CODEWITHSUNDEEP
rpairwise.wilcox.testmultcompview
chiliconcarno
chiliconcarno

Reputation: 89

Problem with argument lengths while using multcompLetters2

I'm trying to obtain the compact letters associated with the p values I generated with the function pairwise.wilcox.test(). I used the function multcompLetters() which works well, but I want the letters to be ordered so that the highest mean gets the letter "a". In the following example, while using the function multcompLetters() to get the letters ordered, I receive the warning : "Error in tapply(data[, fm[[1]]], data[, fm[[2]]], function(x) do.call(mean, : arguments must have same length".

Is there something I don't understand with the usage of the function ?

Thanks a lot.

Adding data frame

As15 <- structure(list(Community = c("Arviat", "Arviat", "Arviat", "Arviat", 
                             "Arviat", "Arviat", "Arviat", "Arviat", "Arviat", "Arviat", "Arviat", 
                             "Arviat", "Arviat", "Arviat", "Arviat", "Arviat", "Arviat", "Arviat", 
                             "Arviat", "Arviat", "Arviat", "Arviat", "Arviat", "Arviat", "Arviat", 
                             "Arviat", "Arviat", "Arviat", "Arviat", "Arviat", "Arviat", "Arviat", 
                             "Arviat", "Arviat", "Arviat", "Arviat", "Arviat", "Arviat", "Arviat", 
                             "Arviat", "Arviat", "Arviat", "Arviat", "Arviat", "Arviat", "Arviat", 
                             "Arviat", "Arviat", "Arviat", "Arviat", "Arviat", "Arviat", "Arviat", 
                             "Arviat", "Arviat", "Arviat", "Arviat", "Arviat", "Arviat", "Arviat", 
                             "Arviat", "Arviat", "Arviat", "Arviat", "Arviat", "Arviat", "Arviat", 
                             "Arviat", "Arviat", "Arviat", "Arviat", "Arviat", "Arviat", "Arviat", 
                             "Arviat", "Arviat", "Arviat", "Arviat", "Arviat", "Arviat", "Arviat", 
                             "Arviat", "Arviat", "Arviat", "Nain", "Nain", "Nain", "Nain", 
                             "Nain", "Nain", "Nain", "Nain", "Nain", "Nain", "Nain", "Nain", 
                             "Nain", "Nain", "Nain", "Nain", "Nain", "Nain", "Nain", "Nain", 
                             "Nain", "Nain", "Nain", "Nain", "Nain", "Nain", "Nain", "Nain", 
                             "Nain", "Nain", "Nain", "Nain", "Nain", "Nain", "Nain", "Nain", 
                             "Nain", "Nain", "Nain", "Nain", "Resolute", "Resolute", "Resolute", 
                             "Resolute", "Resolute", "Resolute", "Resolute", "Resolute", "Resolute", 
                             "Resolute", "Resolute", "Resolute", "Resolute", "Resolute", "Resolute", 
                             "Resolute", "Resolute", "Resolute", "Resolute", "Resolute", "Resolute", 
                             "Resolute", "Resolute", "Resolute", "Resolute", "Resolute", "Resolute", 
                             "Resolute", "Resolute", "Resolute", "Resolute", "Resolute", "Resolute", 
                             "Resolute", "Resolute", "Resolute", "Resolute", "Resolute", "Resolute", 
                             "Resolute", "Resolute", "Resolute", "Resolute", "Resolute", "Resolute", 
                             "Resolute", "Resolute", "Resolute", "Resolute", "Resolute", "Resolute", 
                             "Resolute", "Resolute", "Resolute", "Resolute", "Resolute", "Resolute", 
                             "Resolute", "Resolute", "Resolute", "Resolute", "Resolute", "Resolute", 
                             "Resolute", "Resolute", "Resolute", "Resolute", "Resolute", "Resolute", 
                             "Resolute", "Resolute", "Resolute", "Resolute", "Resolute", "Resolute", 
                             "Resolute", "Resolute", "Resolute", "SachsHarbour", "SachsHarbour", 
                             "SachsHarbour", "SachsHarbour", "SachsHarbour", "SachsHarbour", 
                             "SachsHarbour", "SachsHarbour", "SachsHarbour", "SachsHarbour", 
                             "SachsHarbour", "SachsHarbour", "SachsHarbour", "SachsHarbour", 
                             "SachsHarbour", "SachsHarbour", "SachsHarbour", "SachsHarbour", 
                             "SachsHarbour", "SachsHarbour", "SachsHarbour", "SachsHarbour", 
                             "SachsHarbour", "SachsHarbour", "SachsHarbour", "SachsHarbour", 
                             "SachsHarbour", "SachsHarbour", "SachsHarbour", "SachsHarbour", 
                             "SachsHarbour", "SachsHarbour", "SachsHarbour", "SachsHarbour", 
                             "SachsHarbour", "SachsHarbour", "SachsHarbour", "SachsHarbour", 
                             "SachsHarbour", "SachsHarbour", "SachsHarbour", "SachsHarbour", 
                             "SachsHarbour", "SachsHarbour", "SachsHarbour", "SachsHarbour", 
                             "SachsHarbour", "SachsHarbour", "SachsHarbour", "SachsHarbour", 
                             "SachsHarbour", "SachsHarbour", "SachsHarbour", "SachsHarbour", 
                             "SachsHarbour", "SachsHarbour", "SachsHarbour", "SachsHarbour", 
