R中重复测量的ANOVA和TukeyHSD事后检验

xytpbqjk  于 2022-12-20  发布在  其他
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我想做一个重复测量方差分析的TukeyHSD事后检验,输入公式“TukeyHSD”返回错误,我在论坛中找不到答案,我可以寻求帮助吗?
“treat”是重复测量因子,“vo2”是因变量。
下面是产生此错误的脚本:

my_data <- data.frame(
  stringsAsFactors = FALSE,
  id = c(1L,2L,3L,4L, 5L,1L,2L,3L,4L,5L,1L,2L,3L,4L,5L,1L,2L,3L,4L,5L),
  treat = c("o","o","o","o","o","j","j","j","j","j","z","z","z","z","z","w","w","w","w","w"),
  vo2 = c("47.48","42.74","45.23","51.65","49.11","51.00","43.82","49.88","54.61","52.20","51.31",
          "47.56","50.69","54.88","55.01","51.89","46.10","50.98","53.62","52.77"))

summary(rm_result <- aov(vo2~factor(treat)+Error(factor(id)), data = my_data))
TukeyHSD(rm_result, "treat", ordered = TRUE)
k97glaaz

k97glaaz1#

TukeyHSD()无法处理重复测量ANOVA的aovlist结果。作为替代方法,您可以使用lme4::lmer()拟合等效混合效应模型,然后使用multcomp::glht()进行事后检验。

my_data$vo2 <- as.numeric(my_data$vo2)
my_data$treat <- factor(my_data$treat)
m <- lme4::lmer(vo2 ~ treat + (1|id), data = my_data)
summary(multcomp::glht(m, linfct=mcp(treat="Tukey")))

# Simultaneous Tests for General Linear Hypotheses
# 
# Multiple Comparisons of Means: Tukey Contrasts
# 
# 
# Fit: lmer(formula = vo2 ~ treat + (1 | id), data = my_data)
# 
# Linear Hypotheses:
#            Estimate Std. Error z value Pr(>|z|)    
# o - j == 0   -3.060      0.583  -5.248   <0.001 ***
# w - j == 0    0.770      0.583   1.321   0.5497    
# z - j == 0    1.588      0.583   2.724   0.0327 *  
# w - o == 0    3.830      0.583   6.569   <0.001 ***
# z - o == 0    4.648      0.583   7.972   <0.001 ***
# z - w == 0    0.818      0.583   1.403   0.4974    
# ---
# Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
# (Adjusted p values reported -- single-step method)

混合效应模型的ANOVA表与重复测量ANOVA结果的比较表明,两种方法在处理treat变量的方式方面是等效的:

anova(m)
# Analysis of Variance Table
#       npar Sum Sq Mean Sq F value
# treat    3 61.775  20.592   24.23

summary(rm_result)
# Error: factor(id)
#           Df Sum Sq Mean Sq F value Pr(>F)
# Residuals  4  175.9   43.98               
# 
# Error: Within
#               Df Sum Sq Mean Sq F value   Pr(>F)    
# factor(treat)  3  61.78   20.59   24.23 2.22e-05 ***
# Residuals     12  10.20    0.85                     
# ---
# Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1

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