# Model fitting (compilation) error in "wythamewa" model

**URL:** <https://discourse.mc-stan.org/t/model-fitting-compilation-error-in-wythamewa-model/18184>\
**Category:** Modeling\
**Created:** [September 24, 2020, 1:41pm UTC](https://discourse.mc-stan.org/t/model-fitting-compilation-error-in-wythamewa-model/18184 "2020-09-24T13:41:07Z")\
**Posts on this page:** 15\
**Page:** 1

<div class="post-metadata">

**Author:** ![SeanZ](https://avatars.discourse-cdn.com/v4/letter/s/eb9ed0/32.png) [@SeanZ](https://discourse.mc-stan.org/u/SeanZ)\
**Post date:** [September 24, 2020, 1:41pm UTC](https://discourse.mc-stan.org/t/model-fitting-compilation-error-in-wythamewa-model/18184/1 "2020-09-24T13:41:07Z")

</div>

The problem is as follows: I’m trying to reproduce the results of [Aplin, Sheldon & McElreath (2017)](https://www.pnas.org/content/114/30/7830.short) by using [“wythamewa” package](https://rdrr.io/github/rmcelreath/wythamewa/), i.e., fitting a stan model via [“ewa\_fit” function](https://rdrr.io/github/rmcelreath/wythamewa/man/ewa_fit.html) to [the data](https://rdrr.io/github/rmcelreath/wythamewa/man/WythamUnequal.html) (all provided within the package).  
While the model starts precompiling, the model fitting eventually fails at the compilation stage, producing the following messages and warnings:

```
Error in compileCode(f, code, language = language, verbose = verbose) : 
                   from file166c284c27c5.cpp:14:C:/Users/User/Documents/R/win-library/4.0/StanHeaders/include/stan/math/rev/core/set_zero_all_adjoints.hpp: 
At global scope:C:/Users/User/Documents/R/win-library/4.0/StanHeaders/include/stan/math/rev/core/set_zero_all_adjoints.hpp:14:13: 
warning: 'void stan::math::set_zero_all_adjoints()' defined but not used [-Wunused-function] static void set_zero_all_adjoints() 
{ ^ ~~~~~~~~~~~~~~~~~~~~ make: *** [C:/PROGRA~1/R/R-40~1.2/etc/x64/Makeconf:229: file166c284c27c5.o] Error 1
In addition: Warning message:
In system(paste(CXX, ARGS), ignore.stdout = TRUE, ignore.stderr = TRUE) :
  'C:/rtools40/usr/mingw_/bin/g++' not found
Error in sink(type = "output") : invalid connection

```

My sessionInfo():

```R
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 18363)

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C LC_TIME=English_United States.1252    
system code page: 1251

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

other attached packages:
[1] wythamewa_1.03 rethinking_2.13 rstan_2.21.2 ggplot2_3.3.2 StanHeaders_2.21.0-6     
[6] RcppArmadillo_0.9.900.3.0 Rcpp_1.0.5 inline_0.3.16            

loaded via a namespace (and not attached):
 [1] pillar_1.4.6 compiler_4.0.2 prettyunits_1.1.1 tools_4.0.2 pkgbuild_1.1.0 lattice_0.20-41 jsonlite_1.7.1    
 [8] lifecycle_0.2.0 tibble_3.0.3 gtable_0.3.0 pkgconfig_2.0.3 rlang_0.4.7 cli_2.0.2 rstudioapi_0.11   
[15] curl_4.3 mvtnorm_1.1-1 loo_2.3.1 coda_0.19-3 gridExtra_2.3 withr_2.3.0 dplyr_1.0.2       
[22] generics_0.0.2 vctrs_0.3.4 stats4_4.0.2 grid_4.0.2 tidyselect_1.1.0 glue_1.4.2 R6_2.4.1          
[29] processx_3.4.4 fansi_0.4.1 purrr_0.3.4 callr_3.4.4 magrittr_1.5 MASS_7.3-51.6 codetools_0.2-16  
[36] matrixStats_0.56.0 scales_1.1.1 ps_1.3.4 ellipsis_0.3.1 assertthat_0.2.1 shape_1.4.5 colorspace_1.4-1  
[43] V8_3.2.0 RcppParallel_5.0.2 munsell_0.5.0 crayon_1.3.4      

```

I have browsed through several discussions that seemed relevant to me as a novice to Stan (e.g., “Error in compileCode” kind), yet none of the proposed solutions (e.g., clean installation into default locations without spaces in names) solved the problem thus far .

