mikemeredith
commented
3 years ago The error arises because you loaded package coda after loading jagsUI, which is clear from your sessionInfo output. When you did that, you should have seen a message:
The following object is masked from ‘package:jagsUI’:
traceplotSo when you do traceplot(out5) you are calling coda::traceplot, not jagsUI::traceplot. And, yes, that only works with valid mcmc objects, while out5 is class jagsUI.
There's no call to library(coda) in the script, so it's not a bug. On the other hand it is called in 11.07, so maybe good to specify jagsUI::traceplot everywhere in chapter 11.
Jrogan23
Thank you for reporting a bug in our scripts.
The code here is based on the book, and we update it to work with current versions of JAGS, R and R packages. Please make sure you have the latest version of the script and software (run
update.packages()) before reporting an issue.File name: AHM1_ch11
Lines which produced the error or unexpected output (copy/paste from the console): op <- par(mfrow = c(4,4)) ; traceplot(out5) ; print(out5, dig = 3)
error message: Error in mcmc.list(x) : Arguments must be mcmc objects
Do you have a suggested update for the code:
Coda specifies that in the updated version, older mcmc objects will result in an error message. "n previous releases of CODA, an mcmc object could be a single or multiple chains. A new class mcmc.list has now been introduced to deal with multiple chains and mcmc objects can only have data from a single chain."
mcmcUpgrade(x) can be used to update outdated code for mcmc objects; or objects could be modified to specified correctly under the updated version of the coda package
Run
sessionInfo()and paste the output here:R version 4.0.3 (2020-10-10) Platform: x86_64-apple-darwin17.0 (64-bit) Running under: macOS Catalina 10.15.6
Matrix products: default BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib
locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages: [1] stats graphics grDevices utils datasets methods base
other attached packages: [1] AHMbook_0.2.0 coda_0.19-4 jagsUI_1.5.1 lattice_0.20-41
loaded via a namespace (and not attached): [1] Rcpp_1.0.5 mvtnorm_1.1-1 codetools_0.2-16 unmarked_1.0.1
[5] MASS_7.3-53 grid_4.0.3 plyr_1.8.6 RandomFields_3.3.8
[9] raster_3.3-13 sp_1.4-4 rjags_4-10 RColorBrewer_1.1-2
[13] tools_4.0.3 plotrix_3.7-8 parallel_4.0.3 compiler_4.0.3
[17] RandomFieldsUtils_0.5.3
Other information that may be helpful to pinpoint the issue, eg, screenshots: