e) => { 
+  clearTimeout(text_input_timeout);
+  $("#node_list_node_name").prop("disabled", false);
+});
+
+// Block node change buttons when updating names to avoid infinite looping wonkiness
+// disables buttons when user starts typing in text box
+$("#node_list_node_name").keydown(() => { 
+  $("#shinydag-toolbar-node-list-action button").prop("disabled", true);
+});
+
+// re-enable buttons when Shiny updates or the text bar loses focus (in case no change)
+$(document).on("shiny:value", () => { 
+  $("#shinydag-toolbar-node-list-action button").prop("disabled", false);
+});
+$("#node_list_node_name").blur(() => { 
+  $("#shinydag-toolbar-node-list-action button").prop("disabled", false);
+});
+
+// Block undo/redo buttons during Shiny updates as well
+var undo_disable_timeout = null;
+$("#undo_rv-history_back, #undo_rv-history_forward").on("click", () => {
+  undo_disable_timeout = setTimeout(() => {
+    $("#undo_rv-history_back").parent().addClass("disable-buttons");
+  }, 10);
+})
+
+// Bock undo/redo with a delay for general Shiny updates
+$(document).on("shiny:busy", () => {
+  if (!undo_disable_timeout) {
+    undo_disable_timeout = setTimeout(() => {
+      $("#undo_rv-history_back").parent().addClass("disable-buttons");
+    }, 250);
+  }
+});
+
+// re-enable undo/redo buttons when Shiny is idle
+$(document).on("shiny:idle", () => {
+  clearTimeout(undo_disable_timeout);
+  undo_disable_timeout = null;
+  $("#undo_rv-history_back").parent().removeClass("disable-buttons");
+});
+
+// Animate logo when app is busy
+var app_busy_timeout;
+$(document).on("shiny:busy", e => { 
+  app_busy_timeout = setTimeout(() => {
+    $(".gerkelab-logo").addClass("gerkelab-spinner"); 
+  }, 500);
+});
+$(document).on("shiny:idle", e => { 
+  clearTimeout(app_busy_timeout);
+  $(".gerkelab-logo").removeClass("gerkelab-spinner"); 
+});
--- a/apps/shinyDAG.R
+++ b/apps/shinyDAG.R
@ -0,0 +1,16 @@
+## -----------------------------------------------------------------------------
+## shinyDAG app
+## -----------------------------------------------------------------------------
+## 
+## Copy from https://github.com/gadenbuie/ShinyDAG for local deployment
+## 
+
+old_wd<-getwd()
+
+setwd(paste0(old_wd,"/apps/shinyDAG-1.0.0"))
+shiny::runApp()
+
+source(paste0(old_wd,"/apps/app_deploy.R"))
+
+setwd(old_wd)
+