I have started analyzing my data using R software in 2 way repeated measures according to, "NormalWithR (toronto.edu)". it uses lme4 and car libraries. It worked fine, but when I proceed for # Two-way table of means by command, "Anokhi = meantable[1:4, 4]; Desi Karela = meantable[5:8, 4]" as mentioned in above said pdf, it displayed error message, "Error: object 'meantable' not found".
kindly help me to resolve this issue.
From the console
> ls()
if meantable does not appear, it means that it hasn't been created (is "not in the namespace") and any references to it will produce the error.
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Looking at the pdf, it looks like they forgot to assign this variable. Judging by the context, on page 2 it should be:
meantable = aggregate(rtime,by=list(ear,handed),FUN=mean) # First changes fastest
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I am a PhD student in Food Technology and harvested 10 fruit varieties at 4 maturity stages. I need mixed nodel ANOVA in repeated measures 2 way with simple effects, mean effects, interaction effects and interaction graphs.
Meantable is formed but when proceed for two way mean table then error displayed is, " length of 'dimnames' [2] not equal to array extent" and no two way table is produced. also when I used command "# Want a table of means in a similar format., "> meantable # Again" it shows one way mean table as in middle and now two way table. Your help in this regard will be highly appreciated.
the commands which I used along with their outcome are as under.
library(lme4)
> library(car)
> data <-read.csv(file.choose())
> head(data)
> str(data)
'data.frame': 120 obs. of 4 variables:
$ sub : int 1 1 1 1 1 1 1 1 1 1 ...
$ varieties: chr "Anokhi" "Anokhi" "Anokhi" "Desikarela" ...
$ stages : chr "S1" "S1" "S1" "S1" ...
$ vitc : num 137 135 139 146 141 ...
> attach(dichotic) # Make variable names available
Error in attach(dichotic) : object 'dichotic' not found
> attach(data) # Make variable names available
**The following objects are masked from data (pos = 3):**
** stages, sub, varieties, vitc**
**The following objects are masked from data (pos = 4):**
** stages, sub, varieties, vitc**
> # Sample sizes
> table(varieties, stages)
stages
varieties S1 S2 S3 S4
Anokhi 3 3 3 3
Desikarela 3 3 3 3
Dilbahar 3 3 3 3
Gurh 3 3 3 3
Khobani 3 3 3 3
Mahmoodwali 3 3 3 3
Munirwali 3 3 3 3
Pakwhite 3 3 3 3
Suffon 3 3 3 3
Umran 3 3 3 3
> # Treatment means
> meantable=aggregate(vitc, by=list(stages, varieties), FUN=mean)
> # Two-way table of means
> Anokhi = meantable[1:4, 4]; Desikarela = meantable[5:8, 4]; Dilbahar = meantable[9:12, 4]; Gurh = meantable[13:16, 4]; Khobani = meantable[17:20, 4]; Mahmoodwali = meantable[21:24, 4]; Munirwali = meantable[25:28, 4]; Pakwhite = meantable[29:32, 4]; Suffon = meantable[33:36, 4]; Umran = meantable[37:40, 4]
> aggregate(vitc, by=list(stages, varieties), FUN=mean)
> # Two-way table of means
> Anokhi = meantable[1:4, 4]; Desikarela = meantable[5:8, 4]; Dilbahar = meantable[9:12, 4]; Gurh = meantable[13:16, 4]; Khobani = meantable[17:20, 4]; Mahmoodwali = meantable[21:24, 4]; Munirwali = meantable[25:28, 4]; Pakwhite = meantable[29:32, 4]; Suffon = meantable[33:36, 4]; Umran = meantable[37:40, 4]
> TwoWay = rbind(varieties,stages)
> colnames(TwoWay) = c("S1","S2","S3","S4")
Error in dimnames(x) <- dn :
length of 'dimnames' [2] not equal to array extent
>
> TwoWay
[,1] [,2] [,3] [,4] [,5] [,6]
varieties "Anokhi" "Anokhi" "Anokhi" "Desikarela" "Desikarela" "Desikarela"
stages "S1" "S1" "S1" "S1" "S1" "S1"
[,7] [,8] [,9] [,10] [,11] [,12] [,13] [,14]
varieties "Dilbahar" "Dilbahar" "Dilbahar" "Gurh" "Gurh" "Gurh" "Khobani" "Khobani"
stages "S1" "S1" "S1" "S1" "S1" "S1" "S1" "S1"
[,15] [,16] [,17] [,18] [,19]
varieties "Khobani" "Mahmoodwali" "Mahmoodwali" "Mahmoodwali" "Munirwali"
stages "S1" "S1" "S1" "S1" "S1"
[,20] [,21] [,22] [,23] [,24] [,25]
varieties "Munirwali" "Munirwali" "Pakwhite" "Pakwhite" "Pakwhite" "Suffon"
stages "S1" "S1" "S1" "S1" "S1" "S1"
[,26] [,27] [,28] [,29] [,30] [,31] [,32] [,33]
varieties "Suffon" "Suffon" "Umran" "Umran" "Umran" "Anokhi" "Anokhi" "Anokhi"
stages "S1" "S1" "S1" "S1" "S1" "S2" "S2" "S2"
[,34] [,35] [,36] [,37] [,38] [,39]
varieties "Desikarela" "Desikarela" "Desikarela" "Dilbahar" "Dilbahar" "Dilbahar"
stages "S2" "S2" "S2" "S2" "S2" "S2"
[,40] [,41] [,42] [,43] [,44] [,45] [,46]
varieties "Gurh" "Gurh" "Gurh" "Khobani" "Khobani" "Khobani" "Mahmoodwali"
stages "S2" "S2" "S2" "S2" "S2" "S2" "S2"
[,47] [,48] [,49] [,50] [,51]
varieties "Mahmoodwali" "Mahmoodwali" "Munirwali" "Munirwali" "Munirwali"
stages "S2" "S2" "S2" "S2" "S2"
[,52] [,53] [,54] [,55] [,56] [,57] [,58]
varieties "Pakwhite" "Pakwhite" "Pakwhite" "Suffon" "Suffon" "Suffon" "Umran"
stages "S2" "S2" "S2" "S2" "S2" "S2" "S2"
[,59] [,60] [,61] [,62] [,63] [,64] [,65]
varieties "Umran" "Umran" "Anokhi" "Anokhi" "Anokhi" "Desikarela" "Desikarela"
stages "S2" "S2" "S3" "S3" "S3" "S3" "S3"
[,66] [,67] [,68] [,69] [,70] [,71] [,72]
varieties "Desikarela" "Dilbahar" "Dilbahar" "Dilbahar" "Gurh" "Gurh" "Gurh"
stages "S3" "S3" "S3" "S3" "S3" "S3" "S3"
[,73] [,74] [,75] [,76] [,77] [,78]
varieties "Khobani" "Khobani" "Khobani" "Mahmoodwali" "Mahmoodwali" "Mahmoodwali"
stages "S3" "S3" "S3" "S3" "S3" "S3"
[,79] [,80] [,81] [,82] [,83] [,84]
varieties "Munirwali" "Munirwali" "Munirwali" "Pakwhite" "Pakwhite" "Pakwhite"
stages "S3" "S3" "S3" "S3" "S3" "S3"
[,85] [,86] [,87] [,88] [,89] [,90] [,91] [,92]
varieties "Suffon" "Suffon" "Suffon" "Umran" "Umran" "Umran" "Anokhi" "Anokhi"
stages "S3" "S3" "S3" "S3" "S3" "S3" "S4" "S4"
[,93] [,94] [,95] [,96] [,97] [,98]
varieties "Anokhi" "Desikarela" "Desikarela" "Desikarela" "Dilbahar" "Dilbahar"
stages "S4" "S4" "S4" "S4" "S4" "S4"
[,99] [,100] [,101] [,102] [,103] [,104] [,105]
varieties "Dilbahar" "Gurh" "Gurh" "Gurh" "Khobani" "Khobani" "Khobani"
stages "S4" "S4" "S4" "S4" "S4" "S4" "S4"
[,106] [,107] [,108] [,109] [,110]
varieties "Mahmoodwali" "Mahmoodwali" "Mahmoodwali" "Munirwali" "Munirwali"
stages "S4" "S4" "S4" "S4" "S4"
[,111] [,112] [,113] [,114] [,115] [,116] [,117]
varieties "Munirwali" "Pakwhite" "Pakwhite" "Pakwhite" "Suffon" "Suffon" "Suffon"
stages "S4" "S4" "S4" "S4" "S4" "S4" "S4"
[,118] [,119] [,120]
varieties "Umran" "Umran" "Umran"
stages "S4" "S4" "S4"
> TwoWay(meantable)
Error in TwoWay(meantable) : could not find function "TwoWay"
> # Marginal means
>
> aggregate(rtime,by=list(varieties),FUN=mean)
Error in aggregate(rtime, by = list(varieties), FUN = mean) :
object 'rtime' not found
> aggregate(vitc,by=list(varieties),FUN=mean)
> # Repeated measures with a mixed model
> dichotic = lmer(vitc ~ varieties*stages + (1 | subject))
Error in eval(predvars, data, env) : object 'subject' not found
> dichotic = lmer(rtime ~ handed*ear + (1 | sub))
Error in eval(predvars, data, env) : object 'rtime' not found
> dichotic = lmer(vitc ~ varieties*stages + (1 | sub))
> Anova(dichotic, test="F") # F tests (from car package)
Analysis of Deviance Table (Type II Wald F tests with Kenward-Roger df)
>
> # Multiple comparisons: Which marginal means are different?
