Screening Data

Loading...

The editor below only accepts tab-separated values copied and pasted from Excel/Numbers.


                
                

Type of variables


                

Checking missing/non-numeric values


                

Summary of the data


                

Visualisation of multivariate datasets



Boxplot (applicable for numeric values only)



R session info

              
Note

This web application is developed with Shiny.


List of Packages Used
library(shiny)
library(shinyAce)
library(tabplot)
library(beeswarm)

Code

Source code for this application is based on "The handbook of Research in Foreign Language Learning and Teaching" (Takeuchi & Mizumoto, 2012).

The code for this web application is available at GitHub.

If you want to run this code on your computer (in a local R session), run the code below:
library(shiny)
runGitHub("screenData","mizumot")


Citation in Publications

Mizumoto, A. (2015). Langtest (Version 1.0) [Web application]. Retrieved from http://langtest.jp


Article

Mizumoto, A., & Plonsky, L. (2015). R as a lingua franca: Advantages of using R for quantitative research in applied linguistics. Applied Linguistics, Advance online publication. doi:10.1093/applin/amv025


Recommended

To learn more about R, I suggest this excellent and free e-book (pdf), A Guide to Doing Statistics in Second Language Research Using R, written by Dr. Jenifer Larson-Hall.

Also, if you are a cool Mac user and want to use R with GUI, MacR is defenitely the way to go!


Author

Atsushi MIZUMOTO, Ph.D.
Associate Professor of Applied Linguistics
Faculty of Foreign Language Studies /
Graduate School of Foreign Language Education and Research,
Kansai University, Osaka, Japan



Code for "Screening Data"
by Atsushi Mizumoto

show with app
library(shiny)
library(shinyAce)
library(tabplot)
library(beeswarm)


shinyServer(function(input, output) {


    vartype <- reactive({
        
            dat <- read.csv(text=input$text, header = TRUE, sep="\t", na.strings=c("","NA","."))
            sapply(dat,class)
    
    })
    
    output$vartype.out <- renderPrint({
        vartype()
    })





    missing <- reactive({
        
            dat <- read.csv(text=input$text, header = TRUE, sep="\t", na.strings=c("","NA","."))
            
            # Checking missing values or NAs
            fin <- function(obj){
                sapply(obj,FUN = function(x) all(is.finite(x)))
            }
            
            # Checking non-numeric values
            num <- function(obj){
                sapply(obj,FUN = function(x) all(is.numeric(x)))
            }
            
            res <- data.frame(fin(dat), num(dat))
            colnames(res) <- c("Finite (FALSE=Missing Value)", "Numeric (FALSE=Non-numeric)")
            res
    
    })
    
    output$textarea.out <- renderPrint({
        missing()
    })

    



    min.max <- reactive({
        
            dat <- read.csv(text=input$text, header = TRUE, sep="\t", na.strings=c("","NA","."))
            summary(dat, digits = 1)
    
    })
    
    output$min.max.out <- renderPrint({
        min.max()
    })
    
    
    
    
    
    tabPlot <- function(){
       
        dat <- read.csv(text=input$text, header = TRUE, sep="\t", na.strings=c("","NA","."))
        tableplot(dat)
    
    }
    
    output$tabPlot <- renderPlot({
        print(tabPlot())
    })


    
    

    output$varselect <- renderUI({
        
            dat <- read.csv(text=input$text, header = TRUE, sep="\t", na.strings=c("","NA","."))
            colf <- grep("factor", sapply(dat, class))
            datn <- dat[,-c(colf)] # numeric only
            cols <- names(datn)
            selectInput("vars", "Click the box below and select variables:", choices=cols, multiple=T)

    })
    
    
    
    
    makeboxPlot <- function(){
        
        if (is.null(input$vars)){
            
            NULL
        
        } else {
        
        dat <- read.csv(text=input$text, header = TRUE, sep="\t", na.strings=c("","NA","."))
        dat <- data.frame(dat[,input$vars])
        
        boxplot(dat, las=1, xlab= "Means and +/-1 SDs are displayed in red.")
        
            if (input$beeswarm == 0) {
                NULL
            } else {
                beeswarm(dat, col = 4, pch = 16, vert = TRUE,  add = TRUE)
            }
        
            for (i in 1:ncol(dat)) {
                pts <- 0.2 + i
                mns <- mean(dat[,i], na.rm=TRUE)
                sds <- sd(dat[,i], na.rm=TRUE)
                points(pts, mns, pch = 18, col = "red", cex = 2)
                arrows(pts, mns, pts, mns + sds, length = 0.1, angle = 45, col = "red")
                arrows(pts, mns, pts, mns - sds, length = 0.1, angle = 45, col = "red")
            }

        }
    }
    
    output$boxPlot <- renderPlot({
        print(makeboxPlot())
    })
    
