[R] Order output list od TukeyHSD function by "p adj"
Jim Lemon
drjimlemon at gmail.com
Wed Feb 24 07:48:56 CET 2016
Hi Sergio,
I couldn't get your example data to read in, so I have used the example in
the help page:
fm1 <- aov(breaks ~ wool + tension, data = warpbreaks)
hsd.fit<-TukeyHSD(fm1, "tension", ordered = TRUE)
hsd.fit$tension[order(hsd.fit$tension[,4]),]
diff lwr upr p adj
L-H 14.722222 5.3688015 24.07564 0.001121788
L-M 10.000000 0.6465793 19.35342 0.033626219
M-H 4.722222 -4.6311985 14.07564 0.447421021
Obviously you would have to examine the output of TukeyHSD with str() to
sort out which column to use for ordering.
Jim
On Wed, Feb 24, 2016 at 11:21 AM, Sergio Fonda <sergio.fonda99 at gmail.com>
wrote:
> Hello, It's already for several hours that I try to order the list
> obtained by the function TukeyHSD according to the variable "p adj"
> (in ascending order). Unfortunately, without success.
> In addition to following two lines of code, that offer the result but
> separately so do not correspond to the desired result, I was unable to
> go:
> DF.5 <-lapply(DF.4, function (x) as.data.frame(x[c("patient:Fold.fac")]))
> DF.6 <- DF.5[[1]][order(DF.5[[1]]$patient.Fold.fac.p.adj),]
> Please, I ask some help to answer these two questions:
> 1) is it possible to get directly from the function TukeyHSD sorted
> rows by "p adj"?
> 2) or, may the output list from TukeyHSD() be processed (e.g. by
> lapply) to sort its elements according to "p adj"?
> I attach at bottom a simulation of a list obtained from TukeyHSD which
> should be ordered by "p adj".
> Thanks in advance for any suggestion!
> Sergio
> #
> > dput(DF.4)
> list(structure(list(patient = structure(c(12289274.0619908,
> -2380308.48287107,
> -14669582.5448618, -4176414.56676197, -18845997.1116238, -31135271.1736146,
> 28754962.6907435, 14085380.1458817, 1796106.0838909, 0.186808233632622,
> 0.938592742253258, 0.0922160074633905), .Dim = 3:4, .Dimnames = list(
> c("PARTIAL-COMPLETE", "NO-COMPLETE", "NO-PARTIAL"), c("diff",
> "lwr", "upr", "p adj"))), Fold.fac = structure(c(-12697325.7957036,
> -23938561.4288898, -1456090.1625174, 0.0268617694934425), .Dim = c(1L,
> 4L), .Dimnames = list("middle-low", c("diff", "lwr", "upr", "p adj"
> ))), `patient:Fold.fac` = structure(c(15369710.0977205, 6521960.91205235,
> -4695802.45257667, 4502968.78925385, -16007472.7140147, -8847749.18566819,
> -20065512.5502972, -10866741.3084667, -31377182.8117352, -11217763.364629,
> -2018992.12279849, -22529433.626067, 9198771.24183052, -11311670.261438,
> -20510441.5032685, -12927630.9811041, -21775380.1667723, -33016252.8378897,
> -23817481.5960591, -44327923.0993277, -37145090.2644928, -48385962.9356102,
> -39187191.6937797, -59697633.1970482, -39538213.749942, -30339442.5081115,
> -50849884.01138, -19144769.6082929, -39655211.1115614, -48853982.353392,
> 43667051.1765452, 34819301.990877, 23624647.9327363, 32823419.1745669,
> 12312977.6712983, 19449591.8931564, 8254937.83501579, 17453709.0768463,
> -3056732.42642223, 17102687.020684, 26301458.2625145, 5791016.75924596,
> 37542312.0919539, 17031870.5886854, 7833099.34685487, 0.632098034657304,
> 0.986399530577416, 0.997064140940244, 0.997595806079891, 0.590366152539712,
> 0.948510666498818, 0.330512619876425, 0.883673837089478,
> 0.0198821692150445,