Any help will be greatly appreciated & thanks for reading!

---

<div class="post-metadata">

**Author:** ![torkar](https://yyz2.discourse-cdn.com/flex030/user_avatar/discourse.mc-stan.org/torkar/32/1355_2.png) [@torkar](https://discourse.mc-stan.org/u/torkar)\
**Post date:** [September 28, 2020, 2:53pm UTC](https://discourse.mc-stan.org/t/model-fitting-compilation-error-in-wythamewa-model/18184/2 "2020-09-28T14:53:06Z")

</div>

Hi, I don’t have Windows myself but @andrjohns has helping a lot of people with their Windows issues.

---

<div class="post-metadata">

**Author:** ![andrjohns](https://yyz2.discourse-cdn.com/flex030/user_avatar/discourse.mc-stan.org/andrjohns/32/15297_2.png) [@andrjohns](https://discourse.mc-stan.org/u/andrjohns)\
**Post date:** [September 29, 2020, 1:16am UTC](https://discourse.mc-stan.org/t/model-fitting-compilation-error-in-wythamewa-model/18184/3 "2020-09-29T01:16:35Z")

</div>

Hi Sean,

Sorry I missed this! The first thing to check is your RStan installation. Can you first run:

```
library(rstan)
example(stan_model, run.dontrun=T,verbose=T)

```

And post any lines that start with `error:`?

Next, we need to check how RStan and other packages are configured on your system. Can you post the output from:

```
Sys.getenv("PATH")
Sys.getenv("BINPREF")
readLines("~/.R/Makevars.win")
readLines("~/.Rprofile")
readLines("~/.Renviron")
devtools::session_info("rstan")

```

---

<div class="post-metadata">

**Author:** ![SeanZ](https://avatars.discourse-cdn.com/v4/letter/s/eb9ed0/32.png) [@SeanZ](https://discourse.mc-stan.org/u/SeanZ)\
**Post date:** [September 29, 2020, 4:41am UTC](https://discourse.mc-stan.org/t/model-fitting-compilation-error-in-wythamewa-model/18184/4 "2020-09-29T04:41:11Z")

</div>

Thanks for the response!

Running

> [@andrjohns](#):
>
> ```no-highlight
> example(stan_model, run.dontrun=T,verbose=T)
> 
> ```

results in no error messages, only warnings (the second is harmless, I think):  
Warning messages:

> 1: In find.package(package, lib.loc, verbose = verbose) :  
> package ‘base’ found more than once, using the first from  
> “C:/PROGRA~1/R/R-40~1.2/library/base”,  
> “C:/Program Files/R/R-4.0.2/library/base”  
> 2: In system(paste(CXX, ARGS), ignore.stdout = TRUE, ignore.stderr = TRUE) :  
> ‘C:/rtools40/usr/mingw\_/bin/g++’ not found

