CODEWITHSUNDEEP
rextractanova
Lcat91
Lcat91

Reputation: 794

Extract p-value from anova() from comparison of two linear models in R

My apologies for not including enough information to properly access the issue. Anyway,I want to compare different pairs of linear models and record their p-values into a table. Where my troubles lie is that I cannot extract only the p-value.

TC <- matrix(data=NA, nrow=1, ncol=6)
    ML5 <- 1:5
for(B in ML5) {
    Coop <- anova(M6,Models5[[B]])$"Pr(>F)"
    TC[1,B] <- Coop
}

 >Coop
   NA 2.041767e-05

So how do I only put the number into the table and not the NA into the table?

Thanks a million!

Upvotes: 1

Views: 15088

Answers (3)

Ian
Ian

Reputation: 1

Using aov():

anova_a <- aov(response ~ time + Error(subject), data = all_data)

f_value <- unlist(summary(anova_a)[[2]])[9]

Upvotes: 0

Metrics
Metrics

Reputation: 15458

Using mtcars data from R (I would prefer the solution suggested by @Drew Steen)

myanova<-anova(lm(mpg~cyl,mtcars),lm(mpg~cyl+disp,mtcars))
pval<-summary(myanova)[1,6]

Updated as per question: 

models1<-lm(mpg~cyl,mtcars)
models2<-list(lm(mpg~cyl+disp,mtcars),lm(mpg~cyl+disp+hp,mtcars),lm(mpg~cyl+disp+hp+drat,mtcars))
myp1<-lapply(models2,function(x) anova(models1,x))
myp2<-lapply(myp1,function(x)summary(x)[1,6])
> myp3
[1] "   0.05419  " "   0.09891  " "   0.09661  "

Add:If you are using "$"Pr(>F)"

  myp2<-lapply(myp1,function(x)x$"Pr(>F)")
  myp3<-sapply(myp2,function(x) as.data.frame(x)[2,1])
    > myp3
    [1] 0.05418572 0.09891469 0.09661222

Upvotes: 0

Drew Steen
Drew Steen

Reputation: 16617

You just need quotation marks:

pvalue <- anova(m2,m1)$"Pr(>F)"

You can access the second element of pvalue using normal bracket subsetting:

pvalue[2]

So in your example I believe you'll use 

Coop <- anova(M6,Models5[[B]])$"Pr(>F)"[2]

(Although without access to M6, I can't be totally sure).

The str command is very useful in this sort of situation, to figure out what kind of object you're dealing with: 

str(myanova$"Pr(>F)")

Upvotes: 7

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