Package: microxanox 0.9.3

Owen L. Petchey

microxanox: Oxic-Anoxic Regime Shifts in Microbial Communities

Model to simulate a three functional group system with four chemical substrates using a set of ordinary differential equations. Simulations can be run individually or over a parameter range, to find stable states. The model features multiple species per functional group, where the number is only limited by computational constraints. The R package is constructed in such a way, that the results contain the input parameter used, so that a saved results can be loaded again and thesimulation be repeated.

Authors:Owen L. Petchey [aut, cre], Rainer M. Krug [ctb], Pascal Baertschi [ctb]

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microxanox.pdf |microxanox.html✨
microxanox/json (API)
NEWS

# Install 'microxanox' in R:
install.packages('microxanox', repos = c('https://uzh-peg.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/uzh-peg/microxanox/issues

On CRAN:

4.15 score 35 scripts 44 exports 113 dependencies

Last updated 9 months agofrom:00e345f078. Checks:OK: 3 NOTE: 4. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 11 2024
R-4.5-winNOTENov 11 2024
R-4.5-linuxNOTENov 11 2024
R-4.4-winNOTENov 11 2024
R-4.4-macNOTENov 11 2024
R-4.3-winOKNov 11 2024
R-4.3-macOKNov 11 2024

Exports:add_strain_varbushplus_dynamic_modelevent_definition_1event_definition_2event_definition_symmetricget_final_states_a_Nget_hysteresis_maxget_hysteresis_minget_hysteresis_rangeget_hysteresis_totalget_nonlinearityget_ssbyaN_parameterget_stability_measuresget_stability_measures_replication_ssfind_resultget_stability_measures_temporal_ssfind_resultget_symmetry_measurementsgrowth1growth2inhibitionnew_CB_strain_parameternew_initial_statenew_PB_strain_parameternew_replication_ssfind_parameternew_replication_ssfind_resultsnew_runsim_parameternew_runsim_resultsnew_SB_strain_parameternew_strain_parameternew_temporal_ssfind_resultsplot_dynamicsplot_dynamics_symmetricplot_symmetry_measuresplot_temporal_ssplot_trajectory_symmetryplot_trajectory_symmetry_compactrun_replication_ssfindrun_simulationrun_simulation_symmetricrun_temporal_ssfindrun_temporal_ssfind_experimentrun_temporal_ssfind_symmetricset_diffusivitiesset_temporal_ssfind_initial_statesymmetric_bushplus_dynamic_model

Dependencies:abindaskpassbackportsBHbitbit64bootbroomcallrcarcarDatacellrangerclassclicliprcolorspacecorrplotcowplotcpp11crayoncurldata.tableDerivDescToolsdeSolvedoBydplyre1071ExactexpmfansifarverforcatsFormulagenericsggplot2ggpubrggrepelggsciggsignifgldgluegridExtragtablehavenhmshttrisobandjsonlitelabelinglatticelifecyclelme4lmommagrittrMASSMatrixMatrixModelsmgcvmicrobenchmarkmimeminqamodelrmultidplyrmunsellmvtnormnlmenloptrnnetnumDerivopensslpatchworkpbkrtestpillarpkgconfigpolynomprettyunitsprocessxprogressproxypspurrrqsquantregR6RApiSerializeRColorBrewerRcppRcppEigenRcppParallelreadrreadxlrematchrlangrootSolverstatixrstudioapiscalesSparseMstringfishstringistringrsurvivalsystibbletidyrtidyselecttzdbutf8vctrsviridisLitevroomwithr

SymSys User guide -- Extension of microxanox R Package for microbial oxic and anoxic, symmetric ecosystem simulations

Pascal Bärtschi, Owen Petchey

Rendered fromSymSys-User-guide.Rmdusingknitr::rmarkdownon Nov 11 2024.

Last update: 2024-03-06
Started: 2023-11-13

User guide -- microxanox R Package for microbial oxic and anoxic ecosystem simulations

Owen Petchey, Rainer M Krug

Rendered fromUser-guide.Rmdusingknitr::rmarkdownon Nov 11 2024.

