Problem using function with reactive data in R Shiny

[HABSaremyjam]

Hello,

I tried seeking help a few weeks ago for this problem but no bites, so I'm redoing it in the hope that someone will be interested in solving this for me, as I don't think it's a very complicated problem, I just don't exactly how to do it.

I'm creating an app that takes a .csv file and spits out concentration values after doing some analysis on the back end. The analysis involves running a 5-parameter logistic curve using the drc() package and then storing the model coefficients to use in a function, which is where I'm running into trouble.

Here is some sample data that can be stored into a .csv file for use in the app:

smpdata <- structure(list(Sample = c("Std 0", "Std 0", "Std 1", "Std 1", 
"Std 2", "Std 2", "Std 3", "Std 3", "Std 4", "Std 4"), Absorbance = c(0.854, 
0.876, 0.736, 0.736, 0.551, 0.569, 0.46, 0.414, 0.312, 0.307), 
    Concentration = c(0, 0, 0.05, 0.05, 0.15, 0.15, 0.4, 0.4, 
    1.5, 1.5)), row.names = c(NA, 10L), class = "data.frame")

Now that we have the data, here is the code input and outputs that I am specifically having an issue with, with my comments.

library(ggplot2)
library(dplyr)
library(tidyverse)
library(drc)

library(shiny)

# function that I need to calculate concentration values
concentration <- function(y){
  
  c*(((a-d)/(y-d))^(1/m)-1)^(1/b)
}

# User uploads the .csv file

ui <- fluidPage(
  titlePanel("Microcystin Concentrations from ELISA using 5 PL Curve"),
  fluidRow(
    h4("Upload Data"),
    column(6,
           fileInput("file", "Choose CSV File",
                     multiple = F,
                     accept = c("text/csv",
                                "text/comma-separated-values,text/plain",
                                ".csv"),
                     placeholder = "CSV files only",
                     width = "100%"))),
# Results from data are shown in a table in the server
  fluidRow(
    h4("Results"),
    column(6,
           verbatimTextOutput("results"))))
)

server <- function(input, output, session) {
  
  data <- reactive({
    req(input$file)
    read.csv(input$file$datapath)
  })
  
  dt <- reactive({
    data() %>%
    filter(!Absorbance == 0) %>%
    group_by(Sample) %>%
    mutate(Mean_Absorbance = mean(Absorbance)) %>%
    distinct(Sample, .keep_all = T) %>%
    dplyr::select(Type, Sample, Mean_Absorbance, Concentration)})
  
  
  stds <- reactive({dt() %>%
      filter(Type == "Standard")})
  
  fiveplc <- reactive({drm(Mean_Absorbance ~ Concentration, data=stds(),
                 fct = LL.5(names = c("b", "d", "a", "c", "e")))})
  
  sum.fiveplc <- reactive({summary(fiveplc())})

# THIS IS WHERE THE APP STOPS WORKING
  output$results <- renderTable({
    
    b <- sum.fiveplc()$coefficients[1] # store model coefficients to variable
    d <- sum.fiveplc()$coefficients[2]
    a <- sum.fiveplc()$coefficients[3]
    c <- sum.fiveplc()$coefficients[4]
    m <- sum.fiveplc()$coefficients[5]
    
    dt()$NewConcentration <- concentration(dt()$Mean_Absorbance)
    
    dt()
  
  })

}

shinyApp(ui, server)

I keep getting errors, in this example, the error is Error: object 'd' not found. I have tried all kinds of different formats. I also tried putting the function within the server as a reactive, but then I got the error Error: unused argument (dt()$Mean_Absorbance).

Can anyone sense what is going on wrong here?

Any help would be vastly appreciated. Thank you so much.

[scottyd22]

Hello @HABSaremyjam. It looks like the issue occurs when trying to add NewConcentration to the reactive dt(). I updated output$results as shown below and changed verbatimTextOutput("results") to tableOutput('results') to match the renderTable() call.

output$results <- renderTable({
    
    # you can't modify a reactive directly, so first save it as a new object within the function
    out = dt()
    
    b <- sum.fiveplc()$coefficients[1] # store model coefficients to variable
    d <- sum.fiveplc()$coefficients[2]
    a <- sum.fiveplc()$coefficients[3]
    c <- sum.fiveplc()$coefficients[4]
    m <- sum.fiveplc()$coefficients[5]
    
    # add the new column to the new object (instead of the reactive)
    out$NewConcentration <- concentration(dt()$Mean_Absorbance)
    
    out
    
  })

In the example below, I altered the data you provided by adding a column Type (that is set to "Standard" for all rows) and saved it out as a .csv file (stds filters for Type == "Standard"). This is the result when the .csv is chosen from the app.