Process-Based Modelling of Microbial Populations
Internal function to trade off one trait against another (used when as...
Assigns NA to the MFG data frames for parameter values that are not us...
Internal function to assign stochastic strain traits
Checks whether the all the resources needed are included in the system...
Checks whether the solution generated by the ODE solver contains negat...
Checks whether the stoichiometries in each MFG conserve mass within a ...
combines the growth limitation functions and max growth rates to get t...
Combine microbial growth on different pathways by one microbe
convertFlowsToMoles
convertStatesToMoles
Create a dataframe from a CSV file
Differential Equations called by ODE solver
entry Rate Function
Extra Growth Limitation Function
Makes vector of unique resource names
Convert strain name to its group name e.g. 'Bacteroides.1' becomes 'Ba...
Finds the name of the key resource for each path for each MFG
obtains the none boosting fraction of growth for given MFG if there is...
get the number of metabolic pathways for the given group
get pH corners Function
get strain parameter values from a csv file
get stochastically generated pH corners for each strain
get system quantity (e.g. startValue, inflowRate, washOut) for all sta...
getVNPlotObject
growth rate limitation function
Used for running microPop with multiple compartments Takes the solutio...
makeNetworkMatrices
generic function which assigns values for Rtype or stoichiom to an arr...
Gets parameter values for parameters halfSat, yield and maxGrowthRate ...
mass balance Function
calculate the mean trait at the end of the model run
Microbial Population modelling
Runs the microbial population model
networkDFfromMPinput
networkDFfromMPoutput
Find the pH value which is the centre of mass of the pH limitation fun...
pH Function
pH Limitation Function
Generic plotting of microbes over time
Generic plotting of resources over time
plot changes in trait over time
Production Function
Generic plotting showing results of microPop
Generic plotting showing results of microPop
Generic plotting showing results of microPop Now shows resources and m...
List of functions that are used by the ODE solver these functions can ...
Removal Rate Function
used to replace items in list.in in list.default needed for processing...
reshapeFlowMat
runMicroPopExample
this function is needed due to R dropping the names when it subsets
sumConcOverStrains
sumFlowOverStrains
sumFlowsOverPaths
Uptake Function
Computes the mass ratio of water uptake to substrate uptake (i.e. mass...
Modelling interacting microbial populations - example applications include human gut microbiota, rumen microbiota and phytoplankton. Solves a system of ordinary differential equations to simulate microbial growth and resource uptake over time. This version contains network visualisation functions.