这篇文章How can I extract elements from lists of lists in R?回答了我的一些问题,但这对我来说仍然不起作用,我需要做的事情超出了我的R知识。
我有来自2个环境(=试验),2年和5个感兴趣特征(由trait_id定义)的田间试验的数据。 GID是唯一的行标识符。我在lme4中的模型是:
mods <- dlply(data,.(trial,trait_id),
function(d)
lmer(phenotype_value ~(1|GID)+(1|year)+(1|year:GID)+(1|year:rep),
na.action = na.omit,data=d))
运行它会返回一个包含10个元素的大型列表,我想在数据框中为每个试验的所有特征存储GID的随机效果。我尝试了几件事:
blup=lapply(mods,ranef, drop = FALSE)
blup1=blup[[1]]
blup2=blup1$GID
会给我一个带有每个试验的一个特性的随机效果的df,我希望有更精简的东西,它会在列名中保留一些信息,如$irrigation.GRYLD
。
以下是一个可重复的示例,只有两个特征(GRYLD
,PTHT
),2年(11OBR
,12OBR
)和两个代表:
structure(list(GID = structure(c(1L, 2L, 3L, 4L, 5L, 5L, 1L,
2L, 4L, 3L, 1L, 2L, 3L, 4L, 5L, 5L, 1L, 2L, 4L, 3L, 1L, 2L, 3L,
4L, 5L, 5L, 2L, 1L, 4L, 3L, 1L, 2L, 3L, 4L, 5L, 5L, 2L, 1L, 4L,
3L, 1L, 2L, 3L, 4L, 5L, 5L, 1L, 2L, 4L, 3L, 1L, 2L, 3L, 4L, 5L,
5L, 1L, 2L, 4L, 3L, 1L, 2L, 3L, 4L, 5L, 5L, 2L, 1L, 4L, 3L, 1L,
2L, 3L, 4L, 5L, 5L, 2L, 1L, 4L, 3L), .Label = c("A", "B", "C",
"D", "E"), class = "factor"), year = structure(c(1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L), .Label = c("11OBR",
"12OBR"), class = "factor"), trial = structure(c(1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,
2L, 2L, 2L, 2L, 2L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L), .Label = c("heat",
"irrigation"), class = "factor"), rep = c(1L, 1L, 1L, 1L, 1L,
2L, 2L, 2L, 2L, 2L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 1L,
1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 1L, 1L, 1L, 1L, 1L, 2L, 2L,
2L, 2L, 2L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 1L, 1L, 1L,
1L, 1L, 2L, 2L, 2L, 2L, 2L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L,
2L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L), trait_id = structure(c(1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,
2L, 2L, 2L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L,
2L, 2L, 2L, 2L, 2L, 2L, 2L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L), .Label = c("GRYLD",
"PTHT"), class = "factor"), phenotype_value = c(3.93, 3.38, 1.65,
4.33, 2.45, 2.48, 3.98, 3.3, 4.96, 1.53, 87.5, 69.5, 65.5, 84.5,
77, 81, 94.5, 84.5, 89, 81, 6.56, 4.3, 5.76, 7.3, 5.73, 4.14,
5.93, 6.96, 8.43, 5.81, 114.5, 100, 104.5, 110, 110, 106, 99,
97.5, 105, 100, 0.119, 0.131, 0.681, 0.963, 0.738, 1.144, 0.194,
0.731, 0.895, 0.648, 35, 50, 45, 50, 45, 50, 55, 45, 50, 55,
2.79, 3.73, 3.96, 4.64, 5.03, 2.94, 3.78, 4.14, 3.89, 3.21, 90,
95, 105, 100, 105, 85, 95, 100, 100, 95)), .Names = c("GID",
"year", "trial", "rep", "trait_id", "phenotype_value"), class = "data.frame", row.names = c(NA,
-80L))
答案 0 :(得分:0)
我不是完全确定您想要的输出格式,但是如何:
all_ranef <- function(object) {
rr <- ranef(object)
ldply(rr,function(x) data.frame(group=rownames(x),x,check.names=FALSE))
}
ldply(mods,all_ranef)
## trial trait_id .id group (Intercept)
## 1 heat GRYLD year:GID 11OBR:A 7.935352e-01
## 2 heat GRYLD year:GID 11OBR:B 1.960487e-01
## 3 heat GRYLD year:GID 11OBR:C -1.504116e+00
## ...
## 82 irrigation PTHT year:rep 12OBR:2 -1.595022e+00
## 83 irrigation PTHT year 11OBR 2.915033e+00
## 84 irrigation PTHT year 12OBR -2.915033e+00
这种方法运行得相当好,因为所有随机效果都只是拦截。如果您在模型中有一些随机斜率术语,则可能需要reshape2:::melt()
个别随机效果,或使用rbind.fill()
将数据帧与不同的随机效果列合并。
library("ggplot2"); theme_set(theme_bw())
ggplot(vals, aes(y=group,x=`(Intercept)`))+
geom_point(aes(colour=interaction(trial,trait_id)))+
facet_wrap(~.id,scale="free")
顺便说一下,通常不建议使用只有2级(YEAR
)的因子作为分组变量......