Output issues: dplyr update, using 2 factors and weird plots

[AVGPR]

Hi Brian, I’m having different issues with MixSIAR. First, I am getting the error message below (right after "Plotting Geweke diagnostic" comes up in output_JAGS), that I think may be related to the latest dplyr update (1.0.0):

Error: Problem with summarise() input n. x could not find function "n" i Input n is n(). i The error occured in group 1: Parameter = "deviance", Chain = 1, part = "first". Run rlang::last_error() to see where the error occurred. In addition: Warning message: tbl_df() is deprecated as of dplyr 1.0.0. Please use tibble::as_tibble() instead.

rlang::last_error() <error/dplyr_error> Problem with summarise() input n. x could not find function "n" i Input n is n(). i The error occured in group 1: Parameter = "deviance", Chain = 1, part = "first". Backtrace:

1. MixSIAR::output_JAGS(jags.uninf, mix, source)
2. ggmcmc::ggmcmc(...)
3. ggmcmc::ggs_geweke(D)
4. dplyr::group_by(., Parameter, Chain, part)
5. dplyr::summarize(., m = mean(value), sde0f = sde0f(value), n = n())
6. dplyr:::summarise_cols(.data, ...)

I have been running the same model with different data sets for a while and they suddenly started giving me these errors after I changed the fixed/random factor and error structure specifications. However, when I changed the model specifications back to my original ones, I kept getting the error. Only after re-installing a previous dplyr version was I able to get rid of that error message.

However, now I am getting NAs in my [,] column after the "Plotting Geweke diagnostic" (see below)… which I wasn’t getting before (using the same data and model specifications). It only seems to happen when using two factors (runs perfectly with only one factor). I wouldn't think it has to do with my data as I have been using the same data for a while and I just started getting that now.

Plotting Geweke Diagnostic Time taken to generate the report: 99 seconds. , , 1, 1

           [,1] [,2]

[1,] 0.090742076 NA [2,] 0.069428303 NA [3,] 0.044360332 NA [4,] 0.044162688 NA [5,] 0.117445203 NA [6,] 0.124717812 NA [7,] 0.131961553 NA [8,] 0.148752639 NA

I also get error messages like:

To compare, I tried running the MixSIAR example scripts and while I don't get those issues, I get other error messages (see below) and some plots are weird (see image below of the isoplot for the alligator_length script and for diet proportions for the lake example script).

I don't know if it's a general problem with my whole R and R Studio? If anyone knows what might be happening, it will be greatly appreciated.

Thank you, Adriana