>
> # The combination variable varietiesstages will have 40 values
> n = length(vitc); n
[1] 120
> varietiesstages = character(n) # A character-valued variable of length n
> for(j in 1:n) varietiesstages[j] = paste(varieties[j],stages[j],sep='')
>
> varietiesstages = factor(varietiesstages) # Maybe would be interpreted as a factor anyway
> head(data.frame(varieties,stages,varietiesstages))
varieties stages varietiesstages
1 Anokhi S1 AnokhiS1
2 Anokhi S1 AnokhiS1
3 Anokhi S1 AnokhiS1
4 Desikarela S1 DesikarelaS1
5 Desikarela S1 DesikarelaS1
6 Desikarela S1 DesikarelaS1
>
> table(varietiesstages) # Sample sizes
varietiesstages
AnokhiS1 AnokhiS2 AnokhiS3 AnokhiS4 DesikarelaS1 DesikarelaS2
3 3 3 3 3 3
DesikarelaS3 DesikarelaS4 DilbaharS1 DilbaharS2 DilbaharS3 DilbaharS4
3 3 3 3 3 3
GurhS1 GurhS2 GurhS3 GurhS4 KhobaniS1 KhobaniS2
3 3 3 3 3 3
KhobaniS3 KhobaniS4 MahmoodwaliS1 MahmoodwaliS2 MahmoodwaliS3 MahmoodwaliS4
3 3 3 3 3 3
MunirwaliS1 MunirwaliS2 MunirwaliS3 MunirwaliS4 PakwhiteS1 PakwhiteS2
3 3 3 3 3 3
PakwhiteS3 PakwhiteS4 SuffonS1 SuffonS2 SuffonS3 SuffonS4
3 3 3 3 3 3
UmranS1 UmranS2 UmranS3 UmranS4
3 3 3 3
> # Want a table of means in a similar format.
> meantable # AgainI am a PhD student in Food Technology and harvested 10 fruit varieties at 4 maturity stages. I need mixed nodel ANOVA in repeated measures 2 way with simple effects, mean effects, interaction effects and interaction graphs.
Meantable is formed by command, "aggregate(vitc, by=list(stages, varieties), FUN=mean)" however, command specified by you, "meantable=aggregate(vitc, by=list(stages, varieties), FUN=mean)" produce no results and when proceed for two way mean table by Commands,, "> TwoWay = rbind(varieties,stages)
colnames(TwoWay) = c("S1","S2","S3","S4")
then Error in dimnames(x) <- dn : length of 'dimnames' [2] not equal to array extent" is displayed" and no two way table is produced. also when I used command "# Want a table of means in a similar format., "> meantable # Again" it shows one way mean table as in middle and now two way table. Your help in this regard will be highly appreciated.
the commands which I used along with their outcome are as under.
library(lme4)
> library(car)
> data <-read.csv(file.choose())
> head(data)
> str(data)
'data.frame': 120 obs. of 4 variables:
$ sub : int 1 1 1 1 1 1 1 1 1 1 ...
$ varieties: chr "Anokhi" "Anokhi" "Anokhi" "Desikarela" ...
$ stages : chr "S1" "S1" "S1" "S1" ...
$ vitc : num 137 135 139 146 141 ...