As for the following checks:

```no-highlight
Sys.getenv("PATH")
[1] "C:\\rtools40\\usr\\bin;C:\\Program Files\\R\\R-4.0.2\\bin\\i386;C:\\Program Files (x86)\\Common Files\\Oracle\\Java\\javapath_target_67096062;C:\\Windows\\SysWOW64;C:\\Windows;C:\\Windows\\SysWOW64\\wbem;C:\\Windows\\SysWOW64\\WindowsPowerShell\\v1.0;C:\\Windows\\System32\\OpenSSH\\;C:\\Program Files\\Calibre2;C:\\Users\\User\\AppData\\Local\\Microsoft\\WindowsApps"

Sys.getenv("BINPREF")
[1] ""

readLines("~/.R/Makevars.win")
Error in file(con, "r") : cannot open the connection
In addition: Warning message:
In file(con, "r") :
  cannot open file 'C:/Users/User/Documents/.R/Makevars.win': No such file or directory

readLines("~/.Rprofile")
Error in file(con, "r") : cannot open the connection
In addition: Warning message:
In file(con, "r") :
  cannot open file 'C:/Users/User/Documents/.Rprofile': No such file or directory

readLines("~/.Renviron")
[1] "PATH=\"${RTOOLS40_HOME}\\usr\\bin;${PATH}\""

devtools::session_info("rstan")
- Session info ------------------------------------------------------------------------------------------------------------------------------
 setting value                       
 version R version 4.0.2 (2020-06-22)
 os Windows 10 x64              
 system i386, mingw32               
 ui RStudio                     
 language (EN)                        
 collate English_United States.1252  
 ctype English_United States.1252  
 tz Asia/Jerusalem              
 date 2020-09-29                  

- Packages ----------------------------------------------------------------------------------------------------------------------------------
 ! package * version date lib source        
   assertthat 0.2.1 2019-03-21 [1] CRAN (R 4.0.2)
   backports 1.1.10 2020-09-15 [1] CRAN (R 4.0.2)
   BH 1.72.0-3 2020-01-08 [1] CRAN (R 4.0.0)
   callr 3.4.4 2020-09-07 [1] CRAN (R 4.0.2)
   checkmate 2.0.0 2020-02-06 [1] CRAN (R 4.0.2)
   cli 2.0.2 2020-02-28 [1] CRAN (R 4.0.2)
   colorspace 1.4-1 2019-03-18 [1] CRAN (R 4.0.2)
   crayon 1.3.4 2017-09-16 [1] CRAN (R 4.0.2)
   curl 4.3 2019-12-02 [1] CRAN (R 4.0.2)
   desc 1.2.0 2018-05-01 [1] CRAN (R 4.0.2)
   digest 0.6.25 2020-02-23 [1] CRAN (R 4.0.2)
   ellipsis 0.3.1 2020-05-15 [1] CRAN (R 4.0.2)
   evaluate 0.14 2019-05-28 [1] CRAN (R 4.0.2)
   fansi 0.4.1 2020-01-08 [1] CRAN (R 4.0.2)
   farver 2.0.3 2020-01-16 [1] CRAN (R 4.0.2)
   ggplot2 3.3.2 2020-06-19 [1] CRAN (R 4.0.2)
   glue 1.4.2 2020-08-27 [1] CRAN (R 4.0.2)
   gridExtra 2.3 2017-09-09 [1] CRAN (R 4.0.2)
   gtable 0.3.0 2019-03-25 [1] CRAN (R 4.0.2)
   inline 0.3.16 2020-09-06 [1] CRAN (R 4.0.2)
   isoband 0.2.2 2020-06-20 [1] CRAN (R 4.0.2)
   jsonlite 1.7.1 2020-09-07 [1] CRAN (R 4.0.2)
   labeling 0.3 2014-08-23 [1] CRAN (R 4.0.0)
   lattice 0.20-41 2020-04-02 [2] CRAN (R 4.0.2)
   lifecycle 0.2.0 2020-03-06 [1] CRAN (R 4.0.2)
   loo 2.3.1 2020-07-14 [1] CRAN (R 4.0.2)
   magrittr 1.5 2014-11-22 [1] CRAN (R 4.0.2)
   MASS 7.3-51.6 2020-04-26 [2] CRAN (R 4.0.2)
   Matrix 1.2-18 2019-11-27 [2] CRAN (R 4.0.2)
   matrixStats 0.56.0 2020-03-13 [1] CRAN (R 4.0.2)
   mgcv 1.8-31 2019-11-09 [2] CRAN (R 4.0.2)
   munsell 0.5.0 2018-06-12 [1] CRAN (R 4.0.2)
   nlme 3.1-148 2020-05-24 [2] CRAN (R 4.0.2)
   pillar 1.4.6 2020-07-10 [1] CRAN (R 4.0.2)
   pkgbuild 1.1.0 2020-07-13 [1] CRAN (R 4.0.2)
   pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.0.2)
   pkgload 1.1.0 2020-05-29 [1] CRAN (R 4.0.2)
   praise 1.0.0 2015-08-11 [1] CRAN (R 4.0.2)
   prettyunits 1.1.1 2020-01-24 [1] CRAN (R 4.0.2)
   processx 3.4.4 2020-09-03 [1] CRAN (R 4.0.2)
   ps 1.3.4 2020-08-11 [1] CRAN (R 4.0.2)
   R6 2.4.1 2019-11-12 [1] CRAN (R 4.0.2)
   RColorBrewer 1.1-2 2014-12-07 [1] CRAN (R 4.0.0)
   Rcpp 1.0.5 2020-07-06 [1] CRAN (R 4.0.2)
   RcppEigen 0.3.3.7.0 2019-11-16 [1] CRAN (R 4.0.2)
 D RcppParallel 5.0.2 2020-06-24 [1] CRAN (R 4.0.2)
   rlang 0.4.7 2020-07-09 [1] CRAN (R 4.0.2)
   rprojroot 1.3-2 2018-01-03 [1] CRAN (R 4.0.2)
   rstan 2.21.2 2020-07-27 [1] CRAN (R 4.0.2)
   rstudioapi 0.11 2020-02-07 [1] CRAN (R 4.0.2)
   scales 1.1.1 2020-05-11 [1] CRAN (R 4.0.2)
   StanHeaders 2.21.0-6 2020-08-16 [1] CRAN (R 4.0.2)
   testthat 2.3.2 2020-03-02 [1] CRAN (R 4.0.2)
   tibble 3.0.3 2020-07-10 [1] CRAN (R 4.0.2)
   utf8 1.1.4 2018-05-24 [1] CRAN (R 4.0.2)
   V8 3.2.0 2020-06-19 [1] CRAN (R 4.0.2)
   vctrs 0.3.4 2020-08-29 [1] CRAN (R 4.0.2)
   viridisLite 0.3.0 2018-02-01 [1] CRAN (R 4.0.2)
   withr 2.3.0 2020-09-22 [1] CRAN (R 4.0.2)

[1] C:/Users/User/Documents/R/win-library/4.0
[2] C:/Program Files/R/R-4.0.2/library

 D -- DLL MD5 mismatch, broken installation.

