Structural Equation Modeling (SEM)

Code for "Structural Equation Modeling (SEM)"
by Atsushi Mizumoto

server.R
ui.R

library(shiny)
library(shinyAce)
library(psych)
library(lavaan)
library(semPlot)


shinyServer(function(input, output) {
    
    
    
    bs <- reactive({
        x <- read.csv(text=input$text, sep="\t")
        describe(x)[2:13]
    })
    
    
    
    correl <- reactive({
        x <- read.csv(text=input$text, sep="\t")
        round(cor(cbind(x), use = "complete"),3)
    })
    
    
    makecorPlot <- function(){
        x <- read.csv(text=input$text, sep="\t")
        pairs.panels(x)
    }
    
    output$corPlot <- renderPlot({
        print(makecorPlot())
    })
    
    
    get.text <- reactive({
        input$spec
    })
    
    
    
    est <- reactive({
        dat <- read.csv(text=input$text, sep="\t")
        
        model <- get.text()
        
        fit <- sem(model, data=dat)

        list(fit = fit) #他で使用するため
    })
    
    
    
    result <- reactive({
        
        res <- est()$fit
        summary(res, standardized=TRUE, fit.measures=TRUE)
        
    })
    
    
    
    
    
    makesPlot1 <- function(){
        res <- est()$fit
        semPaths(res, "par", mar=c(3,4,3,4), style="lisrel", edge.label.cex=.8, fade=F, gray=T)
    }


    output$sPlot1 <- renderPlot({
        print(makesPlot1())
     })
    




    makesPlot2 <- function(){
        res <- est()$fit
        semPaths(res, "std", mar=c(3,4,3,4), style="lisrel", edge.label.cex=.8, fade=F, gray=T)
    }

    output$sPlot2 <- renderPlot({
        print(makesPlot2())
    })
    
    
    
    
    
    info <- reactive({
        info1 <- paste("This analysis was conducted with ", strsplit(R.version$version.string, " \\(")[[1]][1], ".", sep = "")# バージョン情報
        info2 <- paste("It was executed on ", date(), ".", sep = "")# 実行日時
        cat(sprintf(info1), "\n")
        cat(sprintf(info2), "\n")
    })
    
    output$info.out <- renderPrint({
        info()
    })





    output$textarea.out <- renderPrint({
        bs()
    })

    output$correl.out <- renderPrint({
        correl()
    })
    
    output$result.out <- renderPrint({
        result()
    })


})

library(shiny)
library(shinyAce)


shinyUI(bootstrapPage(

    headerPanel("Structural Equation Modeling (SEM)"),

########## 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")),

########## Added up untill here ##########

    mainPanel(
        tabsetPanel(

        tabPanel("Main",

            p('Estimation may take a few seconds to minutes depending on the dataset.'),

            h3("Data"),
            p('Input values must be separated by tabs. Copy and paste from Excel/Numbers.'),
            p(HTML("<b><div style='background-color:#FADDF2;border:1px solid black;'>Please make sure that your data includes the header (variable names) in the first row.</div></b>")),

