Package mmgm provides a mixing model that allows to estimate the
degree of decomposition (
You can install the development version of mmgm like so:
remotes::install_github("henningte/mmgm")To estimate the mixing model, one needs to provide a list with two data
frames as elements. The first element, components contains information
on components, and the second element, mixtures, contains information
on the mixtures (peat samples):
library(mmgm)
library(cmdstanr)
#> Warning: package 'cmdstanr' was built under R version 4.3.3
#> This is cmdstanr version 0.8.1
#> - CmdStanR documentation and vignettes: mc-stan.org/cmdstanr
#> - CmdStan path: C:/Users/henni/.cmdstan/cmdstan-2.36.0
#> - CmdStan version: 2.36.0
#>
#> A newer version of CmdStan is available. See ?install_cmdstan() to install it.
#> To disable this check set option or environment variable cmdstanr_no_ver_check=TRUE.
# show structure of the example data
mmgm_example_data
#> $components
#> id_mixture id_component w
#> 1.1 1 1 0.5956979
#> 1.2 1 2 0.4043021
#> 2.1 2 1 0.2799653
#> 2.2 2 2 0.7200347
#> 3.1 3 1 0.5942072
#> 3.2 3 2 0.4057928
#> 4.1 4 1 0.4683780
#> 4.2 4 2 0.5316220
#> 5.1 5 1 0.1578412
#> 5.2 5 2 0.8421588
#>
#> $mixtures
#> # A tibble: 5 × 2
#> id_mixture degree_of_decomposition_2
#> * <int> <quantits>
#> 1 1 0.06227749
#> 2 2 0.01924212
#> 3 3 0.02330240
#> 4 4 0.03896350
#> 5 5 0.12042913To prepare estimation of the mixing model, this list is processed with
mmgm_make_stan_data():
stan_data <-
mmgm_make_stan_data(
x = mmgm_example_data,
id_model_gamma_mirs = 2,
priors = mmgm_make_default_priors(x = mmgm_example_data)
)Here, id_model_gamma_mirs defines the model that was used to predict
irpeatmodels
package (Teickner 2025)). priors defines the priors for the mixing
model and mmgm_make_default_priors() is a helper function that allows
to define default priors for a given list of data.
stan_data can be passed to mmgm_estimate_gamma_mirs_mixing_1() to
estimate the mixing model using CmdStan. Use the CmdStan
arguments
to adjust MCMC sampling:
stan_fit <-
mmgm_estimate_gamma_mirs_mixing_1(
stan_data = stan_data,
iter_warmup = 1000,
iter_sampling = 1000,
chains = 4,
sig_figs = 14,
seed = 7667
)
#> Running MCMC with 4 sequential chains...
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#> Chain 1 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:
#> Chain 1 Exception: gamma_lpdf: Random variable[2] is 0, but must be positive finite! (in 'C:/Users/henni/AppData/Local/Temp/RtmpCCJ84p/model-df0ea5142c.stan', line 43, column 2 to column 40)
#> Chain 1 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,
#> Chain 1 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.
#> Chain 1
#> Chain 1 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:
#> Chain 1 Exception: beta_lpdf: Second shape parameter[2] is 0, but must be positive finite! (in 'C:/Users/henni/AppData/Local/Temp/RtmpCCJ84p/model-df0ea5142c.stan', line 48, column 4 to column 151)
#> Chain 1 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,
#> Chain 1 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.
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#> Chain 1 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:
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#> Chain 1 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,
#> Chain 1 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.
#> Chain 1
#> Chain 1 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:
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#> Chain 1 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,
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#> Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:
#> Chain 2 Exception: beta_lpdf: Second shape parameter[3] is 0, but must be positive finite! (in 'C:/Users/henni/AppData/Local/Temp/RtmpCCJ84p/model-df0ea5142c.stan', line 49, column 4 to column 110)
#> Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,
#> Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.
#> Chain 2
#> Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:
#> Chain 2 Exception: beta_lpdf: First shape parameter[1] is 0, but must be positive finite! (in 'C:/Users/henni/AppData/Local/Temp/RtmpCCJ84p/model-df0ea5142c.stan', line 48, column 4 to column 151)
#> Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,
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#> Chain 3 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.