```

---

<div class="post-metadata">

**Author:** ![andrjohns](https://yyz2.discourse-cdn.com/flex030/user_avatar/discourse.mc-stan.org/andrjohns/32/15297_2.png) [@andrjohns](https://discourse.mc-stan.org/u/andrjohns)\
**Post date:** [September 29, 2020, 4:48am UTC](https://discourse.mc-stan.org/t/model-fitting-compilation-error-in-wythamewa-model/18184/5 "2020-09-29T04:48:10Z")

</div>

Alright, so it looks like RStan is working fine, but there’s an issue with the model being called by `ewa_fit`. I’m not familiar with the package, would you be able to post the code to run the model and reproduce the error?

---

<div class="post-metadata">

**Author:** ![SeanZ](https://avatars.discourse-cdn.com/v4/letter/s/eb9ed0/32.png) [@SeanZ](https://discourse.mc-stan.org/u/SeanZ)\
**Post date:** [September 29, 2020, 5:25am UTC](https://discourse.mc-stan.org/t/model-fitting-compilation-error-in-wythamewa-model/18184/6 "2020-09-29T05:25:14Z")

</div>

Posting the exact Stan code can be a bit tricky in this case, so I’ve attached the links to the package (wythamewa) into original post (reattaching here).

After installing the package

> install.packages(“remotes”)  
> remotes::install\_github(“rmcelreath/wythamewa”)

I’ve loaded the data:

> data(“WythamUnequal”)  
> datx ← WythamUnequal

Then ran:

