Question

我在编写for循环函数时遇到问题，我要求gmulti找到最佳模型。我有以下示例数据集：

dput（数据）

structure(list(Studbook.ID = structure(c(16L, 16L, 16L, 16L, 
16L, 16L, 16L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 6L, 6L, 
 6L, 6L, 6L, 6L, 6L, 6L, 17L, 17L, 17L, 17L, 17L, 17L, 17L, 17L, 
17L, 17L, 17L, 17L, 30L, 30L, 30L), .Label = c("230", "298", 
"308", "329", "357", "358", "374", "382", "385", "394", "397", 
"399", "404", "413", "414", "418", "432", "433", "434", "437", 
"439", "444", "446", "455", "458", "460", "473", "475", "476", 
"477", "478", "492", "495", "496", "499", "503"), class = "factor"), 
Season = structure(c(1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 
2L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 
1L), .Label = c("Breeding", "Nonbreeding"), class = "factor"), 
Year = c(1999L, 2000L, 2000L, 2000L, 2000L, 2000L, 2000L, 
2000L, 2000L, 2000L, 2000L, 2000L, 2000L, 2000L, 2000L, 2000L, 
2000L, 2000L, 2000L, 2000L, 2000L, 2000L, 2000L, 2000L, 2000L, 
2000L, 2000L, 2000L, 2000L, 2000L, 2000L, 2000L, 2000L, 2000L, 
2000L, 2000L, 2000L, 2000L, 2000L, 2000L), Age.Class = 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, 2L, 2L, 2L), .Label = c("Adult", 
"Sub-Adult"), class = "factor"), Sex = 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), .Label = c("Female", "Male"
), class = "factor"), Captive_Wild = structure(c(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, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L), .Label = c("Captive", "Wild"
), class = "factor"), C.SA.F = c(0L, 0L, 0L, 0L, 0L, 0L, 
0L, 0L, 0L, 1L, 0L, 0L, 1L, 0L, 1L, 1L, 0L, 0L, 0L, 0L, 0L, 
0L, 0L, 0L, 1L, 0L, 0L, 1L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 
0L, 0L, 0L, 0L), C.HA.F = c(0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 
0L, 1L, 1L, 0L, 1L, 0L, 1L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 
1L, 1L, 0L, 0L, 1L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 
0L, 0L), W.MW.F = c(0L, 0L, 0L, 0L, 0L, 1L, 0L, 0L, 0L, 1L, 
1L, 1L, 1L, 1L, 1L, 1L, 1L, 0L, 0L, 1L, 1L, 1L, 1L, 1L, 1L, 
0L, 1L, 1L, 0L, 1L, 1L, 1L, 0L, 0L, 1L, 1L, 0L, 0L, 1L, 1L
), W.MW.DUR = c(0L, 0L, 0L, 0L, 0L, 1L, 0L, 0L, 0L, 1L, 1L, 
1L, 1L, 1L, 1L, 1L, 1L, 0L, 0L, 1L, 1L, 1L, 1L, 1L, 1L, 0L, 
1L, 1L, 0L, 1L, 1L, 1L, 0L, 0L, 1L, 1L, 0L, 0L, 1L, 1L), 
C.CHEW.F = c(0L, 0L, 0L, 0L, 0L, 1L, 0L, 0L, 0L, 1L, 1L, 
1L, 1L, 1L, 1L, 1L, 1L, 0L, 0L, 1L, 0L, 1L, 1L, 1L, 1L, 0L, 
1L, 1L, 0L, 1L, 1L, 1L, 0L, 0L, 0L, 1L, 0L, 0L, 1L, 1L)), .Names =c("Studbook.ID", 
"Season", "Year", "Age.Class", "Sex", "Captive_Wild", "C.SA.F", 
"C.HA.F", "W.MW.F", "W.MW.DUR", "C.CHEW.F"), row.names = c(NA, 
40L), class = "data.frame")

我的总循环代码是：

#lmer wrapper for glmulti function
 lmer.glmulti <- function (formula, data, family=binomial, random, ...) {
 lmer(paste(deparse(formula), random), data = data,...)
 }

 #make a dependent variable list for loop
 dep_list<-colnames(Bamboo)
 dep_list<-dep_list[-c(1:6)]

 outglm<-c()
 outdesc<-c()

 #start loop coding
 for (depend in dep_list){

   y <-Bamboo[,depend]

   #gmluti loop
   #glm full model (substitute behavioral variables in place of 'depend') 
   glmmod<-y~Captive_Wild+Sex+Age.Class+Season 
   glm.glmulti<-glmulti(glmmod, random="+(1|Studbook.ID)", data=Bamboo, fitfunc = lmer.glmulti, family=binomial, level=2)
   #make and print table for final best model
   htmlreg(glm.glmulti@objects[[1]], file=paste(depend, ".doc", sep=""), caption = depend, caption.above = TRUE)   
 }

它挂在了glmulti代码上，它给了我这个错误：

Error in model.frame.default(as.formula(paste(y, "~", paste(x, sep = "",  : 
variable lengths differ (found for 'Captive_Wild')

跟踪看起来像：

8 model.frame.default(as.formula(paste(y, "~", paste(x, sep = "", 
collapse = "+"), sep = "")), data = data) 
7 model.frame(as.formula(paste(y, "~", paste(x, sep = "", collapse = "+"), 
sep = "")), data = data) 
6 glmulti(y = "y", data = Bamboo, level = 2, fitfunction = lmer.glmulti, 
random = "+(1|Studbook.ID)", xr = c("Sex", "Season"), exclude = 1) 
5 glmulti(y = "y", data = Bamboo, level = 2, fitfunction = lmer.glmulti, 
random = "+(1|Studbook.ID)", xr = c("Sex", "Season"), exclude = 1) 
4 eval(expr, envir, enclos) 
3 eval(call) 
2 glmulti(y ~ Sex + Season, random = "+(1|Studbook.ID)", data = Bamboo, 
fitfunc = lmer.glmulti, level = 2) 
1 glmulti(y ~ Sex + Season, random = "+(1|Studbook.ID)", data = Bamboo, 
fitfunc = lmer.glmulti, level = 2)

我也尝试过当我逐个手动运行变量时，glmulti工作得很好，当我删除Captive_Wild（我当然不想这样做）时，它给了我同样的错误性与季节同上。我检查了所有变量长度，它们是相同的。

这对我来说意味着glmulti在某处遇到for循环的问题，但我不确定在哪里。任何人都可以建议修复？这是我第一次尝试for循环，所以任何和所有的帮助将不胜感激！

Answer 1

经过一番愚弄后，我在代码中发现了两个问题： 1）lmer包装器是旧的所以需要调用：

glmer.glmulti <- function (formula, data, family=binomial, random, ...) {
glmer(paste(deparse(formula), random), data = data,...)
}

和2）使用在for循环中调用glmulti的替代形式，如下所示：

for (depend in dep_list){

glm.glmulti = glmulti(depend, c("Captive_Wild", "Sex", "Age.Class", "Season"), random="+(1|Studbook.ID)", data=Bamboo, fitfunc=lmer.glmulti, family=binomial, level=2)
#make and print table for final best model
htmlreg(glm.glmulti@objects[[1]], file=paste(depend, ".doc", sep=""), caption = depend, caption.above = TRUE)   
}

glmulti不在for-loop中工作

1 个答案: