I have the following code for an LME:
IDRTlme <- lme(Score ~ Group*Condition, random = ~1|ID, data=IDRT)
I want to check the normality assumption, and so I have completed the following test:
shapiro.test(resid(IDRTlme))
Is this the correct way to undertake the Shapiro test on the output of an lme - if not, then any assistance would be very much appreciated?
Would be so grateful for any help!
Here is the data IDRT:
structure(list(ID = c("1993", "1993", "1993", "1993", "1993",
"1993", "1997", "1997", "1997", "1997", "1997", "1997", "19998",
"19998", "19998", "19998", "19998", "19998", "3122", "3122",
"3122", "3122", "3122", "3122", "3152", "3152", "3152", "3152",
"3152", "3152", "3182", "3182", "3182", "3182", "3182", "3182",
"330", "330", "330", "330", "330", "330", "354", "354", "354",
"354", "354", "354", "363", "363", "363", "363", "363", "363",
"369", "369", "369", "369", "369", "369", "370", "370", "370",
"370", "370", "370", "375", "375", "375", "375", "375", "375",
"377", "377", "377", "377", "377", "377", "378", "378", "378",
"378", "378", "378", "379", "379", "379", "379", "379", "379",
"380", "380", "380", "380", "380", "380", "381", "381", "381",
"381", "381", "381", "3862", "3862", "3862", "3862", "3862",
"3862", "3872", "3872", "3872", "3872", "3872", "3872", "388",
"388", "388", "388", "388", "388", "390", "390", "390", "390",
"390", "390", "392", "392", "392", "392", "392", "392", "393",
"393", "393", "393", "393", "393", "394", "394", "394", "394",
"394", "394", "395", "395", "395", "395", "395", "395", "396",
"396", "396", "396", "396", "396", "399", "399", "399", "399",
"399", "399", "5512", "5512", "5512", "5512", "5512", "5512",
"382", "382", "382", "382", "382", "382", "1001", "1001", "1001",
"1001", "1001", "1001", "1002", "1002", "1002", "1002", "1002",
"1002", "1003", "1003", "1003", "1003", "1003", "1003", "1004",
"1004", "1004", "1004", "1004", "1004", "1005", "1005", "1005",
"1005", "1005", "1005", "1006", "1006", "1006", "1006", "1006",
"1006", "1007", "1007", "1007", "1007", "1007", "1007", "1008",
"1008", "1008", "1008", "1008", "1008", "1009", "1009", "1009",
"1009", "1009", "1009", "1012", "1012", "1012", "1012", "1012",
"1012", "1013", "1013", "1013", "1013", "1013", "1013", "1014",
"1014", "1014", "1014", "1014", "1014", "1015", "1015", "1015",
"1015", "1015", "1015", "1016", "1016", "1016", "1016", "1016",
"1016", "1017", "1017", "1017", "1017", "1017", "1017", "1020",
"1020", "1020", "1020", "1020", "1020", "1021", "1021", "1021",
"1021", "1021", "1021", "1024", "1024", "1024", "1024", "1024",
"1024", "1025", "1025", "1025", "1025", "1025", "1025", "1026",
"1026", "1026", "1026", "1026", "1026", "1027", "1027", "1027",
"1027", "1027", "1027", "1088", "1088", "1088", "1088", "1088",
"1088", "1192", "1192", "1192", "1192", "1192", "1192", "1422",
"1422", "1422", "1422", "1422", "1422", "1492", "1492", "1492",
"1492", "1492", "1492", "1592", "1592", "1592", "1592", "1592",
"1592", "1602", "1602", "1602", "1602", "1602", "1602", "1642",
"1642", "1642", "1642", "1642", "1642", "171", "171", "171",
"171", "171", "171", "1722", "1722", "1722", "1722", "1722",
"1722", "1732", "1732", "1732", "1732", "1732", "1732", "174",
"174", "174", "174", "174", "174", "175", "175", "175", "175",
