microbial-explicit-model / memc Goto Github PK

For the FME-related functions we have adopted a memc_FMEname pattern aka see memc_modfit, would we want this to be the pattern for the other functions as well? This is just a note to save this idea

solve_model --> memc_solve
configure_model --> memc_config

Will need #24 to be completed first!

Add an example vignette that walks through how users can fit the model to their own data!

Something to consider especially if the integration solvers start to struggle or we want more flexibility with the number of pools. Does moving the bulk of the code to Cpp with an R wrapper make sense? Would this be computationally efficient? Consider talking it over with BBL & CRV this would be a post-v1 development enhancement

Right now the the implementation of BAMS in our package uses the following configuration.

We need to confirm that this the correct combination of the dynamics.

Right now the the implementation of MEND in our package uses the following configuration.

1. We need to confirm that this the correct combination of the dynamics.

2. Also confirm that this is the correct reference

Wang, G., Post, W. M., and Mayes, M. A.: Development of microbial-enzyme-mediated decomposition model parameters through steady-state and dynamic analyses, Ecol. Appl., 23, 255–272, 2013.

Right now the the implementation of CORPSE in our package uses the following configuration.

1. We need to confirm that this the correct combination of the dynamics.
2. Do we have the correct citation?

Sulman, B. N., Moore, J. A. M., Abramoff, R., Averill, C., Kivlin, S., Georgiou, K., Sridhar, B., Hartman, M. D., Wang, G., Wieder, W. R., Bradford, M. A., Luo, Y., Mayes, M. A., Morrison, E., Riley, W. J., Salazar, A., Schimel, J. P., Tang, J., and Classen, A. T.: Multiple models and experiments underscore large uncertainty in soil carbon dynamics, Biogeochemistry, 141, 109–123, 2018.

Add more details about the model output!

Update the Github Actions, should be passing

• test-coverage
• R package check on multiple plat forms

• respond to @jianqiuz PR feedback
• add the other kinetic representations
• sensitivity analysis
• optimize parameters
• add linux r cmd build test
• complete documentation
  • add motivation
  • add model structure overview
  • add dynamics documentation
  • expand sens analysis to include the initial pool conditions
  • add an example where find the initial pool conditions?
• add mcmc FME capabilities to the package
• JOSS checklist

Right now we are struggling with calibrating the model configurations to a data set. While we've included functions in the package it is unclear what data set we should be calibrating to and the source of this data set.

Run profvis to diagnosis code performance, this should be minimal effort! If seems like would take too much time or would require a large overhaul should add idea/description of problems to an different issue.

This is a post v1 task, consider revisiting the package dependencies, are packages like data.table really necessary? What are the strengths/limits for this.

One possible idea is to switch from using the data.table/internal package data approach for the model inputs/configurations. This would be quite a bit of work but might be a more user-friendly approach. A potential post-v1 development

script started working on

Right now the the implementation of MEMS in our package uses the following configuration.

1. We need to confirm that this the correct combination of the dynamics.
2. Do we have the correct citation?

Robertson, A. D., Paustian, K., Ogle, S., Wallenstein, M. D., Lugato, E., and Cotrufo, M. F.: Unifying soil organic matter formation and persistence frameworks: the MEMS model, Biogeosciences, 16, 1225–1248, 2019.

Right now the the implementation of MIMCS in our package uses the following configuration.

1. We need to confirm that this the correct combination of the dynamics.
2. Do we have the correct citation?

Wieder, W. R., Allison, S. D., Davidson, E. A., Georgiou, K., Hararuk, O., He, Y., Hopkins, F., Luo, Y., Smith, M. J., Sulman, B., Todd-Brown, K., Wang, Y.-P., Xia, J., and Xu, X.: Explicitly representing soil microbial processes in Earth system models, Global Biogeochem. Cycles, 29, 1782–1800, 2015.

Right now the the implementation of COMISSION in our package uses the following configuration.

1. We need to confirm that this the correct combination of the dynamics.
2. Do we have the correct citation?

Ahrens, B., Braakhekke, M. C., Guggenberger, G., Schrumpf, M., and Reichstein, M.: Contribution of sorption, DOC transport and microbial interactions to the 14C age of a soil organic carbon profile: Insights from a calibrated process model, Soil Biol. Biochem., 88, 390–402, 2015.