Hello, I am really new to R and it's still a challenge to me. Currently I'm working on my Master's Thesis. My supervisor works with SAS and is not familiar with R at all. I want to run an Anova, a tukey-test and as a result I want to have the tukey-grouping ( something like A - AB - B) I came across the HSD.test in the agricolae-package, but... unfortunately I do not get an output (like here in the answer http://stats.stackexchange.com/questions/31547/how-to-obtain-the-results-of-a-tukey-hsd-post-hoc-test-in-a-table-showing-groupe ) I did it like this: ###### ANOVA anova.typabunmit<-aov(ds.typabunmit$abun ~ ds.typabunmit$typ) summary(anova.typabunmit) summary.lm(anova.typabunmit) ###### post HOC tukey.typabunmit<-TukeyHSD(anova.typabunmit) tukey.typabunmit ###### HSD HSD.test(anova.typabunmit, "abun", group=TRUE) and the ONLY output is this: Name: abun ds.typabunmit$typ I would be very pleased about some ides..:! -- View this message in context: http://r.789695.n4.nabble.com/Anova-and-tukey-grouping-tp4644485.html Sent from the R help mailing list archive at Nabble.com.
Anova and tukey-grouping
7 messages · Landi, arun
HI, I guess there is a mistake in your code.? You should have used "typ" instead of "abun" as "abun" is the dependent variable. summary(fm1 <- aov(breaks ~ wool + tension, data = warpbreaks)) myresults??? <-? TukeyHSD(fm1, "tension", ordered = TRUE) library(agricolae) HSD.test(fm1,"wool",group=TRUE) #Study: #HSD Test for breaks #Mean Square Error:? 134.9578 #wool,? means #??? breaks? std.err replication #A 31.03704 3.050609????????? 27 #B 25.25926 1.789963????????? 27 #alpha: 0.05 ; Df Error: 50 #Critical Value of Studentized Range: 2.840532 #Honestly Significant Difference: 6.350628 #Means with the same letter are not significantly different. #Groups, Treatments and means #a ??? ?A ??? ?31.037037037037 #a ??? ?B ??? ?25.2592592592593 ? A.K. ----- Original Message ----- From: Landi <ent-artet at gmx.de> To: r-help at r-project.org Cc: Sent: Friday, September 28, 2012 5:41 AM Subject: [R] Anova and tukey-grouping Hello, I am really new to R and it's still a challenge to me. Currently I'm working on my Master's Thesis. My supervisor works with SAS and is not familiar with R at all. I want to run an Anova, a tukey-test and as a result I want to have the tukey-grouping ( something like A - AB - B) I came across the HSD.test in the agricolae-package, but... unfortunately I do not get an output (like here in the answer http://stats.stackexchange.com/questions/31547/how-to-obtain-the-results-of-a-tukey-hsd-post-hoc-test-in-a-table-showing-groupe ) I did it like this: ######? ANOVA anova.typabunmit<-aov(ds.typabunmit$abun ~ ds.typabunmit$typ) summary(anova.typabunmit) summary.lm(anova.typabunmit) ###### post HOC tukey.typabunmit<-TukeyHSD(anova.typabunmit) tukey.typabunmit ###### HSD HSD.test(anova.typabunmit, "abun", group=TRUE) and the ONLY output is this: Name:? abun ds.typabunmit$typ I would be very pleased about some ides..:! -- View this message in context: http://r.789695.n4.nabble.com/Anova-and-tukey-grouping-tp4644485.html Sent from the R help mailing list archive at Nabble.com. ______________________________________________ R-help at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Hello ! Thanks for your advice. I tried it, but the output is the same:
HSD.test(anova.typabunmit, "typ", group=TRUE)
Name: typ ds.typabunmit$typ I don't get the values...!?!? -- View this message in context: http://r.789695.n4.nabble.com/Anova-and-tukey-grouping-tp4644485p4644513.html Sent from the R help mailing list archive at Nabble.com.
Hi, As I mentioned earlier, these are just guess work until you provide a subset of your data with dput().? Also, please check the structure of the data with str(). A.K.? ----- Original Message ----- From: Landi <ent-artet at gmx.de> To: r-help at r-project.org Cc: Sent: Friday, September 28, 2012 10:35 AM Subject: Re: [R] Anova and tukey-grouping Hello ! Thanks for your advice. I tried it, but the output is the same:
HSD.test(anova.typabunmit, "typ", group=TRUE)
Name:? typ ds.typabunmit$typ I don't get the values...!?!? -- View this message in context: http://r.789695.n4.nabble.com/Anova-and-tukey-grouping-tp4644485p4644513.html Sent from the R help mailing list archive at Nabble.com. ______________________________________________ R-help at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
1 day later
typohne.csv <http://r.789695.n4.nabble.com/file/n4644635/typohne.csv> Hello arun kirshna, I checked str() but I do not see any mistake. Find attached a subset of my data (did you mean this with "dput()" ?) Typ= treatment abun= abundance div= diversity, number of species best wishes. -- View this message in context: http://r.789695.n4.nabble.com/Anova-and-tukey-grouping-tp4644485p4644635.html Sent from the R help mailing list archive at Nabble.com.
