У меня возникли некоторые проблемы с пакетом welchADF в R, и я надеялся, что смогу кое-что понять.
У меня есть следующие данные:
SubjectTag Task Order FSIQ SiteID Gender Age Band Motion L
68200328 2 1 -16.43452381 2 0 -2.557225434 1 0.008024825 35.74936778
68200328 2 1 -16.43452381 2 0 -2.557225434 2 0.008024825 101.5911193
68200328 2 1 -16.43452381 2 0 -2.557225434 3 0.008024825 131.2113343
68200328 2 1 -16.43452381 2 0 -2.557225434 4 0.008024825 89.12478552
68200328 2 1 -16.43452381 2 0 -2.557225434 5 0.008024825 60.73933429
68200328 2 1 -16.43452381 2 0 -2.557225434 6 0.008024825 75.03752888
68200328 2 1 -16.43452381 2 0 -2.557225434 7 0.008024825 63.2052377
68200328 1 2 -16.43452381 2 0 -2.557225434 1 -0.003373914 49.50971077
68200328 1 2 -16.43452381 2 0 -2.557225434 2 -0.003373914 93.27074874
68200328 1 2 -16.43452381 2 0 -2.557225434 3 -0.003373914 129.6672651
68200328 1 2 -16.43452381 2 0 -2.557225434 4 -0.003373914 111.3210527
68200328 1 2 -16.43452381 2 0 -2.557225434 5 -0.003373914 87.01493346
68200328 1 2 -16.43452381 2 0 -2.557225434 6 -0.003373914 71.18978139
68200328 1 2 -16.43452381 2 0 -2.557225434 7 -0.003373914 106.6785894
68201840 2 1 -17.43452381 2 1 2.442774566 1 -0.013665059 46.2357014
68201840 2 1 -17.43452381 2 1 2.442774566 2 -0.013665059 112.9112605
68201840 2 1 -17.43452381 2 1 2.442774566 3 -0.013665059 55.51628871
68201840 2 1 -17.43452381 2 1 2.442774566 4 -0.013665059 94.91140829
68201840 2 1 -17.43452381 2 1 2.442774566 5 -0.013665059 67.52559103
68201840 2 1 -17.43452381 2 1 2.442774566 6 -0.013665059 69.8649204
68201840 2 1 -17.43452381 2 1 2.442774566 7 -0.013665059 65.8327929
68201840 1 2 -17.43452381 2 1 2.442774566 1 -0.013113291 42.99225398
68201840 1 2 -17.43452381 2 1 2.442774566 2 -0.013113291 70.05451222
68201840 1 2 -17.43452381 2 1 2.442774566 3 -0.013113291 54.21563787
68201840 1 2 -17.43452381 2 1 2.442774566 4 -0.013113291 67.92122394
68201840 1 2 -17.43452381 2 1 2.442774566 5 -0.013113291 74.96736338
68201840 1 2 -17.43452381 2 1 2.442774566 6 -0.013113291 56.73479757
68201840 1 2 -17.43452381 2 1 2.442774566 7 -0.013113291 64.46792425
68202519 1 1 15.56547619 2 0 1.542774566 1 -0.017903407 29.20293635
68202519 1 1 15.56547619 2 0 1.542774566 2 -0.017903407 78.8543775
68202519 1 1 15.56547619 2 0 1.542774566 3 -0.017903407 45.17232516
68202519 1 1 15.56547619 2 0 1.542774566 4 -0.017903407 105.1028914
68202519 1 1 15.56547619 2 0 1.542774566 5 -0.017903407 45.70577992
68202519 1 1 15.56547619 2 0 1.542774566 6 -0.017903407 84.68149947
68202519 1 1 15.56547619 2 0 1.542774566 7 -0.017903407 44.29849004
68202519 2 2 15.56547619 2 0 1.542774566 1 -0.013603737 34.76901859
