CODEWITHSUNDEEP
rp-valuegam
a_geo
a_geo

Reputation: 187

Extract p-value from gam.check in R

When I run gam.check(my_spline_gam), I get the following output. 

Method: GCV   Optimizer: magic
Smoothing parameter selection converged after 9 iterations.
The RMS GCV score gradiant at convergence was 4.785628e-06 .
The Hessian was positive definite.
The estimated model rank was 25 (maximum possible: 25)
Model rank =  25 / 25 

Basis dimension (k) checking results. Low p-value (k-index<1) may
indicate that k is too low, especially if edf is close to k'.

         k'    edf k-index p-value
s(x) 24.000 22.098   0.849    0.06

My question is whether I can extract this p-value separately to a table.

Upvotes: 6

Views: 1837

Answers (2)

Vivek Kalyanarangan
Vivek Kalyanarangan

Reputation: 9081

Use capture.output coupled with a little string manipulation - 

gam_obj <- capture.output(gam.check(b,pch=19,cex=.3))
gam_tbl <- gam_obj[12:length(gam_obj)]
str_spl = function(x){
  p_value <- strsplit(x, " ")[[1]]
  output_p <- as.numeric(p_value[length(p_value)])
}
p_values <- data.frame(sapply(gam_tbl, str_spl))

Output

enter image description here

Upvotes: 1

Ravi
Ravi

Reputation: 91

Looks like you cannot store the result in an object the normal way. You could use capture.output to store the console output in an object, and then subsequently use str_split to get the correct value. So for the example in the help file this would be:

library(mgcv)
set.seed(0)
dat <- gamSim(1,n=200)
b <- gam(y~s(x0)+s(x1)+s(x2)+s(x3),data=dat)
r <- capture.output(gam.check(b))
p <- strsplit(r[12], " ")[[1]][11]

But because the p-value is just a string you wouldn't get the exact p-value this way.

Edit: user20650's answer will give you the proper output: 

r <- k.check(b)
r[,'p-value']

Upvotes: 4

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