"175", "175", "1752", "1752", "1752", "1752", "1752", "1752",
"1762", "1762", "1762", "1762", "1762", "1762", "1782", "1782",
"1782", "1782", "1782", "1782", "1802", "1802", "1802", "1802",
"1802", "1802", "182", "182", "182", "182", "182", "182", "184",
"184", "184", "184", "184", "184", "1852", "1852", "1852", "1852",
"1852", "1852", "186", "186", "186", "186", "186", "186", "187",
"187", "187", "187", "187", "187", "188", "188", "188", "188",
"188", "188", "1892", "1892", "1892", "1892", "1892", "1892",
"190", "190", "190", "190", "190", "190", "192", "192", "192",
"192", "192", "192", "1924", "1924", "1924", "1924", "1924",
"1924", "193", "193", "193", "193", "193", "193", "195", "195",
"195", "195", "195", "195", "196", "196", "196", "196", "196",
"196", "197", "197", "197", "197", "197", "197", "1982", "1982",
"1982", "1982", "1982", "1982", "1992", "1992", "1992", "1992",
"1992", "1992", "19922", "19922", "19922", "19922", "19922",
"19922", "1999", "1999", "1999", "1999", "1999", "1999", "19992",
"19992", "19992", "19992", "19992", "19992", "199924", "199924",
"199924", "199924", "199924", "199924", "199945", "199945", "199945",
"199945", "199945", "199945", "199949", "199949", "199949", "199949",
"199949", "199949", "199951", "199951", "199951", "199951", "199951",
"199951", "199952", "199952", "199952", "199952", "199952", "199952",
"199j2", "199j2", "199j2", "199j2", "199j2", "199j2", "490",
"490", "490", "490", "490", "490", "181", "181", "181", "181",
"181", "181", "3812", "3812", "3812", "3812", "3812", "3812",
"199950", "199950", "199950", "199950", "199950", "199950", "191",
"191", "191", "191", "191", "191"), Condition = structure(c(1L,
2L, 3L, 4L, 5L, 6L, 1L, 2L, 3L, 4L, 5L, 6L, 1L, 2L, 3L, 4L, 5L,
6L, 1L, 2L, 3L, 4L, 5L, 6L, 1L, 2L, 3L, 4L, 5L, 6L, 1L, 2L, 3L,
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2L, 3L, 4L, 5L, 6L, 1L, 2L, 3L, 4L, 5L, 6L, 1L, 2L, 3L, 4L, 5L,
6L, 1L, 2L, 3L, 4L, 5L, 6L, 1L, 2L, 3L, 4L, 5L, 6L, 1L, 2L, 3L,
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6L, 1L, 2L, 3L, 4L, 5L, 6L, 1L, 2L, 3L, 4L, 5L, 6L, 1L, 2L, 3L,
4L, 5L, 6L, 1L, 2L, 3L, 4L, 5L, 6L, 1L, 2L, 3L, 4L, 5L, 6L, 1L,
2L, 3L, 4L, 5L, 6L, 1L, 2L, 3L, 4L, 5L, 6L, 1L, 2L, 3L, 4L, 5L,
6L, 1L, 2L, 3L, 4L, 5L, 6L, 1L, 2L, 3L, 4L, 5L, 6L, 1L, 2L, 3L,
4L, 5L, 6L, 1L, 2L, 3L, 4L, 5L, 6L, 1L, 2L, 3L, 4L, 5L, 6L, 1L,
2L, 3L, 4L, 5L, 6L, 1L, 2L, 3L, 4L, 5L, 6L, 1L, 2L, 3L, 4L, 5L,
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4L, 5L, 6L, 1L, 2L, 3L, 4L, 5L, 6L, 1L, 2L, 3L, 4L, 5L, 6L), .Label = c("neutral",
"neutral_social", "no_money", "positive_social", "selfharm",
"win_money"), class = "factor"), Score = c(0.221611076, 0.206888887611111,
0.2319999696, 0.228521740956522, 0.206187486625, 0.220866648533333,
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CodePudding user response:
Is this the correct way to undertake the Shapiro test on the output of an lme
Yes, the results show that the probability of observing these data, if the the data are normally distributed, is extremely low (less than < 2.2e-16).
A histogram and QQ plot is also very useful here:
...which both illustrate that although they are symmetrical, these residuals have extremely short tails, compared to what would be expected if they were normally distributed.