#> Chain 3
#> Chain 3 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:
#> Chain 3 Exception: beta_lpdf: Second shape parameter[2] is 0, but must be positive finite! (in 'C:/Users/henni/AppData/Local/Temp/RtmpCCJ84p/model-df0ea5142c.stan', line 48, column 4 to column 151)
#> Chain 3 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,
#> Chain 3 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.
#> Chain 3
#> Chain 3 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:
#> Chain 3 Exception: beta_lpdf: Second shape parameter[2] is 0, but must be positive finite! (in 'C:/Users/henni/AppData/Local/Temp/RtmpCCJ84p/model-df0ea5142c.stan', line 48, column 4 to column 151)
#> Chain 3 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,
#> Chain 3 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.
#> Chain 3
#> Chain 3 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:
#> Chain 3 Exception: gamma_lpdf: Random variable[2] is 0, but must be positive finite! (in 'C:/Users/henni/AppData/Local/Temp/RtmpCCJ84p/model-df0ea5142c.stan', line 43, column 2 to column 40)
#> Chain 3 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,
#> Chain 3 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.
#> Chain 3
#> Chain 3 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:
#> Chain 3 Exception: beta_lpdf: Second shape parameter[1] is 0, but must be positive finite! (in 'C:/Users/henni/AppData/Local/Temp/RtmpCCJ84p/model-df0ea5142c.stan', line 48, column 4 to column 151)
#> Chain 3 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,
#> Chain 3 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.
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#> Chain 4 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,
#> Chain 4 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.
#> Chain 4
#> Chain 4 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:
#> Chain 4 Exception: beta_lpdf: Second shape parameter[3] is 0, but must be positive finite! (in 'C:/Users/henni/AppData/Local/Temp/RtmpCCJ84p/model-df0ea5142c.stan', line 48, column 4 to column 151)
#> Chain 4 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,
#> Chain 4 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.
#> Chain 4
#> Chain 4 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:
#> Chain 4 Exception: beta_lpdf: First shape parameter[2] is 0, but must be positive finite! (in 'C:/Users/henni/AppData/Local/Temp/RtmpCCJ84p/model-df0ea5142c.stan', line 48, column 4 to column 151)
#> Chain 4 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,
#> Chain 4 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.
#> Chain 4
#> Chain 4 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:
#> Chain 4 Exception: beta_lpdf: Second shape parameter[5] is 0, but must be positive finite! (in 'C:/Users/henni/AppData/Local/Temp/RtmpCCJ84p/model-df0ea5142c.stan', line 48, column 4 to column 151)
#> Chain 4 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,
#> Chain 4 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.
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#> Chain 4 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:
#> Chain 4 Exception: beta_lpdf: Second shape parameter[5] is 0, but must be positive finite! (in 'C:/Users/henni/AppData/Local/Temp/RtmpCCJ84p/model-df0ea5142c.stan', line 49, column 4 to column 110)
#> Chain 4 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,
#> Chain 4 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.
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#>
#> All 4 chains finished successfully.
#> Mean chain execution time: 0.4 seconds.
#> Total execution time: 2.2 seconds.The result is a CmdStanMCMC object for which methods from the
cmdstanr package are available, for example:
stan_fit$diagnostic_summary()
#> $num_divergent
#> [1] 0 0 0 0
#>
#> $num_max_treedepth
#> [1] 0 0 0 0
#>
#> $ebfmi
#> [1] 0.8314510 0.8898877 0.9007872 0.8155281
print(stan_fit$summary(), n = 40)
#> # A tibble: 37 × 10
#> variable mean median sd mad q5 q95 rhat ess_bulk
#> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
#> 1 lp__ -47.0 -46.6 3.79 3.66 -5.37e+1 -41.4 1.00 1393.
#> 2 gamma_com… 0.169 0.117 0.160 0.119 1.24e-2 0.508 1.00 2577.
#> 3 gamma_com… 0.273 0.206 0.238 0.229 1.07e-2 0.754 1.00 2994.
#> 4 gamma_com… 0.327 0.259 0.265 0.286 1.01e-2 0.832 1.00 3250.
#> 5 gamma_com… 0.0421 0.0259 0.0508 0.0245 3.73e-3 0.135 1.00 2236.
#> 6 gamma_com… 0.0967 0.0469 0.128 0.0547 3.65e-3 0.371 1.00 2176.
#> 7 gamma_com… 0.223 0.143 0.228 0.179 3.58e-3 0.712 1.00 2936.
