SYNTAX ERROR, MESSAGE(S) FROM PARSER when editing the ER function in the metab_bayes to (q10temp)

[amina-uwa]

Brief problem description

I have created a new .stan file named "b_np_oipi_tr_psrqkm.stan" following the naming generated by mm_name('bayes', GPP_fun='satlight', ER_fun='q10temp',pool_K600='none'). Then I edited the .stan file to include ER model as function of water temperature as per manual q10temp . However, I get a syntax error when I included temp.water as a variable in the transformed parameter ER_inst[i].

SYNTAX ERROR, MESSAGE(S) FROM PARSER:
Variable identifier may not contain a period (.)

See below for the full code.

Based on Rstan manual variable identifiers in Stan may not contain a period character. And when I changed the variable name to water_temp I got the error

Error in mod$fit_ptr() :
Exception: variable does not exist; processing stage=data initialization; variable name=temp_water; base type=vector_d (in ‘model4b1c66371d71_b_np_oipi_tr_psrqkm’ at line 30)

After troubleshooting in Stan forum, it was found that the temp.water is hard coded in the function and can't be renamed. But the mystery is that DO.sat Do.obs are written in the form DO_stat in the stan data block and they don't cause the same error while only temp_water causes the error above in Italic. Any idea how to include the temperature function without running into this error?

What I saw on my computer

dat<-data.frame(solar.time=as.POSIXct(site$solar.time,tz="UTC",format="%d/%m/%Y %H:%M"),DO.obs=ma(site$DO.obs,10),DO.sat=site$DO.sat,depth=site$depth,temp.water=site$temp.water,light=site$light)

## Sat model with light and ER function
 mm_saturator_ER<-
+   mm_name('bayes', GPP_fun='satlight', ER_fun='q10temp',pool_K600='none') %>%
+   specs(alpha_meanlog=.4,alpha_sdlog=.2,Pmax_mu=6,Pmax_sigma=.3, day_start = 4,day_end = 28,n_cores=4, n_chains=4, burnin_steps=500, saved_steps=500) %>%
+   metab(dat)
SYNTAX ERROR, MESSAGE(S) FROM PARSER:
Variable identifier may not contain a period (.)
    found period at position (indexed from 0)=4
    found identifier=temp.water
Variable identifier may not contain a period (.)
    found period at position (indexed from 0)=4
    found identifier=temp.water
 error in 'model4b1c4e6d2fdf_b_np_oipi_tr_psrqkm' at line 29, column 11
  -------------------------------------------------
    27:   vector[d] DO_obs[n];
    28:   vector[d] DO_sat[n];
    29:   vector[d] temp.water[n];
                  ^
    30:   vector[d] light[n];
  -------------------------------------------------

PARSER EXPECTED: <identifier>
Timing stopped at: 0.08 0 0.09
Warning message:
In metab_fun(specs = specs, data = data, data_daily = data_daily,  :
  Modeling failed
  Errors:
    failed to parse Stan model 'b_np_oipi_tr_psrqkm' due to the above error

Session information

Run the following code line (or sessionInfo() if that doesn't work) and paste in your output.

> sessionInfo()
R version 4.0.3 (2020-10-10)
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   
[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C                          
[5] LC_TIME=English_United States.1252    

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

other attached packages:
 [1] unitted_0.2.9            wql_0.4.9                fpp_0.5                 
 [4] tseries_0.10-47          lmtest_0.9-37            expsmooth_2.3           
 [7] fma_2.4                  forecast_8.12            forcats_0.5.0           
[10] stringr_1.4.0            purrr_0.3.4              readr_1.3.1             
[13] tibble_3.0.3             tidyverse_1.3.0          scales_1.1.1            
[16] cowplot_1.0.0            reshape_0.8.8            lubridate_1.7.9         
[19] xts_0.12-0               zoo_1.8-8                tidyr_1.1.2             
[22] imputeTS_3.1             devtools_2.3.1           usethis_1.6.1           
[25] rstan_2.21.2             StanHeaders_2.21.0-6     ggplot2_3.3.2           
[28] dplyr_1.0.2              streamMetabolizer_0.11.4

loaded via a namespace (and not attached):
 [1] nlme_3.1-149           ggtext_0.1.0           matrixStats_0.56.0    
 [4] fs_1.5.0               httr_1.4.2             LakeMetabolizer_1.5.0 
 [7] rprojroot_1.3-2        tools_4.0.3            backports_1.1.9       
[10] utf8_1.1.4             R6_2.4.1               DBI_1.1.0             
[13] lazyeval_0.2.2         colorspace_1.4-1       nnet_7.3-14           
[16] withr_2.2.0            tidyselect_1.1.0       gridExtra_2.3         
[19] prettyunits_1.1.1      processx_3.4.3         curl_4.3              
[22] compiler_4.0.3         rvest_0.3.6            cli_2.0.2             
[25] xml2_1.3.2             desc_1.2.0             labeling_0.3          
[28] rLakeAnalyzer_1.11.4.1 fracdiff_1.5-1         quadprog_1.5-8        
[31] callr_3.4.3            digest_0.6.25          pkgconfig_2.0.3       
[34] sessioninfo_1.1.1      dbplyr_1.4.4           readxl_1.3.1          
[37] rlang_0.4.9            TTR_0.24.2             rstudioapi_0.11       
[40] quantmod_0.4.17        farver_2.0.3           generics_0.0.2        
[43] jsonlite_1.7.1         inline_0.3.16          magrittr_1.5          
[46] loo_2.3.1              Rcpp_1.0.5             munsell_0.5.0         
[49] fansi_0.4.1            lifecycle_0.2.0        stringi_1.4.6         
[52] pkgbuild_1.1.0         plyr_1.8.6             grid_4.0.3            
[55] blob_1.2.1             parallel_4.0.3         crayon_1.3.4          
[58] lattice_0.20-41        haven_2.3.1            gridtext_0.1.1        
[61] hms_0.5.3              ps_1.3.4               pillar_1.4.6          
[64] reshape2_1.4.4         codetools_0.2-16       stats4_4.0.3          
[67] pkgload_1.1.0          reprex_0.3.0           urca_1.3-0            
[70] glue_1.4.2             V8_3.2.0               modelr_0.1.8          
[73] stinepack_1.4          remotes_2.2.0          RcppParallel_5.0.2    
[76] deSolve_1.28           vctrs_0.3.4            cellranger_1.1.0      
[79] testthat_2.3.2         gtable_0.3.0           assertthat_0.2.1      
[82] broom_0.7.0            timeDate_3043.102      memoise_1.1.0         
[85] ellipsis_0.3.1    

Sample data

sample_data.txt

Stan model file

b_np_oipi_tr_psrqkm.txt