{ "_id": "6a1fd949b401979e73436fc2", "Package": "microxanox", "Version": "0.9.3", "Date": "2023-11-13", "Title": "Oxic-Anoxic Regime Shifts in Microbial Communities", "Description": "Model to simulate a three functional group system with\nfour chemical substrates using a set of ordinary differential\nequations. Simulations can be run individually or over a\nparameter range, to find stable states. The model features\nmultiple species per functional group, where the number is only\nlimited by computational constraints. The R package is\nconstructed in such a way, that the results contain the input\nparameter used, so that a saved results can be loaded again and\nthesimulation be repeated.", "Authors@R": "c(person(given = \"Owen L.\",\nfamily = \"Petchey\",\nrole = c(\"aut\", \"cre\"),\nemail = \"Owen.Petchey@ieu.uzh.ch\",\ncomment = c(ORCID = \"0000-0002-7724-1633\")),\nperson(given = \"Rainer M.\",\nfamily = \"Krug\",\nrole = \"ctb\",\nemail = \"Rainer.Krug@uzh.ch\",\ncomment = c(ORCID = \"0000-0002-7490-0066\")),\nperson(given = \"Pascal\",\nfamily = \"Baertschi\",\nrole = \"ctb\",\nemail = \"compbio.baertschi@gmail.com\",\ncomment = c(ORCID = \"0000-0002-6533-0399\"))\n)", "Maintainer": "Owen L. Petchey ", "URL": "https://github.com/UZH-PEG/microxanox/", "BugReports": "https://github.com/UZH-PEG/microxanox/issues", "License": "MIT + file LICENSE", "RoxygenNote": "7.3.1", "Encoding": "UTF-8", "VignetteBuilder": "knitr", "Config/testthat/edition": "3", "Roxygen": "list(roclets = c(\"collate\", \"namespace\", \"rd\",\n\"roxyglobals::global_roclet\"))", "Config/roxyglobals/filename": "globals.R", "Config/roxyglobals/unique": "FALSE", "Config/pak/sysreqs": "cmake make libicu-dev libuv1-dev libssl-dev\nlibx11-dev zlib1g-dev", "Repository": "https://uzh-peg.r-universe.dev", "Date/Publication": "2024-03-06 13:23:32 UTC", "RemoteUrl": "https://github.com/UZH-PEG/microxanox", "RemoteRef": "HEAD", "RemoteSha": "00e345f078d11f7e8c5322a1e496ffc8b7d40a9c", "NeedsCompilation": "no", "Packaged": { "Date": "2026-06-03 07:29:28 UTC", "User": "root" }, "Author": "Owen L. Petchey [aut, cre] (ORCID:\n),\nRainer M. 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"get_hysteresis_total" ] }, { "page": "get_nonlinearity", "title": "Get the amount of non-linearity in a state-environment relationship.", "topics": [ "get_nonlinearity" ] }, { "page": "get_ssbyaN_parameter", "title": "Extract 'runsim_parameter' from 'replication_ssfind_parameter'", "topics": [ "get_ssbyaN_parameter" ] }, { "page": "get_stability_measures", "title": "Get various measures of the stability", "topics": [ "get_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" ] }, { "page": "get_symmetry_measurements", "title": "Computes measures that make comparisons between collapse and recovery trajectory and between antagonistic environmental variables possible.", "topics": [ "get_symmetry_measurements" ] }, { "page": "growth1", "title": "Growth rate function on one resource X", "topics": [ "growth1" ] }, { "page": 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Is passed to the function 'run_replication_ssfind_parameter()' to run such a set of simulations.", "topics": [ "new_replication_ssfind_parameter" ] }, { "page": "new_replication_ssfind_results", "title": "Create object of type 'replication_ssfind_result' which is returned by the function 'run_replication_ssfind()'.", "topics": [ "new_replication_ssfind_results" ] }, { "page": "new_runsim_parameter", "title": "Create parameter set with which to run a simulation.", "topics": [ "new_runsim_parameter" ] }, { "page": "new_runsim_results", "title": "Create object of type 'runsim_result' which is returned by the function 'run_sim()'.", "topics": [ "new_runsim_results" ] }, { "page": "new_SB_strain_parameter", "title": "Create new 'SB_strain_parameter' object", "topics": [ "new_SB_strain_parameter" ] }, { "page": "new_strain_parameter", "title": "Returns object of class 'strain_parameter'", "topics": [ "new_strain_parameter" ] }, { "page": "new_temporal_ssfind_results", "title": "Create object of type 'temporal_ssfind_result' which is returned by the function 'run_temporal_ssfind_parameter()'.", "topics": [ "new_temporal_ssfind_results" ] }, { "page": "plot_dynamics", "title": "Plot the dynamics of a model run", "topics": [ "plot_dynamics" ] }, { "page": "plot_dynamics_symmetric", "title": "Plot the dynamics of a model run of a symmetric parameter set", "topics": [ "plot_dynamics_symmetric" ] }, { "page": "plot_symmetry_measures", "title": "Visualizes the symmetry measures obtained by the function 'get_symmetry_measures()'", "topics": [ "plot_symmetry_measures" ] }, { "page": "plot_temporal_ss", "title": "Plot the temporal dynamics of a model run of a symmetric parameter set", "topics": [ "plot_temporal_ss" ] }, { "page": "plot_trajectory_symmetry", "title": "Visualizes the symmetry of antagonistic collapse or recovery trajectories, symmetry measures of shift are computed by the function 'get_symmetry_measurements()'", "topics": [ "plot_trajectory_symmetry" ] }, { "page": "plot_trajectory_symmetry_compact", "title": "Visualizes the symmetry of upards and downwards trajectories in the same figure, symmetry measures of shift are computed by the function 'get_symmetry_measurements()'", "topics": [ "plot_trajectory_symmetry_compact" ] }, { "page": "run_replication_ssfind", "title": "Run simulations to determine the steady states by the replication method.", "topics": [ "run_replication_ssfind" ] }, { "page": "run_simulation", "title": "Run the simulation", "topics": [ "run_simulation" ] }, { "page": "run_simulation_symmetric", "title": "Run the symmetric simulation", "topics": [ "run_simulation_symmetric" ] }, { "page": "run_temporal_ssfind", "title": "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.", "topics": [ "run_temporal_ssfind" ] }, { "page": "run_temporal_ssfind_experiment", "title": "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).", "topics": [ "run_temporal_ssfind_experiment" ] }, { "page": "run_temporal_ssfind_symmetric", "title": "Used to find the stable states for a parameter set by increasing and decreasing the oxygen diffusivity in a stepwise fashion. 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