> lms ← list(  
> “mu[1] + a\_bird[bird[i],1] + b\_age[1]\*age[i]”,  
> “mu[2] + a\_bird[bird[i],2] + b\_age[2]\*age[i]”,  
> “mu[3] + a\_bird[bird[i],3] + b\_age[3]\*age[i]”,  
> “mu[4] + a\_bird[bird[i],4] + b\_age[4]\*age[i]”  
> )  
> links ← c(“logit”, “logit”, “log”, “logit”, “”)  
> prior ← "  
> mu ~ normal(0,1);  
> diff\_hi ~ cauchy(0,1);  
> b\_age ~ normal(0,1);  
> to\_vector(z\_bird) ~ normal(0,1);  
> L\_Rho\_bird ~ lkj\_corr\_cholesky(3);  
> sigma\_bird ~ exponential(2);"  
> mod1 ← ewa\_def( model=lms , prior=prior , link=links , data=datx )
> 
> cat(mod1$stan\_code)

`cat(mod1$stan_code)` reproduces the default Stan model code I want to fit:

> data(template\_raw)

Then I ran `ewa_fit` with the following code, which results in the error described in the original post:

> model\_name ← “Sva\_Gva\_Lva\_Pva”
> 
> lms ← list(  
> “mu[1] + a\_bird[bird[i],1] + b\_age[1]\*age[i]”,  
> “mu[2] + a\_bird[bird[i],2] + b\_age[2]\*age[i]”,  
> “mu[3] + a\_bird[bird[i],3] + b\_age[3]\*age[i]”,  
> “mu[4] + a\_bird[bird[i],4] + b\_age[4]\*age[i]”  
> )  
> links ← c(“logit”, “logit”, “log”, “logit”, “”)
> 
> prior ← "  
> mu ~ normal(0,1);  
> diff\_hi ~ cauchy(0,1);  
> b\_age ~ normal(0,1);  
> to\_vector(z\_bird) ~ normal(0,1);  
> L\_Rho\_bird ~ lkj\_corr\_cholesky(3);  
> sigma\_bird ~ exponential(2);"
> 
> mod1 ← ewa\_def( model=lms , prior=prior , link=links )  
> set.seed(1)  
> m ← ewa\_fit( mod1 , warmup=500 , iter=1000 , chains=3 , cores=3 ,  
> control=list( adapt\_delta=0.99 , max\_treedepth=12 ) )

---

<div class="post-metadata">

**Author:** ![andrjohns](https://yyz2.discourse-cdn.com/flex030/user_avatar/discourse.mc-stan.org/andrjohns/32/15297_2.png) [@andrjohns](https://discourse.mc-stan.org/u/andrjohns)\
**Post date:** [September 29, 2020, 5:40am UTC](https://discourse.mc-stan.org/t/model-fitting-compilation-error-in-wythamewa-model/18184/7 "2020-09-29T05:40:22Z")

</div>

Thanks! I’ll dig into it later this afternoon and let you know

---

<div class="post-metadata">

**Author:** ![andrjohns](https://yyz2.discourse-cdn.com/flex030/user_avatar/discourse.mc-stan.org/andrjohns/32/15297_2.png) [@andrjohns](https://discourse.mc-stan.org/u/andrjohns)\
**Post date:** [September 29, 2020, 11:52am UTC](https://discourse.mc-stan.org/t/model-fitting-compilation-error-in-wythamewa-model/18184/8 "2020-09-29T11:52:51Z")

</div>

This is an error we’ve seen before which is specific to this RStan version (2.21). You can workaround this by running the model through `cmdstanR`. It looks like the `rethinking` package has the option to specify using `cmdstanR` as the backend, but the `wythamewa` package is too old for that. As a workaround, you can run the model through cmdstanR and then read the results into the `stanfit` format that would be returned by `ewa_fit`.

First up, install `cmdstanR` and `cmdstan` by following the instructions here: [https://mc-stan.org/cmdstanr/articles/cmdstanr.html](https://mc-stan.org/cmdstanr/articles/cmdstanr.html). If you run into errors with the installation, have a look at the instructions over here as well: [Error caused by missing stan header](https://discourse.mc-stan.org/t/error-caused-by-missing-stan-header/17849/17)

