Last updated on 2026-09-03 20:57:21 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.6.1 | 50.36 | 590.82 | 641.18 | OK | |
| r-devel-linux-x86_64-debian-gcc | 1.6.1 | 31.17 | 384.00 | 415.17 | OK | |
| r-devel-linux-x86_64-fedora-clang | 1.6.1 | 37.00 | 379.67 | 416.67 | OK | |
| r-devel-linux-x86_64-fedora-gcc | 1.6.1 | 36.00 | 411.69 | 447.69 | OK | |
| r-devel-windows-x86_64 | 1.6.1 | 50.00 | 503.00 | 553.00 | ERROR | |
| r-patched-linux-x86_64 | 1.6.1 | 49.13 | 569.97 | 619.10 | OK | |
| r-release-linux-x86_64 | 1.6.1 | 48.57 | 572.97 | 621.54 | OK | |
| r-release-macos-arm64 | 1.6.1 | 13.00 | 116.00 | 129.00 | OK | |
| r-release-macos-x86_64 | 1.6.1 | 38.00 | 528.00 | 566.00 | OK | |
| r-release-windows-x86_64 | 1.6.1 | 50.00 | 532.00 | 582.00 | OK | |
| r-oldrel-macos-arm64 | 1.6.1 | 13.00 | 127.00 | 140.00 | OK | |
| r-oldrel-macos-x86_64 | 1.6.1 | 37.00 | 497.00 | 534.00 | OK | |
| r-oldrel-windows-x86_64 | 1.6.1 | 68.00 | 757.00 | 825.00 | OK |
Version: 1.6.1
Check: examples
Result: ERROR
Running examples in 'missingHE-Ex.R' failed
The error most likely occurred in:
> ### Name: hurdle
> ### Title: Full Bayesian Models to handle missingness in Economic
> ### Evaluations (Hurdle Models)
> ### Aliases: hurdle
> ### Keywords: CEA Hurdle JAGS Models data missing
>
> ### ** Examples
>
> # Quck example to run using subset of MenSS dataset
> MenSS.subset <- MenSS[50:100, ]
>
> # Run the model using the hurdle function assuming a SCAR mechanism
> # Use only 100 iterations to run a quick check
> model.hurdle <- hurdle(data = MenSS.subset, model.eff = e ~ trt, model.cost = c ~ trt,
+ model.se = se ~ 1, model.sc = sc ~ 1, se = 1, sc = 0, dist_e = "norm", dist_c = "norm",
+ type = "SCAR", n.chains = 2, n.iter = 100)
module glm loaded
Compiling model graph
Resolving undeclared variables
Allocating nodes
Graph information:
Observed stochastic nodes: 60
Unobserved stochastic nodes: 152
Total graph size: 1133
Initializing model
Error in ar.yw.default(x, aic = aic, order.max = order.max, na.action = na.action, :
zero-variance series
Error in ar.yw.default(x, aic = aic, order.max = order.max, na.action = na.action, :
zero-variance series
Error in ar.yw.default(x, aic = aic, order.max = order.max, na.action = na.action, :
zero-variance series
Error in ar.yw.default(x, aic = aic, order.max = order.max, na.action = na.action, :
zero-variance series
>
> # Print the results of the JAGS model
> print(model.hurdle)
mean sd 2.5% 50%
alpha[1,1] 0.8552029 0.04086688 7.65e-01 0.8622504
alpha[2,1] 0.0852405 0.08623190 -7.79e-02 0.0965474
alpha[1,2] 1.0000000 0.00000000 1.00e+00 1.0000000
alpha[2,2] 0.0000000 0.00000000 0.00e+00 0.0000000
beta[1,1] 42.7703893 31.47153336 -1.46e+01 42.8872544
beta[2,1] 10.6621597 30.28813438 -3.96e+01 7.5820939
beta[1,2] 0.0000000 0.00000000 0.00e+00 0.0000000
beta[2,2] 0.0000000 0.00000000 0.00e+00 0.0000000
gamma_c -1.2222644 0.74054817 -2.72e+00 -1.1909756
gamma_e -0.3091857 0.47576394 -1.20e+00 -0.2834149
