imbi-heidelberg / descrtab2 Goto Github PK

You can use test_options= list(test_override= "") inside var_options for now. Will fix some time in the future.

todo

In the package website I did not find a description of the computed confidence intervals. If they correspond to the tests, adding them to the test choice tree would probably make sense. I needed it for referencing it in a publication.

good_idx <- names(table(id)[table(id) == 2])
if (!all(id %in% good_idx)) {
warning("Removed paired observations with missings.")
}
tibl <- tibble(
var = var,
group = group,
id = id
)
tibl %<>% filter(id %in% good_idx)
level1 <- levels(group)[1]
level2 <- levels(group)[2]
x <-
tibl %>%
filter(group == level1) %>%
arrange(id) %>%
pull(var)
y <-
tibl %>%
filter(group == level2) %>%
arrange(id) %>%
pull(var)

Warning message should read "Data improperly matched". Also need to check table(id, group) < 2 I think.

When running the standard iris example from here I obtain:

! `fct_explicit_na()` was deprecated in forcats 1.0.0.
Please use `fct_na_value_to_level()` instead.

These situations are most likely associated with some kind of user error.

I am trying to add group labels using the group_labels = list() option. However, the group labels are printed erroneously. The first group gets a tag "(N=)" for specifying the number of group members, but without actually specifying the number of members. The second group does not even print this tag at all. Here is a reproducible example:

---
title: "Reprex"
author: "Author"
date: "10 2 2022"
output: pdf_document
---

```{r setup, include=FALSE}
library(DescrTab2)
library(tidyverse)
knitr::opts_chunk$set(echo = TRUE)
options(print_format="tex")
```
## R Markdown
```{r cars}
data(mtcars)
mtcars %>% select(mpg, am) %>% # mutate(QL = factor(MWS)) %>% 
   descr(., group = "am", group_labels = list("0" = "Automatic trans.", "1" = "Manual trans."),
             format_options = list(print_CI = FALSE, print_Total = FALSE, caption="Fuel efficiency depending on transmission type"))
```

This example produces the following output:

I marked the erroneous and the missing group size tags.

User observed the following error:

<error/rlang_error>
Obsolete data mask.
x Too late to resolve `Alkohol≥5x/Woche` after the end of `dplyr::mutate()`.
i Did you save an object that uses `Alkohol≥5x/Woche` lazily in a column in the `dplyr::mutate()` expression ?

No idea how to reproduce yet, works on my machine.

Within the excellent usage guidance I couldn't find documentation on how to specify the indices argument when using a paired test. Neither in the test choice tree vignette. I figured out that the variable name of the index variable worked in my case.
Maybe you could add something somewhere?

I tried to create a descriptive table within an imbiReport2::imbi_report_tex Markdown document with the following chunk:

# Create data frame with 20 variables
df <- data.frame(
  "x1" = 1:10
)

for(i in 2:20){
  df[[paste0("x", i)]] <- 1:10
}

# Print desription table
df %>%
  descr()

The dataset has 20 variables. When compiling the TeX document, it gives the following error:

! Misplaced \omit.
\multispan ->\omit
@multispan
l.296 ...erscript{tt1} Students one-sample t-test}
\ \*

It seems to be caused by a double star (look for \\** in the TeX document) in the longtable environment. When deleting the second star manually in the TeX document, it can be compiled.
Interestingly, this error only occurs for a certain amount of variables/size of table. With 19 and 21 variables, everything works fine. The problem occurs again for 40 variables.