> attach(dichotic) # Make variable names available
Error in attach(dichotic) : object 'dichotic' not found
> attach(data) # Make variable names available
The following objects are masked from data (pos = 3):
stages, sub, varieties, vitc
The following objects are masked from data (pos = 4):
stages, sub, varieties, vitc
> # Sample sizes
> table(handed,ear)
Error in table(handed, ear) : object 'handed' not found
> table(varieties, stages)
stages
varieties S1 S2 S3 S4
Anokhi 3 3 3 3
Desikarela 3 3 3 3
Dilbahar 3 3 3 3
Gurh 3 3 3 3
Khobani 3 3 3 3
Mahmoodwali 3 3 3 3
Munirwali 3 3 3 3
Pakwhite 3 3 3 3
Suffon 3 3 3 3
Umran 3 3 3 3
> # Treatment means
> meantable=aggregate(vitc, by=list(stages, varieties), FUN=mean)
> # Two-way table of means
> Anokhi = meantable[1:4, 4]; Desikarela = meantable[5:8, 4]; Dilbahar = meantable[9:12, 4]; Gurh = meantable[13:16, 4]; Khobani = meantable[17:20, 4]; Mahmoodwali = meantable[21:24, 4]; Munirwali = meantable[25:28, 4]; Pakwhite = meantable[29:32, 4]; Suffon = meantable[33:36, 4]; Umran = meantable[37:40, 4]
> aggregate(vitc, by=list(stages, varieties), FUN=mean)
> # Two-way table of means
> Anokhi = meantable[1:4, 4]; Desikarela = meantable[5:8, 4]; Dilbahar = meantable[9:12, 4]; Gurh = meantable[13:16, 4]; Khobani = meantable[17:20, 4]; Mahmoodwali = meantable[21:24, 4]; Munirwali = meantable[25:28, 4]; Pakwhite = meantable[29:32, 4]; Suffon = meantable[33:36, 4]; Umran = meantable[37:40, 4]
> TwoWay = rbind(varieties,stages)
> colnames(TwoWay) = c("S1","S2","S3","S4")
Error in dimnames(x) <- dn :
length of 'dimnames' [2] not equal to array extent
>
> TwoWay
[,1] [,2] [,3] [,4] [,5] [,6]
varieties "Anokhi" "Anokhi" "Anokhi" "Desikarela" "Desikarela" "Desikarela"
stages "S1" "S1" "S1" "S1" "S1" "S1"
[,7] [,8] [,9] [,10] [,11] [,12] [,13] [,14]
varieties "Dilbahar" "Dilbahar" "Dilbahar" "Gurh" "Gurh" "Gurh" "Khobani" "Khobani"
stages "S1" "S1" "S1" "S1" "S1" "S1" "S1" "S1"
[,15] [,16] [,17] [,18] [,19]
varieties "Khobani" "Mahmoodwali" "Mahmoodwali" "Mahmoodwali" "Munirwali"
stages "S1" "S1" "S1" "S1" "S1"
[,20] [,21] [,22] [,23] [,24] [,25]
varieties "Munirwali" "Munirwali" "Pakwhite" "Pakwhite" "Pakwhite" "Suffon"
stages "S1" "S1" "S1" "S1" "S1" "S1"
[,26] [,27] [,28] [,29] [,30] [,31] [,32] [,33]
varieties "Suffon" "Suffon" "Umran" "Umran" "Umran" "Anokhi" "Anokhi" "Anokhi"
stages "S1" "S1" "S1" "S1" "S1" "S2" "S2" "S2"
[,34] [,35] [,36] [,37] [,38] [,39]
varieties "Desikarela" "Desikarela" "Desikarela" "Dilbahar" "Dilbahar" "Dilbahar"
stages "S2" "S2" "S2" "S2" "S2" "S2"
[,40] [,41] [,42] [,43] [,44] [,45] [,46]
varieties "Gurh" "Gurh" "Gurh" "Khobani" "Khobani" "Khobani" "Mahmoodwali"
stages "S2" "S2" "S2" "S2" "S2" "S2" "S2"
[,47] [,48] [,49] [,50] [,51]
varieties "Mahmoodwali" "Mahmoodwali" "Munirwali" "Munirwali" "Munirwali"
stages "S2" "S2" "S2" "S2" "S2"
[,52] [,53] [,54] [,55] [,56] [,57] [,58]
varieties "Pakwhite" "Pakwhite" "Pakwhite" "Suffon" "Suffon" "Suffon" "Umran"
stages "S2" "S2" "S2" "S2" "S2" "S2" "S2"
[,59] [,60] [,61] [,62] [,63] [,64] [,65]
varieties "Umran" "Umran" "Anokhi" "Anokhi" "Anokhi" "Desikarela" "Desikarela"
stages "S2" "S2" "S3" "S3" "S3" "S3" "S3"
[,66] [,67] [,68] [,69] [,70] [,71] [,72]
varieties "Desikarela" "Dilbahar" "Dilbahar" "Dilbahar" "Gurh" "Gurh" "Gurh"
stages "S3" "S3" "S3" "S3" "S3" "S3" "S3"
[,73] [,74] [,75] [,76] [,77] [,78]