68202519 2 2 15.56547619 2 0 1.542774566 2 -0.013603737 70.97798267
68202519 2 2 15.56547619 2 0 1.542774566 3 -0.013603737 85.87488696
68202519 2 2 15.56547619 2 0 1.542774566 4 -0.013603737 100.5963616
68202519 2 2 15.56547619 2 0 1.542774566 5 -0.013603737 52.66051211
68202519 2 2 15.56547619 2 0 1.542774566 6 -0.013603737 62.7709995
68202519 2 2 15.56547619 2 0 1.542774566 7 -0.013603737 62.29203598
68203813 2 1 -10.43452381 2 0 1.042774566 1 0.10297146 55.26352953
68203813 2 1 -10.43452381 2 0 1.042774566 2 0.10297146 73.82123836
68203813 2 1 -10.43452381 2 0 1.042774566 3 0.10297146 79.03696001
68203813 2 1 -10.43452381 2 0 1.042774566 4 0.10297146 62.49673835
68203813 2 1 -10.43452381 2 0 1.042774566 5 0.10297146 48.87038596
68203813 2 1 -10.43452381 2 0 1.042774566 6 0.10297146 60.68370317
68203813 2 1 -10.43452381 2 0 1.042774566 7 0.10297146 59.10522803
68203813 1 2 -10.43452381 2 0 1.042774566 1 0.047049044 44.25198487
68203813 1 2 -10.43452381 2 0 1.042774566 2 0.047049044 59.81797027
68203813 1 2 -10.43452381 2 0 1.042774566 3 0.047049044 88.57783191
68203813 1 2 -10.43452381 2 0 1.042774566 4 0.047049044 59.36434895
68203813 1 2 -10.43452381 2 0 1.042774566 5 0.047049044 65.17707813
68203813 1 2 -10.43452381 2 0 1.042774566 6 0.047049044 52.0815453
68203813 1 2 -10.43452381 2 0 1.042774566 7 0.047049044 45.16523765
68205852 2 1 9.56547619 2 1 -1.657225434 1 0.004102858 32.59102712
68205852 2 1 9.56547619 2 1 -1.657225434 2 0.004102858 65.70855965
68205852 2 1 9.56547619 2 1 -1.657225434 3 0.004102858 114.6908268
68205852 2 1 9.56547619 2 1 -1.657225434 4 0.004102858 53.87874146
68205852 2 1 9.56547619 2 1 -1.657225434 5 0.004102858 88.05750134
68205852 2 1 9.56547619 2 1 -1.657225434 6 0.004102858 69.09716175
68205852 2 1 9.56547619 2 1 -1.657225434 7 0.004102858 62.75341116
68205852 1 2 9.56547619 2 1 -1.657225434 1 0.016121302 37.47220195
68205852 1 2 9.56547619 2 1 -1.657225434 2 0.016121302 68.07167045
68205852 1 2 9.56547619 2 1 -1.657225434 3 0.016121302 114.4713806
68205852 1 2 9.56547619 2 1 -1.657225434 4 0.016121302 77.18999387
68205852 1 2 9.56547619 2 1 -1.657225434 5 0.016121302 105.4749687
68205852 1 2 9.56547619 2 1 -1.657225434 6 0.016121302 68.77222643
68205852 1 2 9.56547619 2 1 -1.657225434 7 0.016121302 67.22895844
(фрагмент из 2352 строки данных).
Первоначально я подбирал lmer из lme4:
lmer.out <- lmer(L ~ Age + Gender + FSIQ + Order + SiteID + Task + Band*Motion + (1|SubjectTag),data=data)
Однако остатки значительно ненормальные.
Для решения этой проблемы я хотел использовать welchADF, поскольку он более устойчив к таким нарушениям.
