{"action":"created","issue":{"url":"https://api.github.com/repos/brianstock/MixSIAR/issues/129","repository_url":"https://api.github.com/repos/brianstock/MixSIAR","labels_url":"https://api.github.com/repos/brianstock/MixSIAR/issues/129/labels{/name}","comments_url":"https://api.github.com/repos/brianstock/MixSIAR/issues/129/comments","events_url":"https://api.github.com/repos/brianstock/MixSIAR/issues/129/events","html_url":"https://github.com/brianstock/MixSIAR/issues/129","id":294484201,"number":129,"title":"No diagnostics file or output","user":{"login":"raphael-lavoie","id":28790389,"avatar_url":"https://avatars1.githubusercontent.com/u/28790389?v=4","gravatar_id":"","url":"https://api.github.com/users/raphael-lavoie","html_url":"https://github.com/raphael-lavoie","followers_url":"https://api.github.com/users/raphael-lavoie/followers","following_url":"https://api.github.com/users/raphael-lavoie/following{/other_user}","gists_url":"https://api.github.com/users/raphael-lavoie/gists{/gist_id}","starred_url":"https://api.github.com/users/raphael-lavoie/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/raphael-lavoie/subscriptions","organizations_url":"https://api.github.com/users/raphael-lavoie/orgs","repos_url":"https://api.github.com/users/raphael-lavoie/repos","events_url":"https://api.github.com/users/raphael-lavoie/events{/privacy}","received_events_url":"https://api.github.com/users/raphael-lavoie/received_events","type":"User","site_admin":false},"labels":[{"id":50032761,"url":"https://api.github.com/repos/brianstock/MixSIAR/labels/bug","name":"bug","color":"fc2929","default":true}],"state":"closed","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":3,"created_at":"2018-02-05T17:51:54Z","updated_at":"2018-03-09T05:59:08Z","closed_at":"2018-03-09T05:59:08Z","author_association":"NONE","body":"I cannot get the diagnostics from any model. When I run the model with my data or any runnable examples e.g., wolves, I get:\r\n\r\n`jags.1 <- run_model(run=\"test\", mix, source, discr, model_filename, alpha.prior = c(1,1), resid_err, process_err)`\r\nCompiling model graph\r\n   Resolving undeclared variables\r\n   Allocating nodes\r\nGraph information:\r\n   Observed stochastic nodes: 60\r\n   Unobserved stochastic nodes: 53\r\n   Total graph size: 2213\r\n\r\nInitializing model\r\n\r\n  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100%\r\n  |**************************************************| 100%\r\nWarning messages:\r\n1: In structure(c(), class = c(class(x), class(y))) :\r\n  Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.\r\n  Consider 'structure(list(), *)' instead.\r\n2: In structure(c(), class = c(class(x), class(y))) :\r\n  Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.\r\n  Consider 'structure(list(), *)' instead.\r\n3: In structure(c(), class = c(class(x), class(y))) :\r\n  Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.\r\n  Consider 'structure(list(), *)' instead.\r\n\r\nWhen I call:  \r\n`output_options <- list(summary_save = TRUE,summary_name = \"summary_statistics\",sup_post = FALSE,plot_post_save_pdf = TRUE,plot_post_name = \"posterior_density\",sup_pairs = FALSE,plot_pairs_save_pdf = TRUE,plot_pairs_name = \"pairs_plot\",sup_xy = TRUE,plot_xy_save_pdf = FALSE,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)`\r\n\r\n`output_JAGS(jags.1, mix, source, output_options)`\r\nError: Casting formula contains variables not found in molten data: Var3, Var2, Var1\r\n\r\nI cannot get the diagnostics output (gelman, heidel, geweke) and it does not save the diagnostics file. I can get the posterior graphs, the posterior probabilities, but I don’t know if my model performs well or if it converges because I don’t have the diagnostics. \r\n\r\nI know that the model is working because I have most graphs and the posterior probabilities. I can even get the diagnostics when using the GUI `mixsiar_gui()`, but not when using the scripts. I would rather use the scripts so I would like to solve that issue. \r\n\r\nAny help would be appreciated!\r\nThanks!\r\nRaph"},"comment":{"url":"https://api.github.com/repos/brianstock/MixSIAR/issues/comments/371721488","html_url":"https://github.com/brianstock/MixSIAR/issues/129#issuecomment-371721488","issue_url":"https://api.github.com/repos/brianstock/MixSIAR/issues/129","id":371721488,"user":{"login":"brianstock","id":5124211,"avatar_url":"https://avatars3.githubusercontent.com/u/5124211?v=4","gravatar_id":"","url":"https://api.github.com/users/brianstock","html_url":"https://github.com/brianstock","followers_url":"https://api.github.com/users/brianstock/followers","following_url":"https://api.github.com/users/brianstock/following{/other_user}","gists_url":"https://api.github.com/users/brianstock/gists{/gist_id}","starred_url":"https://api.github.com/users/brianstock/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/brianstock/subscriptions","organizations_url":"https://api.github.com/users/brianstock/orgs","repos_url":"https://api.github.com/users/brianstock/repos","events_url":"https://api.github.com/users/brianstock/events{/privacy}","received_events_url":"https://api.github.com/users/brianstock/received_events","type":"User","site_admin":false},"created_at":"2018-03-09T05:59:08Z","updated_at":"2018-03-09T05:59:08Z","author_association":"OWNER","body":"Hmm, I'm not sure what's causing that. `output_JAGS` uses `cast` from the `reshape` package and `melt` from `reshape2`. I've been using the `tidyverse` set of packages recently, which accomplish the same tasks, but I don't really want to mess with changing the old `reshape` code... \r\n\r\nI solved your original bug report with the error warning coming from the `compositions` package. Download the most recent MixSIAR from Github and check. I'll soon submit a new version to CRAN, but not ready quite yet"}}
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