varieties "Khobani" "Khobani" "Khobani" "Mahmoodwali" "Mahmoodwali" "Mahmoodwali"
stages "S3" "S3" "S3" "S3" "S3" "S3"
[,79] [,80] [,81] [,82] [,83] [,84]
varieties "Munirwali" "Munirwali" "Munirwali" "Pakwhite" "Pakwhite" "Pakwhite"
stages "S3" "S3" "S3" "S3" "S3" "S3"
[,85] [,86] [,87] [,88] [,89] [,90] [,91] [,92]
varieties "Suffon" "Suffon" "Suffon" "Umran" "Umran" "Umran" "Anokhi" "Anokhi"
stages "S3" "S3" "S3" "S3" "S3" "S3" "S4" "S4"
[,93] [,94] [,95] [,96] [,97] [,98]
varieties "Anokhi" "Desikarela" "Desikarela" "Desikarela" "Dilbahar" "Dilbahar"
stages "S4" "S4" "S4" "S4" "S4" "S4"
[,99] [,100] [,101] [,102] [,103] [,104] [,105]
varieties "Dilbahar" "Gurh" "Gurh" "Gurh" "Khobani" "Khobani" "Khobani"
stages "S4" "S4" "S4" "S4" "S4" "S4" "S4"
[,106] [,107] [,108] [,109] [,110]
varieties "Mahmoodwali" "Mahmoodwali" "Mahmoodwali" "Munirwali" "Munirwali"
stages "S4" "S4" "S4" "S4" "S4"
[,111] [,112] [,113] [,114] [,115] [,116] [,117]
varieties "Munirwali" "Pakwhite" "Pakwhite" "Pakwhite" "Suffon" "Suffon" "Suffon"
stages "S4" "S4" "S4" "S4" "S4" "S4" "S4"
[,118] [,119] [,120]
varieties "Umran" "Umran" "Umran"
stages "S4" "S4" "S4"
> TwoWay(meantable)
Error in TwoWay(meantable) : could not find function "TwoWay"
> # Marginal means
>
> aggregate(rtime,by=list(varieties),FUN=mean)
Error in aggregate(rtime, by = list(varieties), FUN = mean) :
object 'rtime' not found
> aggregate(vitc,by=list(varieties),FUN=mean)
> aggregate(vitc,by=list(stages),FUN=mean)
> # Naive fixed effects analysis
>
> anova(lm(vitc ~ varieties*stages))
Analysis of Variance Table
> # Repeated measures with a mixed model
> dichotic = lmer(vitc ~ varieties*stages + (1 | subject))
Error in eval(predvars, data, env) : object 'subject' not found
> dichotic = lmer(rtime ~ handed*ear + (1 | sub))
Error in eval(predvars, data, env) : object 'rtime' not found
> dichotic = lmer(vitc ~ varieties*stages + (1 | sub))
> Anova(dichotic, test="F") # F tests (from car package)
Analysis of Deviance Table (Type II Wald F tests with Kenward-Roger df)
> # Multiple comparisons: Which marginal means are different?
>
> # The combination variable varietiesstages will have 40 values
> n = length(vitc); n
[1] 120
> varietiesstages = character(n) # A character-valued variable of length n
> for(j in 1:n) varietiesstages[j] = paste(varieties[j],stages[j],sep='')
>
> varietiesstages = factor(varietiesstages) # Maybe would be interpreted as a factor anyway
> head(data.frame(varieties,stages,varietiesstages))
varieties stages varietiesstages
1 Anokhi S1 AnokhiS1
2 Anokhi S1 AnokhiS1
3 Anokhi S1 AnokhiS1
4 Desikarela S1 DesikarelaS1
5 Desikarela S1 DesikarelaS1
6 Desikarela S1 DesikarelaS1
>
> table(varietiesstages) # Sample sizes
varietiesstages
AnokhiS1 AnokhiS2 AnokhiS3 AnokhiS4 DesikarelaS1 DesikarelaS2
3 3 3 3 3 3
DesikarelaS3 DesikarelaS4 DilbaharS1 DilbaharS2 DilbaharS3 DilbaharS4
3 3 3 3 3 3
GurhS1 GurhS2 GurhS3 GurhS4 KhobaniS1 KhobaniS2
3 3 3 3 3 3
KhobaniS3 KhobaniS4 MahmoodwaliS1 MahmoodwaliS2 MahmoodwaliS3 MahmoodwaliS4
3 3 3 3 3 3
MunirwaliS1 MunirwaliS2 MunirwaliS3 MunirwaliS4 PakwhiteS1 PakwhiteS2
3 3 3 3 3 3
PakwhiteS3 PakwhiteS4 SuffonS1 SuffonS2 SuffonS3 SuffonS4
3 3 3 3 3 3
UmranS1 UmranS2 UmranS3 UmranS4
3 3 3 3
> # Want a table of means in a similar format.
> meantable # Again
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