I am using this example data.frame and code. I would like to do multiple tests between two group, but when there are no data in one group, it is causing an error. How can I skip the comparisons without two groups and still run the code on the other ones?
library(dplyr)
df <- data.frame(group=c(rep(0,10),rep(1,10)),
apple = as.numeric(c(runif(20, -1, 18))),
pear = as.numeric(c(rep("NA",12), runif(8, 2, 7))),
banana = as.numeric(c(runif(10, 1, 3), runif(10, 2.5, 6))),
cherry = as.numeric(c(runif(9, 5, 12), rep("NA",11))))
df_new <- df %>% summarise(across(!group, ~wilcox.test(.x ~ group)$p.value), exact=NULL) %>%
bind_rows(., p.adjust(., method = 'BH')) %>%
bind_rows(df, .) %>%
mutate(group=replace(group, is.na(group), c('p.values', 'adjusted_p.values')))
# Error in `summarise()`:
# ! Problem while computing `..1 = across(!group, ~wilcox.test(.x ~ group)$p.value)`.
# Caused by error in `across()`:
# ! Problem while computing column `pear`.
# Caused by error in `wilcox.test.formula()`:
# ! grouping factor must have exactly 2 levels
# Run `rlang::last_error()` to see where the error occurred.
As said in the question linked in the comments, you can use try() or tryCatch() in the function in across() to silently capture the error. Basically, it says "if there's no error, return the result (the p-value in your case), and if there's an error, move to the next variable".
df_new <- df %>%
summarise(
across(
!group,
function(x) {
out <- try(wilcox.test(x ~ group)$p.value, silent = TRUE)
if (!inherits(out, "try-error")) {
return(out)
}
}
),
exact = NULL
) %>%
bind_rows(., p.adjust(., method = "BH")) %>%
bind_rows(df, .) %>%
mutate(group = replace(group, is.na(group), c("p.values", "adjusted_p.values")))
df_new
#> group apple pear banana cherry
#> 1 0 7.8559712 NA 2.085272e+00 8.606734
#> 2 0 10.3555136 NA 1.021946e+00 9.759360
#> 3 0 10.9658917 NA 2.839778e+00 7.334473
#> 4 0 1.5944729 NA 2.371802e+00 7.262835
#> 5 0 7.6975703 NA 1.805847e+00 7.527016
#> 6 0 14.3173630 NA 2.029271e+00 10.610466
#> 7 0 6.0701846 NA 1.681383e+00 6.397823
#> 8 0 14.9290293 NA 1.668531e+00 10.541239
#> 9 0 11.0102237 NA 2.202353e+00 8.274926
#> 10 0 6.6343644 NA 2.613700e+00 NA
#> 11 1 10.9747881 NA 3.660303e+00 NA
#> 12 1 14.5043713 NA 3.064596e+00 NA
#> 13 1 5.3523349 4.165088 3.441590e+00 NA
#> 14 1 12.9285923 5.586389 3.768061e+00 NA
#> 15 1 9.0848274 4.119166 3.706076e+00 NA
#> 16 1 1.3605938 2.721709 3.894040e+00 NA
#> 17 1 1.8937699 6.235140 2.826658e+00 NA
#> 18 1 15.5570770 3.414619 2.702846e+00 NA
#> 19 1 0.6901305 6.319984 3.219524e+00 NA
#> 20 1 15.1907810 4.879057 4.147871e+00 NA
#> 21 p.values 0.9705125 NA 4.330035e-05 NA
#> 22 adjusted_p.values 0.9705125 NA 8.660071e-05 NA
Created on 2022-08-11 by the reprex package (v2.0.1)