I am using the dunn.test() function from the dunn.test package to do a pairwise comparison of groups after a Kruskal-Wallis that showed significant differences in means.
The dunn.test() function only reports to the 4th decimal place, though. One of the comparisons is reported as 0.0000. I have attempted to increase the number of digits that it reports using options(digits = 10), but this does not increase the number of decimal places.
This there any way to increase the number of digits this function reports?
Here is an example:
my_data <- structure(list(species =
c("ABIBAL", "ABIBAL", "ABIBAL", "ACEPEN", "ACEPEN", "ACEPEN", "ACERUB", "ACERUB", "ACERUB", "ACESAC", "ACESAC",
"ACESAC", "ACESPI", "ACESPI", "ACESPI", "ARANUD", "ARANUD", "ARANUD",
"ARITRI", "ARITRI", "ARITRI", "ATHANG", "ATHANG", "ATHANG", "BETALL",
"BETALL", "BETALL", "CARARC", "CARARC", "CARARC", "CARINT", "CARINT",
"CARINT", "CINLAT", "CINLAT", "CINLAT", "CLIBOR", "CLIBOR", "CLIBOR",
"DENPUN", "DENPUN", "DENPUN", "DRYCAM", "DRYCAM", "DRYCAM", "DRYINT",
"DRYINT", "DRYINT", "FAGGRA", "FAGGRA", "FAGGRA", "FRAAME", "FRAAME",
"FRAAME", "HUPLUC", "HUPLUC", "HUPLUC", "LONCAN", "LONCAN", "LONCAN",
"MAICAN", "MAICAN", "MAICAN", "MAIRAC", "MAIRAC", "MAIRAC", "MEDVIR",
"MEDVIR", "MEDVIR", "NABSPP", "NABSPP", "NABSPP", "OCLACU", "OCLACU",
"OCLACU", "OXAMON", "OXAMON", "OXAMON", "PARNOV", "PARNOV", "PARNOV",
"PHECON", "PHECON", "PHECON", "PICRUB", "PICRUB", "PICRUB", "RUBIDA",
"RUBIDA", "RUBIDA", "SAMRAC", "SAMRAC", "SAMRAC", "STRAMP", "STRAMP",
"STRAMP", "TIACOR", "TIACOR", "TIACOR", "TRIBOR", "TRIBOR", "TRIBOR",
"TRIERE", "TRIERE", "TRIERE", "TRIUND", "TRIUND", "TRIUND", "TSUCAN",
"TSUCAN", "TSUCAN", "UVUSES", "UVUSES", "UVUSES", "VIBLAN", "VIBLAN",
"VIBLAN", "VIOBLA", "VIOBLA", "VIOBLA", "VIOROT", "VIOROT", "VIOROT"),
name = c("all_3", "topo_spectral_3", "universal", "all_3",
"topo_spectral_3", "universal", "all_3", "topo_spectral_3", "universal",
"all_3", "topo_spectral_3", "universal", "all_3", "topo_spectral_3",
"universal", "all_3", "topo_spectral_3", "universal", "all_3",
"topo_spectral_3", "universal", "all_3", "topo_spectral_3", "universal",
"all_3", "topo_spectral_3", "universal", "all_3", "topo_spectral_3",
"universal", "all_3", "topo_spectral_3", "universal", "all_3",
"topo_spectral_3", "universal", "all_3", "topo_spectral_3", "universal",
"all_3", "topo_spectral_3", "universal", "all_3", "topo_spectral_3",
"universal", "all_3", "topo_spectral_3", "universal", "all_3",
"topo_spectral_3", "universal", "all_3", "topo_spectral_3", "universal",
"all_3", "topo_spectral_3", "universal", "all_3", "topo_spectral_3",
"universal", "all_3", "topo_spectral_3", "universal", "all_3",
"topo_spectral_3", "universal", "all_3", "topo_spectral_3", "universal",
"all_3", "topo_spectral_3", "universal", "all_3", "topo_spectral_3",
"universal", "all_3", "topo_spectral_3", "universal", "all_3",
"topo_spectral_3", "universal", "all_3", "topo_spectral_3", "universal",
"all_3", "topo_spectral_3", "universal", "all_3", "topo_spectral_3",
"universal", "all_3", "topo_spectral_3", "universal", "all_3",
"topo_spectral_3", "universal", "all_3", "topo_spectral_3", "universal",
"all_3", "topo_spectral_3", "universal", "all_3", "topo_spectral_3",
"universal", "all_3", "topo_spectral_3", "universal", "all_3",
"topo_spectral_3", "universal", "all_3", "topo_spectral_3", "universal",
"all_3", "topo_spectral_3", "universal", "all_3", "topo_spectral_3",
"universal", "all_3", "topo_spectral_3", "universal"),
value = c(0.805, 0.729, 0.611, 0.84, 0.729, 0.636, 0.682, 0.592, 0.497, 0.764,
0.762, 0.666, 0.783, 0.668, 0.596, 0.828, 0.735, 0.684, NA, 0.736,
0.715, 0.765, 0.758, 0.636, 0.704, 0.626, NA, NA, NA, NA, 0.771,
0.589, NA, 0.799, 0.649, 0.583, 0.733, 0.753, NA, 0.694, 0.647,
NA, NA, NA, NA, 0.82, 0.833, 0.717, 0.821, 0.821, 0.747, 0.766,
0.717, 0.675, 0.742, 0.667, 0.704, NA, 0.591, NA, 0.793, 0.76,
0.74, 0.782, 0.747, 0.599, 0.755, 0.699, 0.586, 0.738, 0.652,
0.572, 0.62, 0.522, NA, 0.753, 0.531, 0.546, NA, NA, 0.51, 0.736,
0.708, 0.572, 0.657, 0.704, 0.638, 0.694, 0.675, NA, 0.769, 0.739,
0.717, NA, NA, 0.6, 0.77, 0.678, 0.732, 0.735, 0.697, NA, 0.83,
0.705, 0.585, 0.709, 0.683, 0.633, NA, NA, NA, 0.749, 0.748,
0.595, 0.827, 0.725, 0.722, 0.744, 0.676, 0.634, 0.799, 0.793,
0.68)), row.names = c(NA, -123L), class = c("tbl_df", "tbl", "data.frame"))
dunn.test::dunn.test(my_data$value,
my_data$name,
method = "bonferroni")
Thanks!
If you assign the output of that function call to an object name, say res then you can see that the p-values are present:
str(res)
List of 5
$ chi2 : num 39
$ Z : num [1:3] 3.61 6.21 2.8
$ P : num [1:3] 1.54e-04 2.68e-10 2.55e-03
$ P.adjusted : num [1:3] 4.63e-04 8.05e-10 7.66e-03
$ comparisons: chr [1:3] "all_3 - topo_spectral_3" "all_3 - universal" "topo_spectral_3 - universal"
If you want them printed with the default number of significant figures, you can just use the default print operation implied by the REPL behavior of the R console:
res$P.adjusted
[1] 4.629094e-04 8.053304e-10 7.663309e-03
If you want a different number of significant digits then use print() with the digits parameter:
print( res$P.adjusted, dig =10)
[1] 4.629093512e-04 8.053304308e-10 7.663308987e-03
The res object is a list without an additional class, so the material printed to the console is not the result of a class specific print method, but is rather due to code in the body of dunn.test that uses the cat function.