#> 8 gamma_com… 0.202 0.127 0.208 0.150 6.21e-3 0.653 1.00 2850.
#> 9 gamma_com… 0.158 0.0962 0.171 0.111 5.63e-3 0.534 1.00 2547.
#> 10 gamma_com… 0.454 0.438 0.285 0.364 3.78e-2 0.922 1.00 5196.
#> 11 gamma_com… 0.271 0.248 0.164 0.170 5.18e-2 0.578 1.00 2245.
#> 12 phi[1] 0.998 0.942 0.440 0.420 3.96e-1 1.81 1.00 3842.
#> 13 phi[2] 0.995 0.934 0.435 0.417 4.00e-1 1.80 1.00 4334.
#> 14 phi[3] 0.993 0.929 0.449 0.426 3.75e-1 1.83 1.00 4538.
#> 15 phi[4] 0.986 0.912 0.437 0.405 3.94e-1 1.77 1.00 4394.
#> 16 phi[5] 1.01 0.953 0.448 0.433 4.02e-1 1.86 1.00 3903.
#> 17 gamma_mir… 0.148 0.140 0.0701 0.0683 4.73e-2 0.273 1.00 2799.
#> 18 gamma_mir… 0.0499 0.0459 0.0264 0.0259 1.40e-2 0.0991 1.00 3041.
#> 19 gamma_mir… 0.0698 0.0647 0.0365 0.0347 1.97e-2 0.139 1.00 3072.
#> 20 gamma_mir… 0.105 0.0978 0.0525 0.0526 3.14e-2 0.200 1.00 2843.
#> 21 gamma_mir… 0.282 0.266 0.143 0.148 7.53e-2 0.544 1.00 2256.
#> 22 b_interce… -3.52 -3.52 0.131 0.134 -3.73e+0 -3.31 1.00 4827.
#> 23 gamma_mir… 0.154 0.145 0.0734 0.0728 4.83e-2 0.288 1.00 2856.
#> 24 gamma_mir… 0.0571 0.0523 0.0309 0.0297 1.51e-2 0.116 1.00 2933.
#> 25 gamma_mir… 0.0782 0.0728 0.0412 0.0403 2.28e-2 0.155 1.00 2986.
#> 26 gamma_mir… 0.112 0.106 0.0564 0.0576 3.37e-2 0.215 1.00 2518.
#> 27 gamma_mir… 0.286 0.272 0.144 0.150 7.76e-2 0.545 1.00 2193.
#> 28 phi_scale… 200. 188. 88.1 83.9 7.91e+1 362. 1.00 3842.
#> 29 phi_scale… 199. 187. 87.1 83.5 8.00e+1 360. 1.00 4334.
#> 30 phi_scale… 199. 186. 89.8 85.2 7.50e+1 365. 1.00 4538.
#> 31 phi_scale… 197. 182. 87.3 81.0 7.89e+1 353. 1.00 4394.
#> 32 phi_scale… 202. 191. 89.6 86.6 8.04e+1 371. 1.00 3903.
#> 33 gamma_mix… 0.264 0.224 0.162 0.127 7.60e-2 0.591 1.00 2915.
#> 34 gamma_mix… 0.192 0.125 0.178 0.0987 3.38e-2 0.583 1.00 4092.
#> 35 gamma_mix… 0.190 0.138 0.155 0.0939 3.97e-2 0.529 0.999 3282.
#> 36 gamma_mix… 0.220 0.176 0.152 0.112 5.62e-2 0.537 1.00 2622.
#> 37 gamma_mix… 0.373 0.352 0.180 0.178 1.22e-1 0.704 1.00 2872.
#> # ℹ 1 more variable: ess_tail <dbl>Please note that the mmgm project is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.
This study was funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) grant no. KN 929/23-1 to Klaus-Holger Knorr and grant no. PE 1632/18-1 to Edzer Pebesma.
Teickner, Henning. 2025. “irpeatmodels: Mid-infrared Prediction Models for Peat.” Zenodo. https://doi.org/10.5281/ZENODO.17187912.
Teickner, Henning, Julien Arsenault, Mariusz Gałka, and Klaus-Holger Knorr. 2025. “Estimation of the Degree of Decomposition of Peat and Past Net Primary Production from Mid-Infrared Spectra.”