            aceEditor("text", value="Midterm\tFinal\tQuiz\tExam1\tExam2\tExam3\n68\t32\t39\t47\t22\t37\n50\t18\t28\t27\t17\t32\n55\t32\t39\t40\t50\t42\n86\t73\t94\t87\t100\t89\n95\t95\t100\t87\t100\t84\n59\t36\t67\t27\t50\t16\n91\t91\t100\t100\t100\t95\n45\t36\t39\t40\t33\t32\n59\t27\t17\t27\t17\t26\n59\t32\t67\t47\t50\t47\n64\t45\t61\t13\t33\t37\n77\t55\t67\t47\t44\t37\n59\t45\t67\t33\t39\t42\n59\t45\t61\t40\t39\t16\n55\t50\t67\t27\t28\t37\n73\t50\t44\t53\t44\t32\n59\t45\t44\t33\t33\t37\n55\t36\t61\t40\t28\t26\n64\t45\t39\t40\t33\t37\n50\t50\t67\t60\t56\t63\n41\t36\t39\t53\t33\t26\n59\t23\t72\t47\t44\t26\n59\t32\t61\t27\t39\t37\n64\t36\t72\t53\t44\t42\n64\t23\t33\t33\t22\t47\n73\t32\t39\t47\t44\t47\n68\t55\t67\t40\t44\t42\n45\t36\t61\t47\t22\t32\n64\t41\t94\t67\t44\t58\n59\t41\t50\t27\t39\t47\n36\t23\t39\t27\t28\t16\n73\t27\t67\t27\t56\t16\n64\t41\t50\t13\t56\t26\n50\t55\t22\t40\t28\t42\n68\t59\t61\t47\t33\t47\n59\t45\t72\t33\t33\t42\n59\t41\t50\t47\t33\t26\n55\t41\t33\t20\t44\t37\n41\t45\t67\t20\t56\t47\n41\t36\t61\t27\t61\t32\n50\t45\t67\t53\t61\t42\n59\t41\t50\t73\t61\t32\n73\t32\t61\t53\t39\t26\n36\t55\t61\t53\t50\t32\n50\t41\t78\t60\t39\t47\n64\t50\t67\t53\t56\t37\n73\t59\t78\t67\t67\t58\n77\t82\t83\t87\t89\t79\n36\t36\t33\t60\t44\t37\n45\t18\t39\t33\t11\t21\n64\t27\t44\t33\t39\t26\n91\t91\t100\t100\t89\t89\n64\t41\t72\t40\t56\t68\n59\t27\t67\t27\t28\t21\n68\t36\t56\t20\t11\t16\n55\t23\t67\t33\t61\t11\n68\t23\t61\t40\t61\t32\n68\t45\t72\t60\t61\t58\n50\t32\t61\t27\t33\t32\n59\t36\t50\t40\t50\t32\n73\t64\t78\t80\t78\t68\n91\t64\t83\t93\t78\t47\n55\t32\t56\t40\t33\t11\n64\t55\t61\t40\t28\t47\n68\t64\t78\t67\t72\t63\n91\t86\t100\t93\t100\t100\n55\t50\t72\t67\t44\t42\n68\t41\t44\t53\t50\t42\n64\t41\t56\t40\t39\t21\n86\t55\t89\t53\t50\t42\n64\t55\t61\t47\t50\t26\n64\t55\t72\t40\t22\t32\n64\t64\t72\t27\t44\t53\n59\t50\t56\t40\t28\t26\n59\t32\t33\t33\t22\t5\n64\t50\t50\t47\t44\t32\n82\t68\t89\t73\t89\t58\n77\t73\t72\t60\t83\t63\n73\t41\t44\t27\t44\t42\n68\t50\t67\t47\t33\t21\n68\t45\t67\t60\t50\t37\n41\t41\t44\t40\t50\t37\n73\t73\t72\t60\t61\t21\n73\t45\t44\t40\t50\t42\n59\t50\t83\t53\t61\t74\n55\t45\t44\t47\t22\t37\n64\t41\t44\t40\t28\t32\n77\t59\t67\t87\t67\t58\n68\t23\t56\t53\t44\t26\n59\t45\t39\t27\t33\t16\n86\t55\t83\t53\t89\t37\n55\t41\t33\t20\t11\t5\n64\t32\t56\t53\t56\t37\n73\t41\t72\t33\t61\t47\n73\t59\t39\t47\t56\t42\n59\t41\t72\t20\t44\t32\n45\t23\t50\t27\t28\t37\n45\t41\t61\t33\t44\t11\n68\t50\t61\t60\t44\t37\n95\t95\t100\t100\t100\t100\n68\t41\t39\t27\t28\t21\n86\t86\t100\t100\t100\t89\n77\t23\t50\t20\t22\t26\n45\t23\t22\t27\t44\t26\n68\t32\t33\t20\t17\t26\n64\t55\t67\t33\t72\t37\n55\t41\t78\t27\t56\t37\n82\t55\t72\t40\t44\t21\n45\t32\t50\t20\t28\t32\n59\t41\t72\t40\t44\t37\n68\t36\t67\t40\t28\t42\n55\t32\t67\t40\t11\t37\n68\t64\t72\t33\t11\t26\n50\t36\t50\t33\t22\t21\n50\t23\t44\t20\t17\t16\n64\t36\t50\t13\t44\t32\n59\t41\t50\t33\t22\t26\n64\t32\t61\t47\t33\t26\n68\t64\t72\t80\t61\t63\n59\t41\t50\t13\t39\t26\n50\t36\t72\t53\t44\t37\n59\t50\t67\t47\t33\t32\n68\t45\t56\t53\t61\t42\n73\t36\t22\t40\t22\t26\n73\t45\t39\t47\t39\t32\n64\t36\t67\t53\t39\t32\n45\t36\t67\t33\t61\t47\n64\t32\t78\t0\t28\t26\n68\t18\t44\t40\t39\t11\n64\t32\t39\t33\t17\t37\n64\t55\t61\t40\t56\t26\n55\t45\t44\t20\t28\t37\n55\t27\t61\t13\t17\t26\n50\t23\t61\t47\t39\t21\n55\t36\t33\t13\t28\t16\n64\t36\t44\t33\t28\t11\n64\t27\t72\t40\t22\t21\n77\t59\t56\t47\t72\t53\n64\t18\t28\t13\t22\t21\n64\t45\t67\t33\t56\t26\n68\t50\t78\t40\t44\t53\n59