p_c 0.2505798 0.12659831 6.19e-02 0.2330847
p_e 0.4270897 0.11159730 2.32e-01 0.4296181
s_c[1] 231.0436471 50.39006778 1.56e+02 226.9819267
s_c[2] 0.0000100 0.00000000 1.00e-05 0.0000100
s_e[1] 0.1015937 0.02804029 6.06e-02 0.0988762
s_e[2] 0.0000100 0.00000000 1.00e-05 0.0000100
tau_c[1] 0.0000216 0.00000983 9.21e-06 0.0000194
tau_c[2] 9999999999.9999981 0.00000000 1.00e+10 9999999999.9999981
tau_e[1] 118.3102675 60.89067904 3.49e+01 102.2865731
tau_e[2] 9999999999.9999981 0.00000000 1.00e+10 9999999999.9999981
tmu_c 36.0549963 27.18458408 -1.08e+01 36.4539313
tmu_e 0.9422830 0.02451618 8.88e-01 0.9414858
97.5% Rhat n.eff
alpha[1,1] 0.949835 1.010 100
alpha[2,1] 0.261970 1.011 100
alpha[1,2] 1.000000 1.000 1
alpha[2,2] 0.000000 1.000 1
beta[1,1] 98.888679 0.997 100
beta[2,1] 80.512288 1.008 100
beta[1,2] 0.000000 1.000 1
beta[2,2] 0.000000 1.000 1
gamma_c 0.146487 1.068 33
gamma_e 0.637111 1.042 100
p_c 0.536554 1.088 28
p_e 0.654020 1.048 100
s_c[1] 329.502862 1.001 100
s_c[2] 0.000010 1.000 1
s_e[1] 0.169542 1.157 13
s_e[2] 0.000010 1.000 1
tau_c[1] 0.000041 1.001 100
tau_c[2] 9999999999.999998 1.000 1
tau_e[1] 272.131989 1.157 13
tau_e[2] 9999999999.999998 1.000 1
tmu_c 89.688508 1.007 100
tmu_e 0.988371 1.005 100
> #
>
> # Use dic information criterion to assess model fit
> pic.dic <- pic(model.hurdle, criterion = "dic", cases = "cc")
> pic.dic
$d_bar
[1] -36.81777
$pD
[1] 204.8657
$dic
[1] 168.0479
$d_hat
[1] -241.6834
> #
>
> # Extract regression coefficient estimates
> coef(model.hurdle)
$Effects
Mean SD QL QU
(Intercept) 0.855 0.041 0.765 0.950
trt2 0.085 0.086 -0.078 0.262
$Costs
Mean SD QL QU
(Intercept) 42.770 31.472 -14.618 98.889
trt2 10.662 30.288 -39.607 80.512
> #
>
> ## Don't show:
> # Use waic information criterion to assess model fit
> pic.waic <- pic(model.hurdle, criterion = "waic", cases = "cc")
> pic.waic
$elpd
[1] 15.42885
$elpd_se
[1] 40.56594
$p
[1] 5.266018
$p_se
[1] 0.6281658
$waic
[1] -30.8577
$waic_se
[1] 81.13187
$pointwise
elpd_waic p_waic waic
[1,] 18.586768 0.3551583 -37.173536
[2,] -6.502173 0.1919359 13.004346
[3,] -6.303347 0.2478219 12.606694
[4,] 1.604880 0.2168823 -3.209761
[5,] -7.151715 0.4138777 14.303431
[6,] 9.172790 0.5041855 -18.345579
[7,] -7.919465 0.3696665 15.838930
[8,] -7.487206 0.4795243 14.974413
[9,] 18.586768 0.3551583 -37.173536
[10,] 2.929572 0.1750029 -5.859143
[11,] -6.198919 0.1878427 12.397837
[12,] -6.604574 0.4736046 13.209148
[13,] 18.586768 0.3551583 -37.173536
[14,] 2.931216 0.1793959 -5.862431
[15,] -8.802512 0.7608026 17.605023
> ## End(Don't show)
>
> # Assess model convergence using graphical tools
> # Produce histograms of the posterior samples for the mean effects
> diag.hist <- diagnostic(model.hurdle, type = "histogram", param = "mu.e")
Loading required namespace: ggmcmc
Failed with error: 'object 'ggcoef_multinom' is not exported by 'namespace:ggstats''
Error in diagnostic(model.hurdle, type = "histogram", param = "mu.e") :
You need to install the R packages 'ggmcmc', 'coda' and 'mcmcr'.
