tbl_svysummary error: "sum not meaningful for factors" when leaving the weights in the dataset about gtsummary HOT 6 CLOSED

After exploring it, the issue is not coming from gtsummary but from survey. The survey::svytable() is failing if we ask it to summarize a variable named weights. If you change the variable name, there is no problem.

library(dplyr)
#> 
#> Attachement du package : 'dplyr'
#> Les objets suivants sont masqués depuis 'package:stats':
#> 
#>     filter, lag
#> Les objets suivants sont masqués depuis 'package:base':
#> 
#>     intersect, setdiff, setequal, union
library(gtsummary)
library(survey)
#> Le chargement a nécessité le package : grid
#> Le chargement a nécessité le package : Matrix
#> Le chargement a nécessité le package : survival
#> 
#> Attachement du package : 'survey'
#> L'objet suivant est masqué depuis 'package:graphics':
#> 
#>     dotchart
library(WeightIt)

n <- 100000
age <- rnorm(n,60,10)
sex <- rbinom(n,1,0.5)
X <- rbinom(n,1,0.4) * rnorm(n,30,5) + sex * rnorm(n,40,5) + age
X <- round(pnorm(X, mean(X), sd(X)))
Y <- 30*X + age + 40*sex
df <- data.frame(age = age, sex = sex, X = X, Y = Y)
df$w <- weightit(data = df, formula = X ~ age + sex)$weights

svy_tbl <- svydesign(~1, data = df, weights = ~w) %>%
  tbl_svysummary(by = X)
svy_tbl |> 
  as_kable()

^{Created on 2023-10-07 with reprex v2.0.2}

from gtsummary.

On survey side, it could be worth to mention the issue to their team, at lest to mention in the documentation that weights is a reserved named. (even if this variable is something else than the survey weights).

On gtsummary side, we could eventually add a check on the names in include and add a specific error message. @ddsjoberg What do you think?

from gtsummary.

Before we add a message in gtsummary, @zheer-kejlberg can you file a bug report with survey package? Hopefully, they'll just update on their end and we won't need to keep track of this message. Sound good @larmarange ?

from gtsummary.

Good to me

from gtsummary.

Sounds great! Thanks for the quick response. I’ll file a bug with survey and keep you posted once they respond.

from gtsummary.

Great, thank you! Please update us on the outcome! Even if they don't wish to make the update in survey, i hope more informative messaging could be added.

from gtsummary.