                             "SachsHarbour", "SachsHarbour", "SachsHarbour"), ArsenicD = c(0.0254, 
                                                                                           0.121, 0.0726, 0.021, 0.0782, 0.0538, 0.1078, 0.0454, 0.0368, 
                                                                                           0.0618, 0.037, 0.0754, 0.1394, 0.0784, 0.218, 0.1482, 0.0778, 
                                                                                           0.0592, 0.0314, 0.0232, 0.0548, 0.0662, 0.0604, 0.0252, 0.0502, 
                                                                                           0.0768, 0.036, 0.054, 0.0404, 0.0642, 0.0384, 0.0504, 0.0616, 
                                                                                           0.068, 0.0678, 0.06, 0.0526, 0.0454, 0.0574, 0.0462, 0.0558, 
                                                                                           0.0506, 0.0764, 0.0466, 0.0518, 0.0544, 0.0362, 0.0472, 0.0374, 
                                                                                           0.0564, 0.0512, 0.0442, 0.0526, 0.05, 0.047, 0.0456, 0.073, 0.0798, 
                                                                                           0.0544, 0.072, 0.0392, 0.0658, 0.1662, 0.036, 0.0562, 0.0584, 
                                                                                           0.0416, 0.037, 0.046, 0.0334, 0.0384, 0.0654, 0.0528, 0.0274, 
                                                                                           0.0368, 0.0634, 0.0308, 0.0702, 0.0502, 0.058, 0.037, 0.0456, 
                                                                                           0.0404, 0.0516, 0.051, 0.0484, 0.054, 0.0344, 0.064, 0.0548, 
                                                                                           0.032, 0.0532, 0.0562, 0.0464, 0.0334, 0.068, 0.0422, 0.298, 
                                                                                           0.0344, 0.0338, 0.0508, 0.0356, 0.0446, 0.0484, 0.0408, 0.0148, 
                                                                                           0.0374, 0.0244, 0.0644, 0.0574, 0.028, 0.0462, 0.067, 0.0472, 
                                                                                           0.053, 0.0418, 0.0324, 0.054, 0.04, 0.0506, 0.0592, 0.0356, 0.049, 
                                                                                           0.054, 0.296, 0.276, 0.226, 0.0834, 0.452, 0.306, 0.218, 0.33, 
                                                                                           0.208, 0.1628, 0.426, 0.376, 0.0894, 0.438, 0.334, 0.212, 0.1606, 
                                                                                           0.082, 0.1178, 0.1128, 0.142, 0.103, 0.0862, 0.1104, 0.0746, 
                                                                                           0.0954, 0.202, 0.1362, 0.24, 0.21, 0.172, 0.278, 0.1354, 0.274, 
                                                                                           0.228, 0.0854, 0.0924, 0.0992, 0.0648, 0.0548, 0.0768, 0.0996, 
                                                                                           0.1008, 0.063, 0.0372, 0.1582, 0.228, 0.1514, 0.218, 0.1612, 
                                                                                           0.1608, 0.1652, 0.1474, 0.1904, 0.0396, 0.1396, 0.0816, 0.1132, 
                                                                                           0.0968, 1.258, 0.326, 0.236, 0.0854, 0.256, 0.1258, 0.1324, 0.1716, 
                                                                                           0.1642, 0.22, 0.0836, 0.18, 0.274, 0.1918, 0.171, 0.356, 0.298, 
                                                                                           0.1084, 0.1436, 0.238, 0.348, 0.1496, 0.342, 0.434, 0.146, 0.174, 
                                                                                           0.288, 0.396, 0.1834, 0.64, 0.342, 0.686, 0.43, 0.1808, 0.454, 
                                                                                           0.482, 0.352, 0.476, 0.422, 0.286, 0.81, 0.656, 0.564, 0.119, 
                                                                                           0.296, 0.1778, 0.512, 0.278, 0.22, 0.208, 0.1474, 0.55, 0.1526, 
                                                                                           0.1858, 0.128, 0.224, 0.1752, 0.0724, 0.1302, 0.1724, 0.1354, 
                                                                                           0.104, 0.1132, 0.292, 0.238, 0.348, 0.1626, 0.312, 0.238, 0.236, 
                                                                                           0.1276, 0.1228, 0.0978, 0.376, 0.1968, 0.1164, 0.448, 0.2, 0.1322, 
                                                                                           0.117)), row.names = c(NA, -263L), class = c("tbl_df", "tbl", 
                                                                                                                                        "data.frame"))

