There is a newer version of the record available.

Published May 27, 2024 | Version 0.0.0.9000
Software Open

hpmdpredict: Predictions with model HPMe-LE-peat-l0 from Teickner et al. (2024)

Creators

  • 1. University of Münster

Description

hpmdpredict

 

hpmdpredict provides model HPMe-LE-peat-l0 from (Teickner, Pebesma, and Knorr 2024) and functions to make predictions with this model. HPMe-LE-peat-l0 models the fraction of initial mass remaining in Sphagnum litterbag experiments in dependency of species, degree of saturation, and distance below the water table, and it also models the magnitude of initial leaching losses.

Installation

You can install the development version of hpmdpredict in R by downloading the tar.gz file in this repository and executing:

install.packages("hpmdpredict_0.0.0.9000.tar.gz", type = "source")

Example

To make predictions, one first has to define some variables like the incubation duration. Here, we predict remaining masses and initial leaching losses for S. fuscum incubated at a degree of saturation of 0.6 Lwater Lpores-1 during the first five years.

library(hpmdpredict)

d <- 
  tibble::tibble(
    incubation_duration = seq(from = 0, to = 5, length.out = 30),
    m0 = 1,
    layer_degree_of_saturation_1 = 0.6,
    layer_water_table_depth_to_surface_1 = 20,
    sample_depth_lower = 10,
    hpm_taxon_rank_value = "Sphagnum fuscum"
  )

Next, one can pass this data frame to hpmd_predict_fit_4() which makes the predictions.

library(hpmdpredict)
d <- hpmdpredict::hpmd_predict_fit_4(newdata = d)

To illustrate the result, we plot predicted remaining masses versus incubation time:

library(ggplot2)
library(ggdist)

d |>
  ggplot(aes(ydist = mass_relative_mass * 100, x = incubation_duration)) +
  stat_lineribbon() +
  scale_fill_brewer() +
  labs(
    y = "Fraction of initial mass (%)",
    x = "Incubation duration (yr)"
  )

 

Model parameters

Model parameters that can be modified when making predictions are shown in the following table. Column “HPM parameter name” contains the names of the parameters in the Holocene Peatland Model (HPM) (Frolking et al. 2010) for the parameters from the decomposition module of the HPM.

Parameter Description HPM parameter name
phi_2 Precision parameter for the Beta distribution modeling remaining fractions of inital masses predicted by HPMe-LE-peat-l0. Larger values imply smaller errors in remaining masses (-).  
alpha_2 Parameter that controls how fast decomposition rates decrease as mass is lost during the decomposition (-).  
m69_p1 Peat degree of saturation where aerobic decomposition rates are maximal (Lwater Lpores-1). Wopt
m69_p2 Curvature of the relation of aerobic decomposition rates to the degree of saturation (larger values imply a more peaked relation) (-). c1
m68_p1 Minimum anaerobic decomposition rate (yr-1). fmin
m68_p2 Anoxia scale length. Represents limitation of anaerobic decomposition rates with increasing distance below the annual water table depth (m). c2
m68_p3_2 Maximum possible decomposition rate for the Sphagnum species (yr-1). k0,i
hpm_k_2_p1 Shape parameter for the Gamma distribution modeling decomposition rates predicted by the HPM (-).  
hpm_l_2_p1 Intercept for average Sphagnum initial leaching losses at a degree of saturation of 0 Lwater Lpores-1 (logit scale).  
hpm_l_2_p3 Slope for the relation between Sphagnum initial leaching losses and the degree of saturation (logit scale) (Lpores Lwater-1).  
hpm_l_2_p4 Precision parameter for the Beta distribution modeling initial leaching losses predicted by HPMe-LE-peat-l0. Larger values imply smaller errors in leaching losses (-).  

Citation

Please cite this R package as:

Henning Teickner and Klaus-Holger Knorr (2024): “hpmdpredict: Predictions with Model HPMe-LE-Peat-L0 from Teickner et al. (2024). https://doi.org/10.5281/zenodo.11339733”

Licenses

Text and figures : CC BY 4.0

Code : GPL-3 

Acknowledgements

Development of this software 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.

References

Frolking, S., N. T. Roulet, E. Tuittila, J. L. Bubier, A. Quillet, J. Talbot, and P. J. H. Richard. 2010. “A New Model of Holocene Peatland Net Primary Production, Decomposition, Water Balance, and Peat Accumulation.” Earth System Dynamics 1 (1): 1–21. https://doi.org/10.5194/esd-1-1-2010.
Teickner, Henning, Edzer Pebesma, and Klaus-Holger Knorr. 2024. “Underestimation of Anaerobic Decomposition Rates in Sphagnum Litterbag Experiments by the Holocene Peatland Model Depends on Initial Leaching Losses.” Unpublished preprint.

Files

Files (426.2 MB)

Name Size Download all
md5:6b1ef9484f210802303ffebc60540df8
425.6 MB Download
md5:fa94e45abdf36535a839b5ba5e143173
654.3 kB Download

Additional details

Related works

Is derived from
10.5281/zenodo.11276065 (DOI)

Funding

Deutsche Forschungsgemeinschaft
Probabilistic Modeling of Long-term Peatland Carbon Dynamics KN 929/23-1
Deutsche Forschungsgemeinschaft
Probabilistic Modeling of Long-term Peatland Carbon Dynamics PE 1632/18-1

Software

Programming language
R
Development Status
Concept