Problem with "extract_log_lik" in rstan 2.9.0/loo 0.1.5

[Emmanuel Charpentier]

I wanted to explore loo. I loaded some previously fit models, and tried :


> class(Duree.Incr)
[1] "stanfit"
attr(,"package")
[1] "rstan"
> foo <- extract_log_lik(Duree.Incr)
Error in extract_log_lik(Duree.Incr) : Please load the 'rstan' package.

However :

> sessionInfo()
R version 3.2.3 (2015-12-10)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Debian GNU/Linux stretch/sid

locale:
 [1] LC_CTYPE=fr_FR.utf8       LC_NUMERIC=C            
 [3] LC_TIME=fr_FR.utf8        LC_COLLATE=fr_FR.utf8   
 [5] LC_MONETARY=fr_FR.utf8    LC_MESSAGES=fr_FR.utf8  
 [7] LC_PAPER=fr_FR.utf8       LC_NAME=C               
 [9] LC_ADDRESS=C              LC_TELEPHONE=C          
[11] LC_MEASUREMENT=fr_FR.utf8 LC_IDENTIFICATION=C     

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base    

other attached packages:
[1] loo_0.1.5     rstan_2.9.0-3 ggplot2_2.1.0

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.3        matrixStats_0.50.1 lattice_0.20-33    MASS_7.3-45      
 [5] brms_0.8.0.9000    grid_3.2.3         plyr_1.8.3         nlme_3.1-125     
 [9] gtable_0.2.0       stats4_3.2.3       coda_0.18-1        scales_0.4.0     
[13] minqa_1.2.4        nloptr_1.0.4       Matrix_1.2-4       splines_3.2.3    
[17] statmod_1.4.24     lme4_1.1-11        tools_3.2.3        munsell_0.4.3    
[21] abind_1.4-3        parallel_3.2.3     compiler_3.2.3     inline_0.3.14    
[25] colorspace_1.2-6   gridExtra_2.2.1  

What happens ?

--
Emmanuel Charpentier

[Jonah Gabry]

Hi Emmanuel,

Can you post this on the issue tracker for the loo package (github.com/jgabry/loo/issues) and I'll respond over there and we'll get it sorted out?

Thanks,

Jonah

[Emmanuel Charpentier]

Done.

--
Emmanuel Charpentier

[Lei Zhang]

Hi Emmanuel,

last time when I had this same error message, I found out that there was no variable called "log_lik" in my previous fitted model object. 

So probably you do not have it as well?

Best,

Lei

[Jonah Gabry]

Hi Lei, yes this was indeed part of the issue. We sorted it out over at the loo repository (https://github.com/jgabry/loo/issues/29)