> 0.868982868764254, 0.999952294188371, 0.207190890959777, 0.939934594322161,
> 0.86529009598038, 0.306625751897378), .Dim = c(15L, 4L), .Dimnames = list(
> c("PARTIAL:low-COMPLETE:low", "NO:low-COMPLETE:low",
> "COMPLETE:middle-COMPLETE:low",
> "PARTIAL:middle-COMPLETE:low", "NO:middle-COMPLETE:low",
> "NO:low-PARTIAL:low", "COMPLETE:middle-PARTIAL:low",
> "PARTIAL:middle-PARTIAL:low",
> "NO:middle-PARTIAL:low", "COMPLETE:middle-NO:low",
> "PARTIAL:middle-NO:low",
> "NO:middle-NO:low", "PARTIAL:middle-COMPLETE:middle",
> "NO:middle-COMPLETE:middle",
> "NO:middle-PARTIAL:middle"), c("diff", "lwr", "upr", "p adj"
> )))), .Names = c("patient", "Fold.fac", "patient:Fold.fac"
> ), class = c("TukeyHSD", "multicomp"), orig.call = aov(formula = abundance
> ~
> patient * Fold.fac, data = x), conf.level = 0.95, ordered = FALSE),
> structure(list(patient = structure(c(11084928.3849924, -3790273.898858,
> -14875202.2838504, -2565656.8579769, -17440859.1418273,
> -28525787.5268197,
> 24735513.6279617, 9860311.34411127, -1224617.0408811,
> 0.137587687259541,
> 0.791659281224941, 0.028733410253219), .Dim = 3:4, .Dimnames = list(
> c("PARTIAL-COMPLETE", "NO-COMPLETE", "NO-PARTIAL"), c("diff",
> "lwr", "upr", "p adj"))), Fold.fac = structure(c(25003217.9525667,
> 15683872.2084017, 34322563.6967316, 1.59282125378191e-07), .Dim = c(1L,
> 4L), .Dimnames = list("low-high", c("diff", "lwr", "upr",
> "p adj"))), `patient:Fold.fac` = structure(c(6786144.11764773,
> -14136208.8235292, 15255972.7140153, 30625682.8117357,
> 21777933.6260674,
> -20922352.9411769, 8469828.59636761, 23839538.6940879,
> 14991789.5084197,
> 29392181.5375445, 44761891.6352649, 35914142.4495966, 15369710.0977203,
> 6521960.91205206, -8847749.18566828, -16711562.4882314,
> -37633915.4294083,
> -8222591.1541805, 7147118.94353984, -1700630.24212845,
> -44420059.547056,
> -15008735.2718282, 360974.825892106, -8486774.35977618,
> 5913617.6693487,
> 21283327.767069, 12435578.5814008, -8089695.41243546,
> -16937444.5981037,
> -32307154.6958241, 30283850.7235268, 9361497.78234989,
> 38734536.5822112,
> 54104246.6799315, 45256497.4942632, 2575353.66470216, 31948392.4645634,
> 47318102.5622838, 38470353.3766155, 52870745.4057404, 68240455.5034607,
> 59392706.3177924, 38829115.6078761, 29981366.4222079, 14611656.3244875,
> 0.963180623746077, 0.521122619371869, 0.431445001590424,
> 0.00280179326576413, 0.0869916657428951, 0.113173926329674,
> 0.908231706478258, 0.0441523667992262, 0.451984651996765,
> 0.00489618219443777, 9.080596613531e-07, 0.000195613055067767,
> 0.42174023314457, 0.968747601969596, 0.891038899833401), .Dim = c(15L,
> 4L), .Dimnames = list(c("PARTIAL:high-COMPLETE:high",
> "NO:high-COMPLETE:high",
> "COMPLETE:low-COMPLETE:high", "PARTIAL:low-COMPLETE:high",
> "NO:low-COMPLETE:high", "NO:high-PARTIAL:high",
> "COMPLETE:low-PARTIAL:high",
> "PARTIAL:low-PARTIAL:high", "NO:low-PARTIAL:high",
> "COMPLETE:low-NO:high",
> "PARTIAL:low-NO:high", "NO:low-NO:high", "PARTIAL:low-COMPLETE:low",
> "NO:low-COMPLETE:low", "NO:low-PARTIAL:low"), c("diff", "lwr",
> "upr", "p adj")))), .Names = c("patient", "Fold.fac",
> "patient:Fold.fac"
> ), class = c("TukeyHSD", "multicomp"), orig.call = aov(formula =
> abundance ~
> patient * Fold.fac, data = x), conf.level = 0.95, ordered = FALSE))
> >
>
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