Then, setup your priors & model as usual:

```
    model_name <- "Sva_Gva_Lva_Pva"

    lms <- list(
    "mu[1] + a_bird[bird[i],1] + b_age[1]*age[i]",
    "mu[2] + a_bird[bird[i],2] + b_age[2]*age[i]",
    "mu[3] + a_bird[bird[i],3] + b_age[3]*age[i]",
    "mu[4] + a_bird[bird[i],4] + b_age[4]*age[i]"
    )
    links <- c("logit", "logit", "log", "logit", "")

    prior <- "
    mu ~ normal(0,1);
    diff_hi ~ cauchy(0,1);
    b_age ~ normal(0,1);
    to_vector(z_bird) ~ normal(0,1);
    L_Rho_bird ~ lkj_corr_cholesky(3);
    sigma_bird ~ exponential(2);"

    mod1 <- ewa_def( model=lms , prior=prior , link=links )
    set.seed(1)

```

Then compile and run your model through `cmdstanR`:

```
cmd_mod = cmdstan_model(write_stan_tempfile(mod1$stan_code))
cmd_samp = cmd_mod$sample(
    data = your_data,
    num_samples = 500,
    num_warmup = 500,
    num_chains = 3,
    num_cores = 3,
    adapt_delta = 0.99,
    max_treedepth = 12,
    validate_csv = FALSE
)

```

Finally, read the results back in to the same type of object returned by `ewa_fit`:

```
m = rstan::read_stan_csv(cmd_samp$output_files())

```

---

<div class="post-metadata">

**Author:** ![SeanZ](https://avatars.discourse-cdn.com/v4/letter/s/eb9ed0/32.png) [@SeanZ](https://discourse.mc-stan.org/u/SeanZ)\
**Post date:** [September 29, 2020, 1:40pm UTC](https://discourse.mc-stan.org/t/model-fitting-compilation-error-in-wythamewa-model/18184/9 "2020-09-29T13:40:25Z")

</div>

First, thanks for the swift replies!

As for the workaround, after installing `cmdstanR ` I’ve ran  
`cmd_mod = cmdstan_model(write_stan_tempfile(mod1$stan_code))`  
yet it returned the following error:

```
Compiling Stan program...
-
Syntax error in 'C:/Users/User/AppData/Local/Temp/RtmpasdJJx/model-46a062561abe.stan', line 35, column 5 to column 11, parsing error:
   -------------------------------------------------
    33:      
    34: // priors
    35: !priors!
                    ^
    36: // init attractions to preference for low
    37: for ( i in 1:N_birds ) {
   -------------------------------------------------

Ill-formed expression. Found identifier. There are many ways to complete this to a well-formed expression.

mingw32-make.exe: *** [make/program:53: C:/Users/User/AppData/Local/Temp/RtmpasdJJx/model-46a062561abe.hpp] Error 1
Error: An error occured during compilation! See the message above for more information.
In addition: Warning message:
write_stan_tempfile() is deprecated. Please use write_stan_file() instead.

```

running `cmd_samp` afterwards results in sampling failure:

```

Chain 1 Exception: variable does not exist; processing stage=data initialization; variable name=agej; base type=double (in 'C:/Users/User/AppData/Local/Temp/RtmpasdJJx/model-46a0444065db.stan', line 11, column 4 to column 23)
Warning: Chain 1 finished unexpectedly!

Chain 2 Exception: variable does not exist; processing stage=data initialization; variable name=agej; base type=double (in 'C:/Users/User/AppData/Local/Temp/RtmpasdJJx/model-46a0444065db.stan', line 11, column 4 to column 23)
Warning: Chain 2 finished unexpectedly!

Chain 3 Exception: variable does not exist; processing stage=data initialization; variable name=agej; base type=double (in 'C:/Users/User/AppData/Local/Temp/RtmpasdJJx/model-46a0444065db.stan', line 11, column 4 to column 23)
Warning: Chain 3 finished unexpectedly!

Warning: Use read_cmdstan_csv() to read the results of the failed chains.
Warning messages:
1: In cmd_mod$sample(data = datx, num_samples = 500, num_warmup = 500, :
  'num_cores' is deprecated. Please use 'parallel_chains' instead.
2: In cmd_mod$sample(data = datx, num_samples = 500, num_warmup = 500, :
  'num_chains' is deprecated. Please use 'chains' instead.
3: In cmd_mod$sample(data = datx, num_samples = 500, num_warmup = 500, :
  'num_warmup' is deprecated. Please use 'iter_warmup' instead.
4: In cmd_mod$sample(data = datx, num_samples = 500, num_warmup = 500, :
  'num_samples' is deprecated. Please use 'iter_sampling' instead.
5: All chains finished unexpectedly!
 
6: No chains finished successfully. Unable to retrieve the fit. 

