Cannot inject environmental variable into t_test()

[ckfaber]

I'm writing a function wherein I have a user-defined grouping variable in my environment that I would like to inject into t_test() (e.g., t_test({{var}} ~ {{groupvar}})), but I keep getting an error related to pull(), indicating the column cannot be found. I'm not an expert in data-masking and injection, but I've tried every variation that I can think of and continue to get the same issue.

Here is code to generate a toy dataset and the various approaches I have tried, along with the error messages:

groupvar <- "Treatment"
facetvar <- "Sex"
plotvar <- "BodyMass"

df <- tibble(Subject = as.factor(1:10), BodyMass = runif(10,min = 20, max = 30), Sex = as.factor(rep(c("M","F"),5)), Treatment = as.factor(rep(c("Control","Experimental"),each = 5)))

# This works: 
df_ttest <- df %>%
  group_by(Sex) %>% # group by variable that will be used to facet
  t_test(BodyMass ~ Treatment) %>% # 
  adjust_pvalue(method = "bonferroni") %>%
  add_significance() %>%
  add_xy_position(x = "Treatment")

# This breaks:
df_ttest <- df %>%
  group_by({{facetvar}}) %>% # group by variable that will be used to facet
  t_test({{plotvar}} ~ {{groupvar}}) %>% # 
  adjust_pvalue(method = "bonferroni") %>%
  add_significance() %>%
  add_xy_position(x = {{groupvar}})

I've also tried:

• get()
• enquo() and !!
• .env$var

All give a version of the same error indicating the columns don't exist.

Error in `pull()`:
! Can't extract columns that don't exist.
✖ Column `{\n    {\n        groupvar\n    }\n}` doesn't exist.

R Version: 4.2.2 R Studio Version: 2022.07.2 Build 576 rstatix version: 0.7.1.999

I would really appreciate any suggestions as to where to go from here, as I'm hoping to automatically generate plots with summary statistics for many plots from a large dataset.

Thank you!

[GegznaV]

@ckfaber, this is not an rstatix issue so please, close it.

---

Still, I will help you. Construct a formula via as.formula() : as.formula(paste(plotvar, "~", groupvar))

Is this what you expect:

library(rstatix)
#> 
#> Attaching package: 'rstatix'
#> The following object is masked from 'package:stats':
#> 
#>     filter

groupvar <- "Treatment"
facetvar <- "Sex"
plotvar <- "BodyMass"

df <- tibble(
  Subject = as.factor(1:10),
  BodyMass = runif(10,min = 20, max = 30),
  Sex = as.factor(rep(c("M","F"),5)), 
  Treatment = as.factor(rep(c("Control","Experimental"), each = 5))
)

# This works: 
df_ttest <- df %>%
  group_by(Sex) %>% # group by variable that will be used to facet
  t_test(BodyMass ~ Treatment) %>% # 
  adjust_pvalue(method = "bonferroni") %>%
  add_significance() %>%
  add_xy_position(x = "Treatment")

df_ttest
#> # A tibble: 2 × 15
#>   Sex   .y.   group1 group2    n1    n2 statistic    df     p p.adj p.adj.signif
#>   <fct> <chr> <chr>  <chr>  <int> <int>     <dbl> <dbl> <dbl> <dbl> <chr>       
#> 1 F     Body… Contr… Exper…     2     3   1.97     2.48 0.162 0.324 ns          
#> 2 M     Body… Contr… Exper…     3     2  -0.00905  2.69 0.993 1     ns          
#> # ℹ 4 more variables: y.position <dbl>, groups <named list>, xmin <dbl>,
#> #   xmax <dbl>

# This breaks:
df_ttest_2 <- df %>%
  group_by({{facetvar}}) %>% # group by variable that will be used to facet
  t_test(as.formula(paste(plotvar, "~", groupvar))) %>% # 
  adjust_pvalue(method = "bonferroni") %>%
  add_significance() %>%
  add_xy_position(x = {{groupvar}})

df_ttest_2
#> # A tibble: 1 × 15
#>   `"Sex"` .y.      group1  group2          n1    n2 statistic    df     p p.adj
#>   <chr>   <chr>    <chr>   <chr>        <int> <int>     <dbl> <dbl> <dbl> <dbl>
#> 1 Sex     BodyMass Control Experimental     5     5      1.28  7.41 0.239 0.239
#> # ℹ 5 more variables: p.adj.signif <chr>, y.position <dbl>,
#> #   groups <named list>, xmin <dbl>, xmax <dbl>

^{Created on 2023-05-15 with reprex v2.0.2}

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