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Problem with mutate()
input data
.
#114
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I have the same problem, for me it was because on some grouping there is categories that contains only zeros. A rank test like wilcoxon test would be hardly done in this configuration. It would be nice to correct the function to avoid the grouping that is causing this issues whereas some groupings may be testable |
Hi @Ren01230 @BastienBennetot seems to be right with his assumption. If you look at the group-wise examples below, the dependent variable for the third group is 0 in every line and a statistical test for inference doesn't make any sense in this case. I don't think this is an issue that should be fixed by library(tidyverse)
library(rstatix)
#>
#> Attache Paket: 'rstatix'
#> Das folgende Objekt ist maskiert 'package:stats':
#>
#> filter
reprex_data <- structure(list(aid = c("A1", "A2", "A3", "A4", "B1", "B2", "B3",
"B4", "C1", "C2", "C3", "C4", "D1", "D2", "D3", "D4", "E1", "E2",
"E3", "E4", "F1", "F2", "F3", "F4"), tissue = c("sp", "sp", "sp",
"sp", "sp", "sp", "sp", "sp", "sp", "sp", "sp", "sp", "sp", "sp",
"sp", "sp", "sp", "sp", "sp", "sp", "sp", "sp", "sp", "sp"),
group = c("A", "A", "A", "A", "B", "B", "B", "B", "C", "C",
"C", "C", "A", "A", "A", "A", "B", "B", "B", "B", "C", "C",
"C", "C"), sex = c("m", "m", "m", "m", "m", "m", "m", "m",
"m", "m", "m", "m", "f", "f", "f", "f", "f", "f", "f", "f",
"f", "f", "f", "f"), detail = c("mCD4", "mCD4", "mCD4", "mCD4",
"mCD4", "mCD4", "mCD4", "mCD4", "mCD4", "mCD4", "mCD4", "mCD4",
"mCD4", "mCD4", "mCD4", "mCD4", "mCD4", "mCD4", "mCD4", "mCD4",
"mCD4", "mCD4", "mCD4", "mCD4"), value = c(0, 0, 0, 0, 0,
0, 0, 0.46, 0, 0, 0, 0, 0, 0, 0, 0.31, 0, 0, 0, 0.47, 0,
0, 0, 0)), class = c("spec_tbl_df", "tbl_df", "tbl", "data.frame"
), row.names = c(NA, -24L), spec = structure(list(cols = list(
aid = structure(list(), class = c("collector_character",
"collector")), tissue = structure(list(), class = c("collector_character",
"collector")), group = structure(list(), class = c("collector_character",
"collector")), sex = structure(list(), class = c("collector_character",
"collector")), detail = structure(list(), class = c("collector_character",
"collector")), value = structure(list(), class = c("collector_double",
"collector"))), default = structure(list(), class = c("collector_guess",
"collector")), skip = 1), class = "col_spec"))
# Nest the data for quick examination
reprex_data_nested <- reprex_data %>%
group_by(group, detail) %>%
nest()
# This works just fine
reprex_data_nested %>%
pluck("data", 1) %>%
wilcox_test(value ~ sex)
#> # A tibble: 1 x 7
#> .y. group1 group2 n1 n2 statistic p
#> * <chr> <chr> <chr> <int> <int> <dbl> <dbl>
#> 1 value f m 4 4 10 0.453
# This one as well
reprex_data_nested %>%
pluck("data", 2) %>%
wilcox_test(value ~ sex)
#> # A tibble: 1 x 7
#> .y. group1 group2 n1 n2 statistic p
#> * <chr> <chr> <chr> <int> <int> <dbl> <dbl>
#> 1 value f m 4 4 8.5 1
# Here, the error occurs
reprex_data_nested %>%
pluck("data", 3) %>%
wilcox_test(value ~ sex)
#> Error in if (f.lower <= 0) return(mumin): Fehlender Wert, wo TRUE/FALSE nötig ist
# As can be seen, all values are 0
reprex_data_nested %>%
pluck("data", 3)
#> # A tibble: 8 x 4
#> aid tissue sex value
#> <chr> <chr> <chr> <dbl>
#> 1 C1 sp m 0
#> 2 C2 sp m 0
#> 3 C3 sp m 0
#> 4 C4 sp m 0
#> 5 F1 sp f 0
#> 6 F2 sp f 0
#> 7 F3 sp f 0
#> 8 F4 sp f 0 Created on 2021-10-06 by the reprex package (v2.0.1) |
#statistical test run
#error
Error: Problem with mutate() input data.
x missing value where TRUE/FALSE needed
ℹ️ Input data is map(.data$data, .f, ...).
#data for reference
dput(spleen)
structure(list(aid = c("A1", "A2", "A3", "A4", "B1", "B2", "B3",
"B4", "C1", "C2", "C3", "C4", "D1", "D2", "D3", "D4", "E1", "E2",
"E3", "E4", "F1", "F2", "F3", "F4"), tissue = c("sp", "sp", "sp",
"sp", "sp", "sp", "sp", "sp", "sp", "sp", "sp", "sp", "sp", "sp",
"sp", "sp", "sp", "sp", "sp", "sp", "sp", "sp", "sp", "sp"),
group = c("A", "A", "A", "A", "B", "B", "B", "B", "C", "C",
"C", "C", "A", "A", "A", "A", "B", "B", "B", "B", "C", "C",
"C", "C"), sex = c("m", "m", "m", "m", "m", "m", "m", "m",
"m", "m", "m", "m", "f", "f", "f", "f", "f", "f", "f", "f",
"f", "f", "f", "f"), detail = c("mCD4", "mCD4", "mCD4", "mCD4",
"mCD4", "mCD4", "mCD4", "mCD4", "mCD4", "mCD4", "mCD4", "mCD4",
"mCD4", "mCD4", "mCD4", "mCD4", "mCD4", "mCD4", "mCD4", "mCD4",
"mCD4", "mCD4", "mCD4", "mCD4"), value = c(0, 0, 0, 0, 0,
0, 0, 0.46, 0, 0, 0, 0, 0, 0, 0, 0.31, 0, 0, 0, 0.47, 0,
0, 0, 0)), class = c("spec_tbl_df", "tbl_df", "tbl", "data.frame"
), row.names = c(NA, -24L), spec = structure(list(cols = list(
aid = structure(list(), class = c("collector_character",
"collector")), tissue = structure(list(), class = c("collector_character",
"collector")), group = structure(list(), class = c("collector_character",
"collector")), sex = structure(list(), class = c("collector_character",
"collector")), detail = structure(list(), class = c("collector_character",
"collector")), value = structure(list(), class = c("collector_double",
"collector"))), default = structure(list(), class = c("collector_guess",
"collector")), skip = 1), class = "col_spec"))
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