Last update: 2023-11-13
Started: 2021-04-16

Readme and manuals

Help Manual

Help pageTopics
R/microxanox: Microbial oxic and anoxic ecosystem simulations-package microxanox-package microxanox
Create variability in strain parametersadd_strain_var
The rate equations, as published in the Bush et al 2017 doi:10.1093/clinchem/39.5.766 <https://doi.org/10.1093/clinchem/39.5.766> paper, but with forcing of oxygen diffusivity 'a_0' potential added, and the possibility to simulate multiple strains per functional groupbushplus_dynamic_model
Event definition for the simulation.event_definition_1
Event definition for the simulation.event_definition_2
Event definition for the symmetric simulation.event_definition_symmetric
Get the steady state solutions for a set of oxygen diffusivity and initial states.get_final_states_a_N
Get the maximum of environmental conditions for which alternate stable states existget_hysteresis_max
Get the minimum of environmental conditions for which alternate stable states existget_hysteresis_min
Get the range of environmental conditions for which alternate stable states existget_hysteresis_range
Get the total hysteresis of a system variable.get_hysteresis_total
Get the amount of non-linearity in a state-environment relationship.get_nonlinearity
Extract 'runsim_parameter' from 'replication_ssfind_parameter'get_ssbyaN_parameter
Get various measures of the stabilityget_stability_measures get_stability_measures.replication_ssfind_result get_stability_measures.temporal_ssfind_result get_stability_measures_replication_ssfind_result get_stability_measures_temporal_ssfind_result
Computes measures that make comparisons between collapse and recovery trajectory and between antagonistic environmental variables possible.get_symmetry_measurements
Growth rate function on one resource Xgrowth1
Growth rate function on two resources X and Ygrowth2
Growth inhibition functioninhibition
Create CB strain parameter valuesnew_CB_strain_parameter
Create initial state of the system, selecting them from various preset options.new_initial_state
Create PB strain parameternew_PB_strain_parameter
Create parameter set to run a set of simulations to find stable states. Is passed to the function 'run_replication_ssfind_parameter()' to run such a set of simulations.new_replication_ssfind_parameter
Create object of type 'replication_ssfind_result' which is returned by the function 'run_replication_ssfind()'.new_replication_ssfind_results
Create parameter set with which to run a simulation.new_runsim_parameter
Create object of type 'runsim_result' which is returned by the function 'run_sim()'.new_runsim_results
Create new 'SB_strain_parameter' objectnew_SB_strain_parameter
Returns object of class 'strain_parameter'new_strain_parameter
Create object of type 'temporal_ssfind_result' which is returned by the function 'run_temporal_ssfind_parameter()'.new_temporal_ssfind_results
Plot the dynamics of a model runplot_dynamics
Plot the dynamics of a model run of a symmetric parameter setplot_dynamics_symmetric
Visualizes the symmetry measures obtained by the function 'get_symmetry_measures()'plot_symmetry_measures
Plot the temporal dynamics of a model run of a symmetric parameter setplot_temporal_ss
Visualizes the symmetry of antagonistic collapse or recovery trajectories, symmetry measures of shift are computed by the function 'get_symmetry_measurements()'plot_trajectory_symmetry
Visualizes the symmetry of upards and downwards trajectories in the same figure, symmetry measures of shift are computed by the function 'get_symmetry_measurements()'plot_trajectory_symmetry_compact
Run simulations to determine the steady states by the replication method.run_replication_ssfind
Run the simulationrun_simulation
Run the symmetric simulationrun_simulation_symmetric
Used to find the stable states for a parameter set by increasing and decreasing the oxygen diffusivity in a stepwise fashion. If increasing 'parameter$sim_duration' while keeping the length of 'parameter$log10_series' doesn't change response dynanimcs, stable states have been found.run_temporal_ssfind
Run a stable state finding experiment via the temporal method (e.g. get the stable states for different levels of oxygen diffusivity when oxygen diffusivity is varied in a stepwise fashion).run_temporal_ssfind_experiment
Used to find the stable states for a parameter set by increasing and decreasing the oxygen diffusivity in a stepwise fashion. If increasing 'parameter$sim_duration' while keeping the length of 'parameter$log10_series' doesn't change response dynanimcs, stable states have been found.run_temporal_ssfind_symmetric
Used to update the asymmetry factor with logaO_series & log10aS_series accordinglyset_diffusivities
Convenience function for setting initial states during the process of finding stable states using the function 'run_temporal_ssfind_experiment' Should only be used internally.set_temporal_ssfind_initial_state
The rate equations, modified from publication of Bush et al 2017 doi:10.1093/clinchem/39.5.766 <https://doi.org/10.1093/clinchem/39.5.766>. Equations of antagonistic environmental variables are identical, while the oxygen and sulfide diffusivities are forced in antisymmetric manner. Possibility to simulate multiple strain per functional group as published in doi:10.1111/ele.14217 <https://doi.org/10.1111/ele.14217> by Limberger et al 2023 remains.symmetric_bushplus_dynamic_model