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I am fitting a gam using the MGCV package in R using the bam function:

gam_model = bam(y ~ s(time, k = -1) + 
                    s(ID, bs = 're'),
                  family = 'gaussian',
                  data = dat,
                  method = "fREML",
                  select = FALSE,
                  nthreads = 64,
                  discrete = TRUE,
                  control = ctrl)

The size of the dataset is 10,388 observations. The GAM fits quite quickly (483 seconds), however the summary.gam function takes significantly longer: ~18 minutes (measured using the tictoc package).

Might anyone know what could be causing this?

This is the R version information:

platform       x86_64-pc-linux-gnu         
arch           x86_64                      
os             linux-gnu                   
system         x86_64, linux-gnu           
status                                     
major          3                           
minor          6.3                         
year           2020                        
month          02                          
day            29                          
svn rev        77875                       
language       R                           
version.string R version 3.6.3 (2020-02-29)
nickname       Holding the Windsock 
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1 Answer 1

5
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The test for random effects is extremely costly computation-wise, especially so if there are lots of levels in the random effect factor.

Use

summary(gam_model, re.test = FALSE)

to exclude the test for the random effect term from the model summary.

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