Error in eval(predvars, data, env) : object 'Practice' not found

Question

I have the code below, but I have error when executing the FUN function

library(table1)
library(RVAideMemoire)

Practice<-c(rep("Clippings",14),rep("Irrigation",14),rep("MowHeight",14),rep("SoilTest",14))
Response<-c(rep("No",23),rep("Yes",33))
Student<-c(rep("a",4),rep("b",4),rep("c",4),rep("d",4),rep("e",4),rep("f",4),rep("g",4),rep("h",4),rep("i",4),rep("j",4),rep("k",4),rep("l",4),rep("m",4),rep("n",4))
dataset<-data.frame(Practice,Student,Response)

Fun<-function(data,var,Response,ID) {
  
  
  tab<-table1(~ Response | var, data=data,topclass="Rtable1-zebra")
  tab<-as.data.frame(tab)
  
  test<-cochran.qtest(Response ~ var | ID,data = data)

  pvalue<-test$p.value
  
  list<-c(pvalue,tab)
  
  return(list)
}


Fun(dataset,Practice,Response,Student)

I want to print both pvalue and tab, and this is the error I got

is there any possibility to correct it ?

The function `table1` is not defined, can you please post it or the package where we can find it? — Rui Barradas, Dec 05 '21 at 14:58

Rui Barradas · Accepted Answer · 2021-12-05T15:26:46.947

Base function table is not finding the variables, they must be extracted from the data but not with the operator $, see this SO post.

Fun <- function(data, var, Response, ID) {
  
  v <- deparse(substitute(var))
  r <- deparse(substitute(Response))

  tab <- table1(~ Response | var, data=data, topclass = "Rtable1-zebra")
  tab <- as.data.frame(tab)
  
  tbl <- table(data[[v]], data[[r]])
  test <- chisq.test(tbl)
  
  pvalue <- test$p.value
  
  list(p.value = pvalue, table = tab)
}

Fun(dataset, Practice, Response, Student)
#$p.value
#[1] 2.82287e-09
#
#$table
#           Clippings Irrigation MowHeight  SoilTest    Overall
#1             (N=14)     (N=14)    (N=14)    (N=14)     (N=56)
#2 Response                                                    
#3       No 14 (100%)  9 (64.3%)    0 (0%)    0 (0%) 23 (41.1%)
#4      Yes    0 (0%)  5 (35.7%) 14 (100%) 14 (100%) 33 (58.9%)

Edit

With the new test, cochran.test there is an error.
The updated function below runs both tests, Cochran's with tryCatch and the error message is output.

Fun <- function(data, var, Response, ID) {
  
  v <- deparse(substitute(var))
  r <- deparse(substitute(Response))

  tab <- table1(~ Response | var, data=data, topclass = "Rtable1-zebra")
  tab <- as.data.frame(tab)
  
  tbl <- table(data[[v]], data[[r]])
  test1 <- chisq.test(tbl)
  test2 <- tryCatch(
    cochran.qtest(Response ~ var | ID, data = data),
    error = function(e) e
  )
  pv2 <- if(inherits(test2, "error"))
    paste("Error:", conditionMessage(test2))
  else test2$p.value
  pvalue <- list(test1$p.value, pv2)
  pvalue <- setNames(pvalue, c("chisq", "cochran"))
  
  list(p.value = pvalue, table = tab)
}

yes thank you it works like that, but when I change the test, for example cochran test I gave same error, I added the code of cochran on the post — Ruser-lab9, Dec 05 '21 at 15:21
@Ruser-lab9 See the edit. If I complicated too much, say so and I will edit again. — Rui Barradas, Dec 05 '21 at 15:27

Error in eval(predvars, data, env) : object 'Practice' not found

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