Error in output_posteriors, not producing values

[naalipalo]

I have run through the wolf data and have no problem. I am unable to get the alligator data to work as I continually get an error Error in if (n.chains == 1) return(coda::mcmc(sims[, 1, ], thin = n.thin)) : argument is of length zero So I can't test it there.

Ive no idea why when I use the exact same script as the wolf example to run my 1 model, I am missing information. no posterior draws are produced or saved.

jags.mod$BUGSoutput$sims.list$p.fac1[,1,1] produces NAs or ZERO

g.post <- output_posteriors(jags.mod, mix, source, output_options)
names(g.post)
[1] "both"    "epsilon"

There is nothing to plot. Even though I have 2 fixed effects Age and Treatment, nothing is registering. What have I done wrong? what am I missing? Ive been working on this issue for 10 days almost and its really disheartening so any assistance would be extremely appreciated.

mix<- load_mix_data(filename=mix.filename,
                           iso_names=c("d13C","d15N"),
                           factors=c("age_class","treatment"),
                           fac_random=c(FALSE, FALSE),
                           fac_nested=c(FALSE,FALSE),
                           cont_effects=NULL)




mainDir <- "~/StableIsotope/5 MixSIAR/BestModelRun"
  subDir <- paste0("model_", mod)
  dir.create(file.path(getwd(), subDir), showWarnings = FALSE)
  setwd(file.path(getwd(), subDir))
 source[[mod]] <- load_source_data(filename=source.filename,
                                    source_factors=NULL,
                                    conc_dep=FALSE,
                                    data_type="means",
                                    mix[[mod]])
  discr[[mod]] <- load_discr_data(filename=discr.filename, mix[[mod]])
  
 plot_data(filename=paste0("isospace_plot_", mod),
            plot_save_pdf=FALSE,
            plot_save_png=TRUE,
            mix[[mod]], source[[mod]], discr[[mod]], 
            return_obj = TRUE)

  model_filename <- paste0("MixSIAR_model_", mod, ".txt")
  resid_err <- TRUE
  process_err <- TRUE
  write_JAGS_model(model_filename, resid_err, process_err, mix[[mod]], source[[mod]])
  
    jags.mod[[mod]] <- run_model(run="long", mix[[mod]], source[[mod]], discr[[mod]], model_filename, alpha.prior=1)
  
  # Process diagnostics, summary stats, and posterior plots
  output_options <- list(summary_save = TRUE,                 
                       summary_name = "summary_statistics", 
                       sup_post = TRUE,                    
                       plot_post_save_pdf = FALSE,           
                       plot_post_name = "posterior_density",
                       sup_pairs = TRUE,             
                       plot_pairs_save_pdf = TRUE,    
                       plot_pairs_name = "pairs_plot",
                       sup_xy = TRUE,           
                       plot_xy_save_pdf = TRUE,
                       plot_xy_name = "xy_plot",
                       gelman = TRUE,
                       heidel = FALSE,  
                       geweke = TRUE,   
                       diag_save = TRUE,
                       diag_name = "diagnostics",
                       indiv_effect = FALSE,       
                       plot_post_save_png = FALSE, 
                       plot_pairs_save_png = FALSE,
                       plot_xy_save_png = FALSE,
                       diag_save_ggmcmc = FALSE,
                       return_obj = TRUE)
  
  output_JAGS(jags.mod, mix[[mod]], source[[mod]], output_options)

 ..$ BUGSoutput        :List of 24
  .. ..$ n.chains       : int 3
  .. ..$ n.iter         : num 3e+05
  .. ..$ n.burnin       : num 2e+05
  .. ..$ n.thin         : num 100
  .. ..$ n.keep         : int 1000
  .. ..$ n.sims         : int 3000
  .. ..$ sims.array     : num [1:1000, 1:3, 1:108] 271 269 268 264 261 ...
  .. .. ..- attr(*, "dimnames")=List of 3
  .. .. .. ..$ : NULL
  .. .. .. ..$ : NULL
  .. .. .. ..$ : chr [1:108] "deviance" "ilr.fac1[1,1]" "ilr.fac1[2,1]" "ilr.fac1[3,1]" ...
  .. ..$ sims.list      :List of 7
  .. .. ..$ deviance  : num [1:3000, 1] 269 264 272 268 273 ...
  .. .. ..$ ilr.fac1  : num [1:3000, 1:3, 1:3] 0 0 0 0 0 0 0 0 0 0 ...
  .. .. ..$ ilr.fac2  : num [1:3000, 1:2, 1:3] 0 0 0 0 0 0 0 0 0 0 ...
  .. .. ..$ ilr.global: num [1:3000, 1:3] -1.168 -0.708 -0.754 0.556 0.521 ...
  .. .. ..$ loglik    : num [1:3000, 1:83] -0.532 -0.408 -1.064 -0.885 -0.854 ...
  .. .. ..$ p.global  : num [1:3000, 1:4] 0.02041 0.00424 0.0069 0.03996 0.08206 ...
  .. .. ..$ resid.prop: num [1:3000, 1:2] 0.969 0.266 0.543 0.626 0.807 ...
.. ..$ sims.matrix    : num [1:3000, 1:108] 269 264 272 268 273 ...
  .. .. ..- attr(*, "dimnames")=List of 2
  .. .. .. ..$ : NULL
  .. .. .. ..$ : chr [1:108] "deviance" "ilr.fac1[1,1]" "ilr.fac1[2,1]" "ilr.fac1[3,1]" ...
  .. ..$ summary        : num [1:108, 1:9] 267.06 0 -0.219 0.263 0 ...
  .. .. ..- attr(*, "dimnames")=List of 2
  .. .. .. ..$ : chr [1:108] "deviance" "ilr.fac1[1,1]" "ilr.fac1[2,1]" "ilr.fac1[3,1]" ...
  .. .. .. ..$ : chr [1:9] "mean" "sd" "2.5%" "25%" ...