Having trouble running Shiny app script for mini meta analysis

Question

I'm trying to load a script from a seminar on meta analysis, which supposedly gives you an app/tool to run meta analysis. The script looks like this:

if(!require(shiny)){install.packages('shiny')}
if(!require(shinythemes)){install.packages('shinythemes')}
if(!require(rstudioapi)){install.packages('rstudioapi')}

library(shiny)
library(shinythemes)
ui <- fluidPage(theme=shinytheme("flatly"),
                titlePanel("Mini meta-analysis of your own studies (correlations)"),
                sidebarLayout(
                  sidebarPanel(
                    h6("To create the mini meta-analysis, you need to upload a CSV file with the following columns:"),                
                    h6("Study: Name of the study/experiment [String]"),        
                    h6("N    : Sample size"),                    
                    h6("R    : Correlation between X and Y"),
                    fileInput("file1", "Choose CSV File",
                              accept = c(
                                "text/csv",
                                "text/comma-separated-values,text/plain",
                                ".csv"))
                  ),
                  mainPanel(h3("Loaded file:"), br(),
                            tableOutput("fileload"), br(),
                            h3("Meta analysis Results:"), br(),
                            h5(verbatimTextOutput("metaresult")), br(),
                            plotOutput("forestplot"),br(),
                            plotOutput("funnelplot"),br(),
                            h3("Test for asymmetry & trim-fill procedure"), br(),
                            h5(verbatimTextOutput("metaresult3")), br(),                            
                            h5(verbatimTextOutput("metaresult2")), br(),                            
                            plotOutput("funnelplottrim"))
                )
)

server <- function(input, output) {
  
  this.dir <- dirname(rstudioapi::getActiveDocumentContext()$path)
  setwd(this.dir)
  source("minimetacor.R")
  
  
  InFile <- reactive({
    
    validate(
      need(input$file1, "Choose a file to see meta-analysis output results!")
    )
    
    inFile <- input$file1
    
    if (is.null(inFile))
      return(NULL)
    
    idataset <- read.table(inFile$datapath, header=TRUE, sep=",", na.strings="NA", dec=".", strip.white=TRUE)
    
  })
  
  MetaFile <- reactive({
    idata <-InFile()
    odataset<-CorMeta(idata$R, idata$N,idata$Study)
  })
  
  
  
  output$forestplot <- renderPlot({
    
    PrintPlotMetaR(MetaFile())
  })
  
  output$metaresult <- renderPrint({ 
    summary(MetaFile())
  })
  
  output$metaresult2 <- renderPrint({ 
    taf <- trimfill(MetaFile())
    taf
  })
  
  output$metaresult3 <- renderPrint({ 
    regtest(MetaFile())
  })
  
  output$fileload <- renderTable({ 
    
    InFile()
    
  })
  
  output$funnelplot <- renderPlot({
    
    PrintFunnelMetaR(MetaFile())
  })
  
  output$funnelplottrim <- renderPlot({
    taf <- trimfill(MetaFile())
    taf
    PrintFunnelMetaR(taf)
  })
  
}
shinyApp(ui = ui, server = server)

However when I ran it, it briefly showed what I wanted, then gave me this error:

Listening on http://127.0.0.1:4427 Warning: Error in setwd: cannot change working directory 50: setwd 49: server [#4] Error in setwd(this.dir) : cannot change working directory

I'm not sure what this means. I assume its referring to this specific part of the code, however, I'm not sure if I should fiddle with this:

  this.dir <- dirname(rstudioapi::getActiveDocumentContext()$path)
  setwd(this.dir)
  source("minimetacor.R")

Can anybody offer some insight? I don't wanna edit the wrong thing and it becomes unworkable.

Are you running this from inside RStudio? Have you saved the script file in the same place that the `minimetacor.R` file exists? You can try commending out the first two of the three lines you highlighted and just keep the `source()` one. It's not really a good practice to put `setwd()` in a script anyway, — MrFlick, Aug 18 '21 at 02:01
As far as I'm aware, I don't have such a file, I only copied this script and pasted it into R Studio. I deleted the first two parts you mentioned and it spit out this: Listening on http://127.0.0.1:6565 Warning in file(filename, "r", encoding = encoding) : cannot open file 'minimetacor.R': No such file or directory Warning: Error in file: cannot open the connection 51: file 50: source 49: server [#4] Error in file(filename, "r", encoding = encoding) : cannot open the connection — Shawn Hemelstrand, Aug 18 '21 at 02:13
Well make sure to save the file after copy/pasting into RStudio. And you'll need to locate and download the `minimetacor.R` file as well. You'll have to ask whomever gave the seminar or created the tool where that file is. — MrFlick, Aug 18 '21 at 02:22
I think I found that same file somewhere in his dropbox. Is there somewhere specific I should save each file? — Shawn Hemelstrand, Aug 18 '21 at 02:43
Save both files in the same folder. Then open the non-"minimetacor" file in RStudio, but this time run the original code without the lines removed. — MrFlick, Aug 18 '21 at 02:44
Not sure why my previous comment wasn't saved, but it worked! Thanks a bunch. I've included an answer to the problem below. — Shawn Hemelstrand, Aug 18 '21 at 03:04

score 0 · Accepted Answer · answered Aug 18 '21 at 02:59

It looks like I just needed to download another file, the "minimetacor" file shown in this directory code I mentioned:

  this.dir <- dirname(rstudioapi::getActiveDocumentContext()$path)
  setwd(this.dir)
  source("minimetacor.R")

Once I downloaded both the minimetacor file and downloaded the script I was using, I put them in the same folder and ran the script again. It worked right away.

Thanks to MrFlick for the help!

Having trouble running Shiny app script for mini meta analysis

1 Answers1