    




    info <- reactive({
        info1 <- paste("This analysis was conducted with ", strsplit(R.version$version.string, " \\(")[[1]][1], ".", sep = "")
        info2 <- paste("It was executed on ", date(), ".", sep = "")
        cat(sprintf(info1), "\n")
        cat(sprintf(info2), "\n")
    })
    
    output$info.out <- renderPrint({
        info()
    })


})
library(shiny)
library(shinyAce)



shinyUI(bootstrapPage(

    headerPanel("Screening Data"),


########## Adding loading message #########

tags$head(tags$style(type="text/css", "
#loadmessage {
position: fixed;
top: 0px;
left: 0px;
width: 100%;
padding: 10px 0px 10px 0px;
text-align: center;
font-weight: bold;
font-size: 100%;
color: #000000;
background-color: #CCFF66;
z-index: 105;
}
")),

conditionalPanel(condition="$('html').hasClass('shiny-busy')",
tags$div("Loading...",id="loadmessage")),

#-----------------------------------------#

    mainPanel(
        tabsetPanel(

        tabPanel("Main",

            p(HTML("<b><div style='background-color:#FADDF2;border:1px solid black;'>The editor below only accepts tab-separated values copied and pasted from Excel/Numbers. </div></b>")),

            aceEditor("text", value="Group\tGender\tAbility\tPre\tPost\nA\tMale\t130\t29\t36\nA\tMale\t152\t37\t35\nA\tMale\t148\t29\t41\nA\tMale\t\t47\t52\nA\tMale\t122\t29\t41\nA\tMale\t126\t17\t35\nA\tMale\t122\t33\t35\nA\tMale\t150\t32\t48\nA\tMale\t148\t34\t39\nA\tMale\t124\t35\t34\nA\tMale\t136\t11\t18\nA\tMale\t128\t29\t48\nA\tMale\t132\t44\t45\nA\tMale\t\t39\t43\nA\tMale\t144\t30\t38\nA\tMale\t130\t36\t27\nA\tMale\t128\t30\t24\nA\tMale\t132\t28\t37\nA\tMale\t124\t38\t38\nA\tMale\t130\t28\t28\nA\tMale\t130\t46\t46\nA\tFemale\t136\t43\t38\nA\tFemale\t\t28\t33\nA\tFemale\t120\t45\t46\nA\tFemale\t138\t28\t24\nA\tFemale\t120\t14\t27\nA\tFemale\t152\t50\t49\nA\tFemale\t136\t30\t30\nA\tFemale\t140\t27\t46\nA\tFemale\t134\t47\t54\nA\tFemale\t122\t32\t38\nA\tFemale\t134\t37\t34\nA\tFemale\t152\t34\t47\nA\tFemale\t90\t26\t32\nA\tFemale\t144\t36\t34\nA\tFemale\t\t27\t38\nA\tFemale\t130\t26\t32\nA\tFemale\t128\t38\t38\nA\tFemale\t140\t38\t37\nA\tFemale\t148\t27\t32\nA\tFemale\t146\t38\t38\nA\tFemale\t134\t29\t32\nB\tMale\t148\t37\t49\nB\tMale\t134\t29\t35\nB\tMale\t102\t22\t31\nB\tMale\t118\t19\t43\nB\tMale\t136\t36\t41\nB\tMale\t152\t35\t53\nB\tMale\t126\t17\t22\nB\tMale\t126\t26\t21\nB\tMale\t136\t41\t51\nB\tMale\t148\t25\t37\nB\tMale\t114\t37\t51\nB\tMale\t128\t38\t47\nB\tMale\t128\t33\t50\nB\tMale\t110\t29\t40\nB\tMale\t128\t30\t37\nB\tMale\t\t23\t40\nB\tMale\t140\t33\t44\nB\tMale\t132\t15\t29\nB\tMale\t124\t32\t40\nB\tMale\t146\t25\t43\nB\tMale\t150\t32\t44\nB\tFemale\t148\t35\t42\nB\tFemale\t138\t27\t40\nB\tFemale\t128\t36\t42\nB\tFemale\t126\t31\t35\nB\tFemale\t138\t24\t37\nB\tFemale\t134\t31\t41\nB\tFemale\t136\t21\t34\nB\tFemale\t134\t28\t40\nB\tFemale\t122\t31\t41\nB\tFemale\t130\t35\t44\nB\tFemale\t142\t31\t34\nB\tFemale\t122\t35\t41\nB\tFemale\t138\t35\t41\nB\tFemale\t140\t36\t45\nB\tFemale\t128\t23\t47\nB\tFemale\t142\t34\t45\nB\tFemale\t140\t44\t50\nB\tFemale\t112\t40\t36\nB\tFemale\t128\t26\t38\nC\tMale\t126\t16\t35\nC\tMale\t\t27\t34\nC\tMale\t96\t20\t23\nC\tMale\t122\t27\t23\nC\tMale\t118\t14\t14\nC\tMale\t134\t26\t41\nC\tMale\t94\t20\t20\nC\tMale\t144\t31\t30\nC\tMale\t112\t30\t43\nC\tMale\t126\t22\t24\nC\tMale\t146\t37\t43\nC\tMale\t128\t36\t34\nC\tMale\t134\t26\t39\nC\tMale\t128\t30\t34\nC\tMale\t116\t15\t20\nC\tMale\t116\t28\t33\nC\tMale\t140\t24\t29\nC\tMale\t152\t39\t41\nC\tMale\t134\t29\t36\nC\tMale\t\t19\t23\nC\tMale\t130\t34\t27\nC\tFemale\t132\t21\t35\nC\tFemale\t104\t12\t15\nC\tFemale\t110\t30\t39\nC\tFemale\t130\t18\t31\nC\tFemale\t126\t25\t38\nC\tFemale\t118\t21\t36\nC\tFemale\t98\t16\t26\nC\tFemale\t126\t33\t43\nC\tFemale\t100\t28\t36\nC\tFemale\t134\t32\t32\nC\tFemale\t122\t35\t29\nC\tFemale\t134\t20\t20\nC\tFemale\t144\t36\t38\nC\tFemale\t\t16\t24\nC\tFemale\t126\t37\t39\nC\tFemale\t120\t29\t21\nC\tFemale\t142\t20\t21\nC\tFemale\t132\t24\t22\nC\tFemale\t122\t26\t32\nC\tFemale\t138\t37\t27",
                mode="r", theme="cobalt"),

