Shiny应用中已定义变量Z未被识别问题求助

我在Shiny应用中尝试使用变量Z，但系统提示该变量不存在。明明在lme函数调用的前几行就定义了Z，为何Z的数值无法被保留？

应用代码 #

#
# This is a Shiny web application. You can run the application by clicking
# the 'Run App' button above.
#
# Find out more about building applications with Shiny here:
#
#    http://shiny.rstudio.com/
#

library(shiny)
library(nlme)

# Define UI for application that draws a histogram

ui = fluidPage(
  titlePanel("Use csv"),
  sidebarLayout(
    sidebarPanel(
      fileInput('file1', 'Choose csv file',
                accept = c(".csv")
      ),
      sliderInput("p",
                  "p:",
                  min = -2,
                  max = 3,
                  value = 1),
      sliderInput("q",
                  "q:",
                  min = -2,
                  max = 3,
                  value = 2),
    ),

    mainPanel(
      plotOutput('sscPlot')
    )
  )
)

server = function(input, output){
 
  output$sscPlot<-renderPlot({
    inFile <- input$file1
    
    if(is.null(inFile))
      return(NULL)
    file.rename(inFile$datapath,
                paste(inFile$datapath, ".csv", sep=""))
    df=read.csv(paste(inFile$datapath, ".csv", sep=""), 1)
    
    visit=df$visit
    K=round(length(unique(visit))/4)
    knots=quantile(unique(visit), seq(0.05, 0.95, length=K))
    Z=outer(visit,knots,"-")
    Z=Z*(Z>0)

    model=lme(data=df, y ~ group + visit, random=list(group=pdIdent(~Z+-1), id=~1))
    
    plot(1:10)
  })
}



# Run the application 
shinyApp(ui = ui, server = server)

错误信息 #

Warning: Error in eval: object 'Z' not found

测试数据 #

structure(list(id = c(101, 102, 102, 103, 103, 103, 104, 104, 
104, 104, 104, 105, 105, 105, 105, 105, 106, 106, 106, 106, 106, 
107, 107, 107, 107, 107, 108, 108, 108, 108), visit = c(0, 0, 
4, 0, 28, 27, 0, 20, 19, 15, 6, 0, 12, 29, 27, 14, 0, 15, 1, 
26, 5, 0, 9, 28, 19, 3, 0, 19, 4, 6), y = c(-1, -1, -1, -1, 0, 
0, -1, 0, -1, 0, 1, -1, 1, 0, 1, 0, -1, -1, -1, 0, -1, -1, -1, 
1, -1, 0, -1, 0, 0, 1), group = structure(c(1L, 2L, 2L, 2L, 2L, 
2L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 1L, 1L, 1L, 1L, 1L, 
2L, 2L, 2L, 2L, 2L, 1L, 1L, 1L, 1L), .Label = c("0", "1"), class = "factor")), row.names = c(NA, 
-30L), class = c("tbl_df", "tbl", "data.frame"))

原因与解决方法 #

原因 #

lme函数解析公式时，只会在data参数指定的数据框（此处为df）范围内查找变量。你定义的Z是独立于df的外部变量，因此函数无法在指定数据源中找到它，从而报错。

解决方法 #

将Z合并到数据框df中，让lme能从指定数据源读取该变量。修改后的server函数代码如下：

server = function(input, output){
 
  output$sscPlot<-renderPlot({
    inFile <- input$file1
    
    if(is.null(inFile))
      return(NULL)
    file.rename(inFile$datapath,
                paste(inFile$datapath, ".csv", sep=""))
    # 明确指定row.names参数，避免歧义
    df=read.csv(paste(inFile$datapath, ".csv", sep=""), row.names = 1)
    
    visit=df$visit
    K=round(length(unique(visit))/4)
    knots=quantile(unique(visit), seq(0.05, 0.95, length=K))
    Z=outer(visit,knots,"-")
    Z=Z*(Z>0)
    
    # 将Z合并到数据框df中
    df <- cbind(df, Z)
    
    # 此时lme可从df中读取Z变量
    model=lme(data=df, y ~ group + visit, random=list(group=pdIdent(~Z+-1), id=~1))
    
    plot(1:10)
  })
}

补充说明 #

• Z是矩阵类型，cbind后会自动将其列命名为Z.1、Z.2等，lme的公式~Z+-1会自动识别整个矩阵作为随机效应的设计矩阵，无需额外修改公式。
• 原代码中read.csv的第二个参数1建议明确写成row.names=1，避免因参数位置歧义导致的读取错误。

内容的提问来源于stack exchange，提问作者Vons