From 97929393072f039e464f4cd1ed877047994247b0 Mon Sep 17 00:00:00 2001 From: jo Date: Wed, 9 May 2018 11:03:46 +0200 Subject: [PATCH] updated man pages --- man/Arena-class.Rd | 2 +- man/Organism.Rd | 2 ++ man/chemotaxis.Rd | 6 ++++-- man/constrain.Rd | 10 +++++----- man/diffuse.Rd | 6 ++++-- man/simBac.Rd | 2 +- 6 files changed, 17 insertions(+), 11 deletions(-) diff --git a/man/Arena-class.Rd b/man/Arena-class.Rd index 1183cc6..0799a8b 100644 --- a/man/Arena-class.Rd +++ b/man/Arena-class.Rd @@ -26,7 +26,7 @@ Structure of the S4 class \code{Arena} to represent the environment in which Org \item{\code{mflux}}{A vector containing highly used metabolic reactions within the arena} -\item{\code{exchanges}}{A Matrix containing last exchanges of each organism.} +\item{\code{exchanges}}{A data.frame containing last exchanges of each organism.} \item{\code{shadow}}{A vector containing shadow prices of metabolites present in the arena} diff --git a/man/Organism.Rd b/man/Organism.Rd index 29e504d..fa2df73 100644 --- a/man/Organism.Rd +++ b/man/Organism.Rd @@ -49,5 +49,7 @@ Structure of the S4 class \code{Organism} representing the organisms present in \item{\code{algo}}{Algorithm to be used during optimization (default fba)} \item{\code{rbiomass}}{Name of biomass reactions which is used for growth model (set automatically but needs input if objective is not biomass optimization)} + +\item{\code{limit_growth}}{If true then a upper bound on growth will be set, see maxweight (default: True).} }} diff --git a/man/chemotaxis.Rd b/man/chemotaxis.Rd index 90cb99f..5565e4a 100644 --- a/man/chemotaxis.Rd +++ b/man/chemotaxis.Rd @@ -6,9 +6,9 @@ \alias{chemotaxis,Bac-method} \title{Function for chemotaxis of bacteria to their prefered substrate} \usage{ -chemotaxis(object, population, j) +chemotaxis(object, population, j, chemo) -\S4method{chemotaxis}{Bac}(object, population, j) +\S4method{chemotaxis}{Bac}(object, population, j, chemo) } \arguments{ \item{object}{An object of class Bac.} @@ -16,6 +16,8 @@ chemotaxis(object, population, j) \item{population}{An object of class Arena.} \item{j}{The number of the iteration of interest.} + +\item{chemo}{The vector that contains the prefered substrate.} } \description{ The generic function \code{chemotaxis} implements a bacterial movement in the Moore neighbourhood to the highest substrate concentration. diff --git a/man/constrain.Rd b/man/constrain.Rd index 70bcce1..99b2dd6 100644 --- a/man/constrain.Rd +++ b/man/constrain.Rd @@ -6,10 +6,10 @@ \alias{constrain,Organism-method} \title{Function for constraining the models based on metabolite concentrations} \usage{ -constrain(object, reacts, lb, ub, dryweight, tstep, scale, j) +constrain(object, reacts, lb, dryweight, tstep, scale, j, cutoff = 1e-06) -\S4method{constrain}{Organism}(object, reacts, lb, ub, dryweight, tstep, scale, - j) +\S4method{constrain}{Organism}(object, reacts, lb, dryweight, tstep, scale, j, + cutoff = 1e-06) } \arguments{ \item{object}{An object of class Organisms.} @@ -18,8 +18,6 @@ constrain(object, reacts, lb, ub, dryweight, tstep, scale, j) \item{lb}{A numeric vector giving the constraint values of lower bounds (e.g. avaible metabolite concentrations} -\item{ub}{A numeric vector giving the constraint values of upper bounds.} - \item{dryweight}{A number giving the current dryweight of the organism.} \item{tstep}{A number giving the time intervals for each simulation step.} @@ -27,6 +25,8 @@ constrain(object, reacts, lb, ub, dryweight, tstep, scale, j) \item{scale}{A numeric defining the scaling (units for linear programming has to be in certain range)} \item{j}{debuging index to track cell} + +\item{cutoff}{value used to define numeric accuracy while interpreting optimization results} } \value{ Returns the lower bounds, which carry the constraints and names of relevant reactions. diff --git a/man/diffuse.Rd b/man/diffuse.Rd index 7517767..3b8d61f 100644 --- a/man/diffuse.Rd +++ b/man/diffuse.Rd @@ -6,9 +6,9 @@ \alias{diffuse,Arena-method} \title{Function for diffusion} \usage{ -diffuse(object, lrw, sublb) +diffuse(object, lrw, sublb, verbose = TRUE) -\S4method{diffuse}{Arena}(object, lrw, sublb) +\S4method{diffuse}{Arena}(object, lrw, sublb, verbose = TRUE) } \arguments{ \item{object}{An object of class Arena.} @@ -16,6 +16,8 @@ diffuse(object, lrw, sublb) \item{lrw}{A numeric value needed by solver to estimate array size (by default lwr is estimated in the simEnv() by the function estimate_lrw())} \item{sublb}{A matrix with the substrate concentration for every individual in the environment based on their x and y position.} + +\item{verbose}{Set to false if no status messages should be printed.} } \description{ The generic function \code{diffuse} computes the media distribution via diffusion diff --git a/man/simBac.Rd b/man/simBac.Rd index 97f883a..daaf941 100644 --- a/man/simBac.Rd +++ b/man/simBac.Rd @@ -38,7 +38,7 @@ Returns the updated enivironment of the \code{population} parameter with all new The generic function \code{simBac} implements all neccessary functions for the individuals to update the complete environment. } \details{ -Bacterial individuals undergo step by step the following procedures: First the individuals are constrained with \code{constrain} to the substrate environment, then flux balance analysis is computed with \code{optimizeLP}, after this the substrate concentrations are updated with \code{consume}, then the bacterial growth is implemented with \code{growth}, the potential new phenotypes are added with \code{checkPhen}, finally the additional and conditional functions \code{lysis}, \code{move} or \code{chemotaxis} are performed. Can be used as a wrapper for all important bacterial functions in a function similar to \code{simEnv}. +Bacterial individuals undergo step by step the following procedures: First the individuals are constrained with \code{constrain} to the substrate environment, then flux balance analysis is computed with \code{optimizeLP}, after this the substrate concentrations are updated with \code{consume}, then the bacterial growth is implemented with \code{growth}, the potential new phenotypes are added with \code{checkPhen}, finally the additional and conditional functions \code{lysis}, \code{move} or \code{chemotaxis} are performed. In case of many compounds in the vector of \code{chemotaxis}, the change of the position takes place by the order of the compounds in the vector of \code{chemotaxis}. Can be used as a wrapper for all important bacterial functions in a function similar to \code{simEnv}. } \examples{ NULL