Wilcoxon Test

As15Wilcox <- suppressWarnings(pairwise.wilcox.test(As15$ArsenicD, As15$Community, p.adjust.method = "BH"))
As15pvals <- c(na.omit(setNames(c(As15Wilcox$p.value),
                            do.call("paste", c(as.list(expand.grid(rownames(As15Wilcox$p.value), 
                                                                   colnames(As15Wilcox$p.value))), sep = "-")))))

Obtaining Letters

multcompLetters2(ArsenicD ~ Community, As15pvals, As15)

I verified with length(), and both ArsenicD and Community possess the same length.

Upvotes: 0

Views: 217

Answers (1)

Allan Cameron
Allan Cameron

Reputation: 173793

It's not clear why you think you can pass the output of pairwise.wilcox.test to the second argument of multcompLetters2 (the parameter x). According to the docs:

x

  • One of the following: (1) A square, symmetric matrix with row names. (2) A vector with hyphenated names, which identify individual items or factor levels after "strsplit". (3) An object of class "dist". If x (or x[1]) is not already of class "logical", it is replaced with do.call(compare, list(x, threshold)), which by default converts numbers (typically p-values) less than 0.05 to TRUE and everything else to FALSE. If x is a matrix, its diagonal must be or must convert to FALSE.

...whereas wilcox1 is an object of class "pairwise.htest".

However, it does contain a matrix of p values of the comparisons, which we can convert into one of the above formats. Let's demonstrate with a dataset similar to yours.

library(multcompView)

wilcox1 <- suppressWarnings(
  pairwise.wilcox.test(site21$ArsenicD, site21$Community, 
                       p.adjust.method = "BH"))

Using your code, we get an error:

multcompLetters2(ArsenicD ~ Community, wilcox1, site21)
#> Error in vec2mat2(namx, sep): Names must contain exactly one '-' each;  
#> instead got method, data.name, p.value, p.adjust.method

Let us take the p values from our wilcox1 object and convert to a named vector with the correct pair names:

pvals <- c(na.omit(setNames(c(wilcox1$p.value),
           do.call("paste", c(as.list(expand.grid(rownames(wilcox1$p.value), 
           colnames(wilcox1$p.value))), sep = "-")))))

pvals
#>   North-East   South-East    West-East  South-North   West-North   West-South 
#> 4.746437e-14 1.077333e-04 3.164291e-14 3.164291e-14 3.164291e-14 7.175058e-08

And now we can do:

multcompLetters2(ArsenicD ~ Community, pvals, site21)
#>  West South  East North 
#>   "a"   "b"   "c"   "d"

Data used

Obviously, we don't have your data, so here is a reproducible example with the same names and basic structure that I used for this example:

set.seed(1)

site21 <- data.frame(Community = rep(c("North", "East", 
                                       "South", "West"), each = 25),
                     ArsenicD = c(rnorm(25, 5), rnorm(25, 8),
                                  rnorm(25, 9), rnorm(25, 11)))

Created on 2023-07-26 with reprex v2.0.2

Upvotes: 1

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