Однако, похоже, что большинство команд, которые я запускаю, выдает различные ошибки:
welchADF.test(lmer.out)
Error in .check.parameters(data, response, between.s, within.s, subject, :
argument "response" is missing, with no default
welchADF.test(data, response = "L", between.s = c("SiteID","Age","FSIQ","Gender"), within.s = c("Task","Band"), subject = "SubjectTag")
Error in .check.parameters(data, response, between.s, within.s, subject, :
ERROR: response L not found in the data
welchADF.test(data, response = "L", between.s = c("Age"), within.s = c("Task","Band"), subj
ect = "SubjectTag")
Error in if (det(r %*% sigma %*% t(r)) == 0) { :
missing value where TRUE/FALSE needed
In addition: Warning message:
In if (within.s == "multivariate") { :
the condition has length > 1 and only the first element will be used
welchADF.test(L ~ Age + Gender + FSIQ + Order + SiteID + Task + Band*Motion + (SubjectTag), data)
Error in table(betweenSubjectData) :
attempt to make a table with >= 2^31 elements
welchADF.test(data, response = "L", between.s = c("SiteID","Age","FSIQ","Gender"), within.s
= c("Task","Band"), subject = "SubjectTag")
Error in .reshape.data(data, response, between.s, within.s, subject, nlevelslist) :
Data corresponding to some between-subjects factor combination(s) are missing:
In addition: Warning message:
In if (within.s == "multivariate") { :
the condition has length > 1 and only the first element will be used
For Gender AND SiteID
welchADF.test(data, response = "L", between.s = c("Gender","SiteID"), within.s = c("Task","
Band"), subject = "SubjectTag")
Error in .reshape.data(data, response, between.s, within.s, subject, nlevelslist) :
Data corresponding to some between-subjects factor combination(s) are missing:
In addition: Warning message:
In if (within.s == "multivariate") { :
the condition has length > 1 and only the first element will be used
Я знаю, что ни одна из этих точек данных отсутствует (все NA были удалены из импортированного .csv)
Однако, кажется, что следующее работает просто отлично:
Call:
welchADF.test(formula = data, response = "L", between.s = c("SiteID"),
within.s = c("Task", "Band"), subject = "SubjectTag")
Welch-James Approximate DF Test (Least squares means & variances)
Omnibus test(s) of effect and/or interactions
SiteID Task Band Task:Band SiteID : Task
Pr(>WJ) 0.003974401 3.0870916e-05 0 1.1627199e-10 0.66542166
SiteID : Band SiteID : Task:Band
Pr(>WJ) 4.1840975e-12 0.22652975
Warning message:
In if (within.s == "multivariate") { :
the condition has length > 1 and only the first element will be used
welchADF.test(formula = L ~ SiteID * Band * Task + (Band * Task |
SubjectTag), data = data)
Welch-James Approximate DF Test (Least squares means & variances)
Omnibus test(s) of effect and/or interactions
SiteID Band Task Band:Task SiteID : Band
Pr(>WJ) 0.003974401 0 3.0870916e-05 1.1627199e-10 4.1840975e-12
SiteID : Task SiteID : Band:Task
Pr(>WJ) 0.66542166 0.22652975
Warning message:
In if (within.s == "multivariate") { :
the condition has length > 1 and only the first element will be used
For Gender or SiteID:
Call:
welchADF.test(formula = data, response = "L", between.s = c("Gender"),
within.s = c("Task", "Band"), subject = "SubjectTag")
Welch-James Approximate DF Test (Least squares means & variances)
Omnibus test(s) of effect and/or interactions
Gender Task Band Task:Band Gender : Task Gender : Band
Pr(>WJ) 0.46913667 1.7342508e-06 0 6.1087843e-09 0.075641611 1.3068659e-05
Gender : Task:Band
Pr(>WJ) 0.71917955
Warning message:
In if (within.s == "multivariate") { :
the condition has length > 1 and only the first element will be used
Любые предложения относительно того, что может быть неправильным, будут оценены.
Руководство и код пакета находятся:
https://cran.r-project.org/web/packages/welchADF/welchADF.pdf
https://rdrr.io/cran/welchADF/src/R/welch-wrapper.R