I am trying to obtain the significance letters with the function cldList() (package rcompanion) after performing a Peto-Peto one factor test with the function cen1way()(package NADA2).
After obtaining the p values from the test, I am unable to call them correctly, as the output of cldList() is null.
I believe the p values output might not be in an appropriate object type to be called in cldList(), but I can't figure out how to get it in a usable form.
Here is the code I tried using a subset of my data.
Adding Data
set1 <- structure(list(ID = c("A", "A", "A", "A", "A", "A",
"A", "A", "A", "A", "B", "B", "B", "B", "B", "B", "B",
"B", "C", "C", "C", "D", "D", "D", "D", "D", "D", "D",
"D", "D", "D", "E", "E", "E", "E", "E", "E", "E", "E",
"E", "F", "F", "F", "F", "F", "F", "F", "F", "F", "F",
"F", "F", "F", "G", "G", "G", "G", "G", "G", "G", "G",
"G", "G", "G", "G", "G", "H", "H", "H", "H", "H", "H",
"H", "H"), original = c(0.0034397051289882, 1.1895195198828e-05,
2.80463220089782e-05, 5.40349098831069e-05, 2.80463220089782e-05,
6.54592102975903e-05, 8.42044278641221e-05, 0.00110045642460291,
5.83998369803433e-06, 6.62922790737467e-05, 5.97908405798548e-05,
2.80463220089782e-05, 0.000485444017223116, 7.59323332783847e-05,
9.34269632583946e-05, 2.80463220089782e-05, 0.000202856928583584,
2.80463220089782e-05, 0.000628230889994026, 9.13108026060008e-05,
0.000162375214276451, 0.00124474651246522, 6.05143500495826e-05,
0.000765789119095523, 0.000705778973990029, 0.000439267485838453,
0.000271485757636799, 0.000264355137702171, 0.000913605153098551,
0.000841832877175541, 0.00150097653600645, 0.000440713522584867,
0.000333725382308514, 0.000440771063101499, 0.000330888958820384,
0.000335177057648398, 0.00027488295896592, 0.000518376675120886,
0.000258107439200671, 0.000295378252143169, 1.33813016467029e-05,
0.000170515172372076, 0.000160470677229974, 9.8859042573522e-05,
4.77094034798514e-06, 0.000779128855726363, 2.80463220089782e-05,
0.000407571008174826, 4.76025086993255e-05, 1.6605450183472e-05,
0.000437149280986268, 5.37106562163918e-05, 4.82654666645295e-05,
5.56927962541369e-05, 6.13875350181571e-05, 7.23571226639171e-05,
0.000139020374377688, 0.000183535432147331, 2.80463220089782e-05,
0.00027648488631673, 0.000168280725021817, 5.21403981691148e-05,
2.80463220089782e-05, 2.80463220089782e-05, 2.80463220089782e-05,
2.80463220089782e-05, 2.80463220089782e-05, 2.80463220089782e-05,
3.53603278692284e-05, 0.000774068073825739, 8.72875026642225e-05,
0.000231402667811853, 2.51299208991313e-05, 7.37528096121726e-05
), LOD = c(0.0034397051289882, 5.68047780523916e-05, 5.68047780523916e-05,
5.68047780523916e-05, 5.68047780523916e-05, 6.54592102975903e-05,
8.42044278641221e-05, 0.00110045642460291, 5.68047780523916e-05,
6.62922790737467e-05, 5.97908405798548e-05, 5.68047780523916e-05,
0.000485444017223116, 7.59323332783847e-05, 9.34269632583946e-05,
5.68047780523916e-05, 0.000202856928583584, 5.68047780523916e-05,
0.000628230889994026, 9.13108026060008e-05, 0.000162375214276451,
0.00124474651246522, 6.05143500495826e-05, 0.000765789119095523,
0.000705778973990029, 0.000439267485838453, 0.000271485757636799,
0.000264355137702171, 0.000913605153098551, 0.000841832877175541,
0.00150097653600645, 0.000440713522584867, 0.000333725382308514,
0.000440771063101499, 0.000330888958820384, 0.000335177057648398,
0.00027488295896592, 0.000518376675120886, 0.000258107439200671,
0.000295378252143169, 5.68047780523916e-05, 0.000170515172372076,
0.000160470677229974, 9.8859042573522e-05, 5.68047780523916e-05,
0.000779128855726363, 5.68047780523916e-05, 0.000407571008174826,
5.68047780523916e-05, 5.68047780523916e-05, 0.000437149280986268,
5.68047780523916e-05, 5.68047780523916e-05, 5.68047780523916e-05,
6.13875350181571e-05, 7.23571226639171e-05, 0.000139020374377688,
0.000183535432147331, 5.68047780523916e-05, 0.00027648488631673,
0.000168280725021817, 5.68047780523916e-05, 5.68047780523916e-05,
5.68047780523916e-05, 5.68047780523916e-05, 5.68047780523916e-05,
5.68047780523916e-05, 5.68047780523916e-05, 5.68047780523916e-05,
0.000774068073825739, 8.72875026642225e-05, 0.000231402667811853,
5.68047780523916e-05, 7.37528096121726e-05), cen = c(0, 1,
1, 1, 1, 0, 0, 0, 1, 0, 0, 1, 0, 0, 0, 1, 0, 1, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0,
1, 0, 1, 0, 1, 1, 0, 1, 1, 1, 0, 0, 0, 0, 1, 0, 0, 1, 1, 1, 1,
1, 1, 1, 1, 0, 0, 0, 1, 0)), class = c("tbl_df", "tbl", "data.frame"
), row.names = c(NA, -74L))
Peto-Peto one-factor test
pval <- cen1way(set1$LOD,
set1$cen, set1$ID, mcomp.method = "BH", printstat = TRUE)
Obtaining the significance letters
CLD <- cldList(P.adj ~ Comparison, data=pval$res)
CLD
You have to dig through the structure of the output from cen1way() to get the part you want. And then I think you need to convert it to a complete square matrix to pass it to multcompView.
cldList() doesn't handle p-values in that kind of matrix format.
You can examine the structure of the output with e.g. str(Cen1), as defined below.
library(NADA2)
Cen1 <- cen1way(set1$LOD,
set1$cen, set1$ID, mcomp.method = "BH", printstat = TRUE)
Pval = Cen1$mcomp$p.value
Pval
library(rcompanion)
PT = fullPTable(Pval)
PT
library(multcompView)
multcompLetters(PT)
### A B C D E F G H
### "ab" "a" "ab" "b" "b" "a" "a" "a"