feature request for `PMCMRplus`

[Indrajeet Patil]

# setup
set.seed(123)
library(tidyverse)
library(PMCMRplus)

# custom function
PMCMR_to_tidy <- function(mod, ...) {
  # custom function to convert from a matrix to a tidy dataframe
  matrix_to_tidy <- function(m, col_name = "value") {
    result <-
      data.frame(
        group1 = rep(rownames(m), each = ncol(m)),
        group2 = rep(colnames(m), times = nrow(m)),
        col3 = as.numeric(base::t(m)),
        stringsAsFactors = FALSE
      )

    names(result)[3] <- col_name
    stats::na.omit(result)
  }

  # combine all components of the object in a single dataframe
  tibble::as_tibble(dplyr::bind_cols(
    dplyr::full_join(
      matrix_to_tidy(mod$statistic, col_name = "statistic"),
      matrix_to_tidy(mod$p.value, col_name = "p.value"),
      by = c("group1", "group2")
    ),
    purrr::flatten_dfr(list(mod$parameter)),
    tibble::tibble(method = mod$method),
    tibble::tibble(distribution = mod$dist),
    tibble::tibble(p.adjust.method = mod$p.adjust.method)
  ))
}

# example PMCMRplus object
ans <- kwAllPairsConoverTest(count ~ spray, data = InsectSprays, p.adjust.method = "single-step")
#> Warning in kwAllPairsConoverTest.default(c(10, 7, 20, 14, 14, 12, 10, 23, : Ties
#> are present. Quantiles were corrected for ties.

# using the function
PMCMR_to_tidy(ans)
#> # A tibble: 15 x 9
#>    group1 group2 statistic  p.value nmeans    df method distribution
#>    <chr>  <chr>      <dbl>    <dbl>  <int> <int> <chr>  <chr>       
#>  1 B      A          0.890 9.88e- 1      6    66 Conov~ q           
#>  2 C      A        -13.6   0.            6    66 Conov~ q           
#>  3 C      B        -14.5   0.            6    66 Conov~ q           
#>  4 D      A         -8.87  4.61e- 7      6    66 Conov~ q           
#>  5 D      B         -9.76  3.61e- 8      6    66 Conov~ q           
#>  6 D      C          4.71  1.70e- 2      6    66 Conov~ q           
#>  7 E      A        -11.0   1.12e- 9      6    66 Conov~ q           
#>  8 E      B        -11.8   7.57e-11      6    66 Conov~ q           
#>  9 E      C          2.63  4.37e- 1      6    66 Conov~ q           
#> 10 E      D         -2.09  6.81e- 1      6    66 Conov~ q           
#> 11 F      A          1.15  9.64e- 1      6    66 Conov~ q           
#> 12 F      B          0.264 1.00e+ 0      6    66 Conov~ q           
#> 13 F      C         14.7   0.            6    66 Conov~ q           
#> 14 F      D         10.0   1.68e- 8      6    66 Conov~ q           
#> 15 F      E         12.1   3.05e-11      6    66 Conov~ q           
#> # ... with 1 more variable: p.adjust.method <chr>

^{Created on 2020-10-14 by the reprex package (v0.3.0.9001)}

[Indrajeet Patil]

Added in 1.7.0:
https://www.rdocumentation.org/packages/PMCMRplus/versions/1.7.0/topics/toTidy

[Indrajeet Patil]

Keeping this open until this is actually adapted in the current package:

# function body
PMCMR_to_tibble <- function(mod, ...) {
  dplyr::select(PMCMRplus::toTidy(mod), -dplyr::contains("method")) %>%
    dplyr::rename(.data = ., group2 = group1, group1 = group2)
}