\t50\t67\t40\t72\t42\n55\t55\t56\t40\t33\t32\n64\t9\t39\t13\t33\t26\n55\t36\t61\t33\t50\t26\n55\t27\t56\t33\t22\t37\n50\t27\t67\t53\t56\t42\n59\t59\t67\t53\t22\t47\n73\t50\t44\t33\t44\t42\n68\t45\t50\t47\t61\t26\n55\t27\t56\t47\t44\t42\n59\t27\t56\t33\t39\t26\n73\t50\t78\t47\t50\t47\n68\t41\t72\t67\t89\t58\n59\t23\t44\t33\t6\t26\n82\t59\t78\t73\t83\t53\n59\t59\t67\t40\t67\t53\n73\t32\t61\t47\t11\t42\n59\t45\t67\t67\t50\t58\n73\t32\t67\t33\t28\t26\n55\t50\t39\t20\t44\t42\n59\t27\t61\t40\t44\t58\n73\t68\t89\t53\t61\t58\n73\t36\t61\t53\t72\t42\n68\t59\t89\t40\t33\t42\n64\t41\t61\t47\t33\t42\n77\t50\t61\t60\t56\t47\n55\t55\t56\t40\t44\t53\n50\t36\t56\t40\t56\t26\n64\t18\t78\t40\t33\t16\n59\t36\t67\t53\t72\t37\n64\t36\t61\t40\t44\t37\n59\t41\t56\t27\t39\t37\n68\t45\t56\t53\t50\t37\n77\t36\t44\t60\t33\t21\n59\t23\t50\t33\t17\t42\n55\t36\t56\t40\t33\t42\n82\t59\t67\t53\t61\t63\n55\t9\t39\t33\t22\t21\n77\t36\t72\t47\t44\t26\n55\t18\t39\t60\t39\t16\n55\t45\t56\t40\t28\t32\n59\t36\t67\t20\t28\t26\n64\t45\t67\t73\t33\t26\n59\t45\t28\t40\t39\t21\n50\t41\t78\t47\t56\t37\n77\t32\t72\t47\t67\t47\n64\t36\t61\t7\t33\t37\n64\t41\t44\t60\t39\t32\n45\t36\t67\t40\t50\t21\n68\t55\t61\t20\t17\t26\n64\t41\t67\t47\t44\t32\n59\t32\t39\t27\t39\t37\n27\t18\t22\t40\t39\t16\n55\t41\t44\t20\t28\t26\n68\t32\t61\t33\t39\t42\n45\t32\t33\t27\t44\t21\n68\t45\t67\t60\t89\t42\n59\t5\t50\t13\t22\t21\n77\t32\t56\t40\t39\t37\n86\t55\t72\t53\t72\t63\n55\t18\t61\t33\t33\t32\n50\t45\t72\t53\t33\t32\n59\t27\t56\t13\t33\t16\n59\t18\t67\t13\t22\t11\n68\t55\t56\t67\t44\t63\n77\t27\t61\t53\t56\t37\n68\t32\t61\t27\t39\t53\n41\t23\t56\t7\t44\t11\n64\t50\t61\t33\t28\t21\n41\t14\t33\t20\t28\t26\n64\t23\t33\t20\t28\t37\n59\t27\t56\t20\t22\t26\n64\t41\t56\t53\t44\t37\n59\t45\t61\t33\t56\t47\n50\t45\t61\t40\t22\t37\n50\t32\t56\t20\t22\t32\n55\t41\t50\t20\t28\t16\n64\t41\t44\t27\t39\t37\n45\t36\t22\t27\t28\t21\n68\t32\t44\t53\t50\t42\n55\t23\t61\t33\t28\t37\n55\t18\t67\t33\t44\t42\n55\t23\t39\t33\t33\t21\n55\t36\t72\t47\t50\t37\n55\t36\t44\t13\t17\t21\n50\t41\t72\t53\t39\t42\n68\t55\t56\t40\t44\t21\n55\t41\t67\t47\t61\t32\n64\t41\t61\t33\t33\t37\n41\t41\t33\t53\t56\t26\n59\t55\t72\t80\t72\t53\n64\t77\t67\t20\t50\t47\n73\t45\t67\t67\t72\t58\n64\t59\t83\t73\t78\t37\n59\t55\t67\t67\t44\t42\n55\t45\t72\t80\t83\t53\n73\t36\t61\t47\t50\t42\n77\t59\t83\t67\t78\t47\n45\t36\t50\t47\t28\t47\n68\t68\t83\t67\t67\t68\n73\t23\t56\t47\t56\t42\n82\t73\t67\t80\t72\t58\n64\t32\t67\t20\t22\t32\n64\t45\t83\t73\t78\t63\n73\t73\t72\t100\t94\t84\n86\t73\t83\t60\t72\t68\n82\t73\t89\t80\t83\t58\n73\t55\t72\t67\t72\t74\n77\t59\t67\t87\t61\t63\n64\t45\t56\t33\t33\t32\n86\t77\t78\t73\t56\t42\n55\t50\t67\t53\t67\t42\n59\t41\t50\t67\t56\t58\n68\t27\t61\t53\t39\t42\n50\t36\t72\t53\t56\t26\n59\t36\t72\t67\t50\t37\n64\t50\t72\t40\t50\t32\n41\t32\t61\t40\t50\t53\n64\t50\t78\t33\t33\t37\n77\t64\t72\t67\t67\t68\n64\t27\t61\t40\t56\t26\n55\t55\t44\t47\t50\t37\n64\t41\t50\t60\t33\t58\n64\t32\t61\t40\t56\t58\n55\t27\t72\t47\t22\t32\n50\t32\t61\t60\t44\t37\n68\t59\t78\t80\t72\t79\n55\t41\t67\t53\t61\t58\n59\t41\t50\t60\t89\t68\n86\t86\t94\t93\t83\t84\n68\t41\t39\t27\t22\t42\n73\t36\t28\t33\t39\t32\n64\t32\t67\t60\t33\t42\n55\t41\t44\t47\t44\t16\n68\t36\t67\t47\t56\t37\n73\t55\t61\t47\t39\t26\n77\t64\t78\t53\t67\t58\n59\t23\t39\t47\t0\t32\n95\t95\t100\t100\t94\t100\n95\t95\t100\t100\t100\t100\n82\t82\t83\t93\t94\t89\n45\t18\t22\t7\t17\t26\n95\t86\t94\t100\t100\t95",
                mode="r", theme="terminal"),