```

---

<div class="post-metadata">

**Author:** ![andrjohns](https://yyz2.discourse-cdn.com/flex030/user_avatar/discourse.mc-stan.org/andrjohns/32/15297_2.png) [@andrjohns](https://discourse.mc-stan.org/u/andrjohns)\
**Post date:** [September 29, 2020, 2:35pm UTC](https://discourse.mc-stan.org/t/model-fitting-compilation-error-in-wythamewa-model/18184/10 "2020-09-29T14:35:06Z")

</div>

It looks like the priors block wasn’t correctly picked up by `ewa_def`.

If you run:

```
lms <- list(
    "mu[1] + a_bird[bird[i],1] + b_age[1]*age[i]",
    "mu[2] + a_bird[bird[i],2] + b_age[2]*age[i]",
    "mu[3] + a_bird[bird[i],3] + b_age[3]*age[i]",
    "mu[4] + a_bird[bird[i],4] + b_age[4]*age[i]"
)
links <- c("logit", "logit", "log", "logit", "")

prior <- "
    mu ~ normal(0,1);
    diff_hi ~ cauchy(0,1);
    b_age ~ normal(0,1);
    to_vector(z_bird) ~ normal(0,1);
    L_Rho_bird ~ lkj_corr_cholesky(3);
    sigma_bird ~ exponential(2);"

mod1 <- ewa_def( model=lms , prior=prior , link=links )

```

And then run:

```
cat(mod1$stan_code)

```

You should be able to see a section in the `model` block with:

```
    // priors
    
    mu ~ normal(0,1);
    diff_hi ~ cauchy(0,1);
    b_age ~ normal(0,1);
    to_vector(z_bird) ~ normal(0,1);
    L_Rho_bird ~ lkj_corr_cholesky(3);
    sigma_bird ~ exponential(2);
    // init attractions to preference for low
    for ( i in 1:N_birds ) {
        A[i,1] = 0;
        A[i,2] = A_init[i]; // should be STRENGTH_PREF_PREVEXP
    }

```

---

<div class="post-metadata">

**Author:** ![SeanZ](https://avatars.discourse-cdn.com/v4/letter/s/eb9ed0/32.png) [@SeanZ](https://discourse.mc-stan.org/u/SeanZ)\
**Post date:** [September 29, 2020, 2:49pm UTC](https://discourse.mc-stan.org/t/model-fitting-compilation-error-in-wythamewa-model/18184/11 "2020-09-29T14:49:06Z")

</div>

Thanks, the compilation seems to complete successfully this time:

```
Compiling Stan program...
Warning message:
write_stan_tempfile() is deprecated. Please use write_stan_file() instead.

```

However, the sampling with `cmd_samp` leads to the same error as above:

```
Chain 1 Exception: variable does not exist; processing stage=data initialization; variable name=agej; base type=double (in 'C:/Users/User/AppData/Local/Temp/RtmpasdJJx/model-46a02fbc6ee2.stan', line 11, column 4 to column 23)
Warning: Chain 1 finished unexpectedly!

Chain 2 Exception: variable does not exist; processing stage=data initialization; variable name=agej; base type=double (in 'C:/Users/User/AppData/Local/Temp/RtmpasdJJx/model-46a02fbc6ee2.stan', line 11, column 4 to column 23)
Warning: Chain 2 finished unexpectedly!

Chain 3 Exception: variable does not exist; processing stage=data initialization; variable name=agej; base type=double (in 'C:/Users/User/AppData/Local/Temp/RtmpasdJJx/model-46a02fbc6ee2.stan', line 11, column 4 to column 23)
Warning: Chain 3 finished unexpectedly!

Warning: Use read_cmdstan_csv() to read the results of the failed chains.
Warning messages:
1: In cmd_mod$sample(data = datx, num_samples = 500, num_warmup = 500, :
  'num_cores' is deprecated. Please use 'parallel_chains' instead.
2: In cmd_mod$sample(data = datx, num_samples = 500, num_warmup = 500, :
  'num_chains' is deprecated. Please use 'chains' instead.
3: In cmd_mod$sample(data = datx, num_samples = 500, num_warmup = 500, :
  'num_warmup' is deprecated. Please use 'iter_warmup' instead.
4: In cmd_mod$sample(data = datx, num_samples = 500, num_warmup = 500, :
  'num_samples' is deprecated. Please use 'iter_sampling' instead.
5: All chains finished unexpectedly!
 
6: No chains finished successfully. Unable to retrieve the fit.