Hi,
I got your data from Nabble.? I meant to do it by dput() because the .csv files may not get through the R-help mailing list.
This is what I got:
dat1<-read.delim("typohne.csv")
?str(dat1)
#'data.frame':??? 60 obs. of? 3 variables:
# $ typ : Factor w/ 5 levels "A","B","C","D",..: 1 2 3 4 5 1 2 3 4 5 ...
# $ abun: int? 7 3 14 8 15 5 21 19 9 21 ...
# $ div : int? 7 3 11 6 14 5 12 15 8 12 ...
summary(fm1<-aov(abun~typ,data=dat1))
#??????????? Df Sum Sq Mean Sq F value Pr(>F)?
#typ????????? 4??? 847? 211.69?? 3.654 0.0104 *
#Residuals?? 55?? 3186?? 57.93????????????????
#---
#Signif. codes:? 0 ?***? 0.001 ?**? 0.01 ?*? 0.05 ?.? 0.1 ? ? 1
?myresults<-TukeyHSD(fm1,"typ",ordered=TRUE)
?myresults
#? Tukey multiple comparisons of means
#??? 95% family-wise confidence level
#??? factor levels have been ordered
#Fit: aov(formula = abun ~ typ, data = dat1)
#
#$typ
#???????? diff??????? lwr????? upr???? p adj
#B-A? 6.500000 -2.2633699 15.26337 0.2382355
#D-A? 6.750000 -2.0133699 15.51337 0.2055350
#E-A? 9.083333? 0.3199635 17.84670 0.0386441
#C-A 11.166667? 2.4032968 19.93004 0.0060292
#D-B? 0.250000 -8.5133699? 9.01337 0.9999902
#E-B? 2.583333 -6.1800365 11.34670 0.9197106
#C-B? 4.666667 -4.0967032 13.43004 0.5657010
#E-D? 2.333333 -6.4300365 11.09670 0.9432637
#C-D? 4.416667 -4.3467032 13.18004 0.6167517
#C-E? 2.083333 -6.6800365 10.84670 0.9619249
library(agricolae)
?HSD.test(fm1,"typ",group=TRUE)
#Study:
#HSD Test for abun
#Mean Square Error:? 57.92879
#typ,? means
#????? abun?? std.err replication
#A? 6.25000 0.6976693????????? 12
#B 12.75000 2.4061947????????? 12
#C 17.41667 2.9062585????????? 12
#D 13.00000 2.6198543????????? 12
#E 15.33333 1.5970301????????? 12
#alpha: 0.05 ; Df Error: 55
#Critical Value of Studentized Range: 3.988545
#Honestly Significant Difference: 8.76337
#Means with the same letter are not significantly different.
#Groups, Treatments and means
#a ??? ?C ??? ?17.4166666666667
#a ??? ?E ??? ?15.3333333333333
#ab ??? ?D ??? ?13
#ab ??? ?B ??? ?12.75
# b ??? ?A ??? ?6.25
I am not sure why you didn't get the results as above.? Check str() to see whether the str() I got matches with yours.
Have a great day!
A.K.
???
----- Original Message -----
From: Landi <ent-artet at gmx.de>
To: r-help at r-project.org
Cc:
Sent: Friday, September 28, 2012 10:35 AM
Subject: Re: [R] Anova and tukey-grouping
Hello !
Thanks for your advice. I tried it, but the output is the same:
HSD.test(anova.typabunmit, "typ", group=TRUE)
Name:? typ ds.typabunmit$typ I don't get the values...!?!? -- View this message in context: http://r.789695.n4.nabble.com/Anova-and-tukey-grouping-tp4644485p4644513.html Sent from the R help mailing list archive at Nabble.com. ______________________________________________ R-help at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Hello again ! It worked exactly the same way as yours! I'm kind of astonished, because in "my" opinion our skripts are the same (obviously not...). Whatever! It works :-D Tomorrow (as where I live it's already evening...sunday) will be a great day, indeed, and I can go on with analysis ! I really appreciate the conversation with you and your support! -- View this message in context: http://r.789695.n4.nabble.com/Anova-and-tukey-grouping-tp4644485p4644642.html Sent from the R help mailing list archive at Nabble.com.