            br(),

            h3("Specifying the model"),
            p('See',
            a("lavaan", href="http://lavaan.ugent.be/", target="_blank"),
            'for the syntax.'),

            aceEditor("spec", mode="r", value="# latent variables\nAchievement =~ Midterm + Final + Quiz\nProficiency =~ Exam1 + Exam2 + Exam3\n# regression\nProficiency ~ Achievement\n"),

            br(),

            h3("Basic statistics"),
            verbatimTextOutput("textarea.out"),

            br(),

            h3("Correlation"),
            verbatimTextOutput("correl.out"),

            br(),

            strong("Scatter plot matrices"),
            br(),

            plotOutput("corPlot"),

            br(),

            h3("SEM result"),

            verbatimTextOutput("result.out"),

            br(),

            h3("Path diagram (Unstandardized estimates)"),

            plotOutput("sPlot1"),

            br(),

            h3("Path diagram (Standardized estimates)"),

            plotOutput("sPlot2"),

            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(psych)'),br(),
            code('library(lavaan)'),br(),
            code('library(semPlot)'),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/sem', 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("sem","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(),
            '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

Structural Equation Modeling (SEM)

Data

Specifying the model

Basic statistics

Correlation

SEM result

Path diagram (Unstandardized estimates)

Path diagram (Standardized estimates)

Code for "Structural Equation Modeling (SEM)" by Atsushi Mizumoto

Code for "Structural Equation Modeling (SEM)"
by Atsushi Mizumoto