```

Does it indicate a problem in the “wythamewa” model itself? (i.e., specification of a variable not provided in the data)

---

<div class="post-metadata">

**Author:** ![andrjohns](https://yyz2.discourse-cdn.com/flex030/user_avatar/discourse.mc-stan.org/andrjohns/32/15297_2.png) [@andrjohns](https://discourse.mc-stan.org/u/andrjohns)\
**Post date:** [September 29, 2020, 2:56pm UTC](https://discourse.mc-stan.org/t/model-fitting-compilation-error-in-wythamewa-model/18184/12 "2020-09-29T14:56:35Z")

</div>

It looks the `ewa_def` function does some custom data pre-processing. So you need to use the data from that function in the cmdstanr call:

```
cmd_samp = cmd_mod$sample(
    data = mod1$data,
    num_samples = 500,
    num_warmup = 500,
    num_chains = 3,
    num_cores = 3,
    adapt_delta = 0.99,
    max_treedepth = 12,
    validate_csv = FALSE
)

```

---

<div class="post-metadata">

**Author:** ![andrjohns](https://yyz2.discourse-cdn.com/flex030/user_avatar/discourse.mc-stan.org/andrjohns/32/15297_2.png) [@andrjohns](https://discourse.mc-stan.org/u/andrjohns)\
**Post date:** [September 29, 2020, 2:59pm UTC](https://discourse.mc-stan.org/t/model-fitting-compilation-error-in-wythamewa-model/18184/13 "2020-09-29T14:59:08Z")

</div>

Also, it’s probably best practice not to use the deprecated functions (I’m a bit behind on `cmdstanR`!), so the workflow should be:

```
cmd_mod = cmdstan_model(write_stan_file(mod1$stan_code))
cmd_samp = cmd_mod$sample(
    data = mod1$data,
    iter_sampling = 500,
    iter_warmup = 500,
    chains = 3,
    parallel_chains = 3,
    adapt_delta = 0.99,
    max_treedepth = 12,
    validate_csv = FALSE
)

m = rstan::read_stan_csv(cmd_samp$output_files())

```

---

<div class="post-metadata">

**Author:** ![SeanZ](https://avatars.discourse-cdn.com/v4/letter/s/eb9ed0/32.png) [@SeanZ](https://discourse.mc-stan.org/u/SeanZ)\
**Post date:** [September 29, 2020, 3:18pm UTC](https://discourse.mc-stan.org/t/model-fitting-compilation-error-in-wythamewa-model/18184/14 "2020-09-29T15:18:41Z")

</div>

The workaround with `cmdstanR ` did the job.

```
All 3 chains finished successfully.
Mean chain execution time: 12583.6 seconds.
Total execution time: 15676.8 seconds.

```

Many thanks for your help, it’s deeply appreciated!  
Sean

---

<div class="post-metadata">

**Author:** ![andrjohns](https://yyz2.discourse-cdn.com/flex030/user_avatar/discourse.mc-stan.org/andrjohns/32/15297_2.png) [@andrjohns](https://discourse.mc-stan.org/u/andrjohns)\
**Post date:** [September 30, 2020, 5:01am UTC](https://discourse.mc-stan.org/t/model-fitting-compilation-error-in-wythamewa-model/18184/15 "2020-09-30T05:01:34Z")

</div>

No worries, glad that we could get you sorted!