CODEWITHSUNDEEP
r
A.Fowler
A.Fowler

Reputation: 101

R - TableOne -- Error in ModuleStopIfNoVarsLeft : No valid variables

I'm trying to use TableOne [https://cran.r-project.org/web/packages/tableone/tableone.pdf] in R to create a table. The data I'm using looks at patients who have undergone surgery and need a table of their existing medical conditions. I tried with the full dataset (30+ cols), but made a smaller df of just four to try and get this working.

Comorbidities (htn, hl, cv) are coded as TRUE/FALSE; and I have converted them to numeric using: 

df$data <- as.numeric(df$data)

I have put my code below, and the associated error.

For reference:

tp is the dataframe
htn/hl/cv are three separate columns, each is True/False within tp
age is a column of continuous within tp

Convert logical to numeric

> tp$htn <- as.numeric(tp$htn)
> tp$hl <- as.numeric(tp$hl)
> tp$cv <- as.numeric(tp$cv)

Check all numeric

> str(tp)
Classes ‘tbl_df’, ‘tbl’ and 'data.frame':   1199 obs. of  4 variables:
 $ htn : num  0 0 0 0 1 0 1 1 1 1 ...
 $ hl  : num  0 0 0 0 0 0 1 0 1 1 ...
 $ cv  : num  0 0 1 0 0 0 0 1 1 1 ...
 $ age : num  81.2 85.5 80.4 69.4 67.3 ...

Create variable list for table

> listvars <- tp[c("htn", "hl", "cv", "age")]

Create categorical variable list for table

> catvars <- tp[c("htn", "hl", "cv")]

Create table

> table1 <- CreateTableOne(vars = listvars, data = tp, factorVars = catvars)

Error is as follows:

**Error in ModuleStopIfNoVarsLeft(vars) : No valid variables.
In addition: Warning message:
In ModuleReturnVarsExist(vars, data) :**

I have attempted to fix it, firstly as above by ensuring all the variables are numeric, not just logical. Secondly, cut the dataset to only four columns as above, as I thought perhaps it required using all variables in the dataset.

I'm unsure how to proceed, any help greatly appreciated.

Upvotes: 1

Views: 2403

Answers (1)

kaz_yos
kaz_yos

Reputation: 325

I'm the maintainer. Please use the following.

listvars <- c("htn", "hl", "cv", "age")
catvars  <- c("htn", "hl", "cv")

vars and factorVars expect character vectors of variable NAMES.

Upvotes: 1

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