            br(),

            h3("Type of variables"),
            verbatimTextOutput("vartype.out"),

            br(),

            h3("Checking missing/non-numeric values"),
            verbatimTextOutput("textarea.out"),

            br(),

            h3("Summary of the data"),
            verbatimTextOutput("min.max.out"),

            br(),

            h3("Visualisation of multivariate datasets"),
            plotOutput("tabPlot", width="100%"),

            br(),
            br(),

            h3("Boxplot (applicable for numeric values only)"),
            uiOutput("varselect"),
            checkboxInput("beeswarm", label = strong("Plot individual data points."), value = T),

            plotOutput("boxPlot"), #, width="80%"

            br(),
            br(),

            strong('R session info'),
            verbatimTextOutput("info.out")

            ),


        tabPanel("About",

            strong('Note'),
            p('This web application is developed with',
            a("Shiny.", href="http://www.rstudio.com/shiny/", target="_blank"),
            ''),

            br(),

            strong('List of Packages Used'), br(),
            code('library(shiny)'),br(),
            code('library(shinyAce)'),br(),
            code('library(tabplot)'),br(),
            code('library(beeswarm)'),br(),

            br(),

            strong('Code'),
            p('Source code for this application is based on',
            a('"The handbook of Research in Foreign Language Learning and Teaching" (Takeuchi & Mizumoto, 2012).', href='http://mizumot.com/handbook/', target="_blank")),

            p('The code for this web application is available at',
            a('GitHub.', href='https://github.com/mizumot/screenData', target="_blank")),

            p('If you want to run this code on your computer (in a local R session), run the code below:',
            br(),
            code('library(shiny)'),br(),
            code('runGitHub("screenData","mizumot")')
            ),

            br(),

            strong('Citation in Publications'),
            p('Mizumoto, A. (2015). Langtest (Version 1.0) [Web application]. Retrieved from http://langtest.jp'),

            br(),

            strong('Article'),
            p('Mizumoto, A., & Plonsky, L. (2015).', a("R as a lingua franca: Advantages of using R for quantitative research in applied linguistics.", href='http://applij.oxfordjournals.org/content/early/2015/06/24/applin.amv025.abstract', target="_blank"), em('Applied Linguistics,'), 'Advance online publication. doi:10.1093/applin/amv025'),

            br(),

            strong('Recommended'),
            p('To learn more about R, I suggest this excellent and free e-book (pdf),',
            a("A Guide to Doing Statistics in Second Language Research Using R,", href="http://cw.routledge.com/textbooks/9780805861853/guide-to-R.asp", target="_blank"),
            'written by Dr. Jenifer Larson-Hall.'),

            p('Also, if you are a cool Mac user and want to use R with GUI,',
            a("MacR", href="https://sites.google.com/site/casualmacr/", target="_blank"),
            'is defenitely the way to go!'),

            br(),

            strong('Author'),
            p(a("Atsushi MIZUMOTO,", href="http://mizumot.com", target="_blank"),' Ph.D.',br(),
            'Associate Professor of Applied Linguistics',br(),
            'Faculty of Foreign Language Studies /',br(),
            'Graduate School of Foreign Language Education and Research,',br(),
            'Kansai University, Osaka, Japan'),

            br(),

            a(img(src="http://i.creativecommons.org/p/mark/1.0/80x15.png"), target="_blank", href="http://creativecommons.org/publicdomain/mark/1.0/"),

            p(br())

            )

))
))
Code license: GPL-3