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