Please run in your R terminal:
install.packages('ggmcmc', 'coda', 'mcmcr')
Execution halted
Flavor: r-devel-windows-x86_64
Version: 1.6.1
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building 'Fitting_MNAR_models_in_missingHE.Rmd' using rmarkdown
--- finished re-building 'Fitting_MNAR_models_in_missingHE.Rmd'
--- re-building 'Introduction_to_missingHE.Rmd' using rmarkdown
Warning in eng_r(options) :
Failed to tidy R code in chunk 'diag1'. Reason:
Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored.
Failed with error: 'object 'ggcoef_multinom' is not exported by 'namespace:ggstats''
Quitting from Introduction_to_missingHE.Rmd:326-328 [fig2]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `diagnostic()`:
! You need to install the R packages 'ggmcmc', 'coda' and 'mcmcr'.
Please run in your R terminal:
install.packages('ggmcmc', 'coda', 'mcmcr')
---
Backtrace:
▆
1. └─missingHE::diagnostic(x = sm1_mar, type = "traceplot", param = "sd.e")
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'Introduction_to_missingHE.Rmd' failed with diagnostics:
You need to install the R packages 'ggmcmc', 'coda' and 'mcmcr'.
Please run in your R terminal:
install.packages('ggmcmc', 'coda', 'mcmcr')
--- failed re-building 'Introduction_to_missingHE.Rmd'
--- re-building 'Longitudinal_models_in_missingHE.Rmd' using rmarkdown
Warning in eng_r(options) :
Failed to tidy R code in chunk 'diag1'. Reason:
Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored.
Failed with error: 'object 'ggcoef_multinom' is not exported by 'namespace:ggstats''
Quitting from Longitudinal_models_in_missingHE.Rmd:225-227 [fig2]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `diagnostic()`:
! You need to install the R packages 'ggmcmc', 'coda' and 'mcmcr'.
Please run in your R terminal:
install.packages('ggmcmc', 'coda', 'mcmcr')
---
Backtrace:
▆
1. └─missingHE::diagnostic(x = lmdm1_mar, type = "denplot", param = "beta.f")
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'Longitudinal_models_in_missingHE.Rmd' failed with diagnostics:
You need to install the R packages 'ggmcmc', 'coda' and 'mcmcr'.
Please run in your R terminal:
install.packages('ggmcmc', 'coda', 'mcmcr')
--- failed re-building 'Longitudinal_models_in_missingHE.Rmd'
--- re-building 'Model_customisation_in_missingHE.Rmd' using rmarkdown
Warning in eng_r(options) :
Failed to tidy R code in chunk 'selprint'. Reason:
Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored.
Failed with error: 'object 'ggcoef_multinom' is not exported by 'namespace:ggstats''
Quitting from Model_customisation_in_missingHE.Rmd:228-230 [figplotdiag]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `diagnostic()`:
! You need to install the R packages 'ggmcmc', 'coda' and 'mcmcr'.
Please run in your R terminal:
install.packages('ggmcmc', 'coda', 'mcmcr')
---
Backtrace:
▆
1. └─missingHE::diagnostic(x = sm1_nn_cov, type = "acf", param = "alpha")
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'Model_customisation_in_missingHE.Rmd' failed with diagnostics:
You need to install the R packages 'ggmcmc', 'coda' and 'mcmcr'.
Please run in your R terminal:
install.packages('ggmcmc', 'coda', 'mcmcr')
--- failed re-building 'Model_customisation_in_missingHE.Rmd'
SUMMARY: processing the following files failed:
'Introduction_to_missingHE.Rmd'
'Longitudinal_models_in_missingHE.Rmd'
'Model_customisation_in_missingHE.Rmd'
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-windows-x86_64