init

Author: TorkelE

docs/src/catalyst_functionality/network_analysis.md

@@ -52,7 +52,7 @@ the reaction rate equation ODE model for the repressilator is
 ## Matrix-vector reaction rate equation representation
 In general, reaction rate equation (RRE) ODE models for chemical reaction networks can
 be represented as a first-order system of ODEs in a compact matrix-vector notation. Suppose
-we have a reaction network with ``K`` reactions and ``M`` species, labelled by the state vector
+we have a reaction network with ``K`` reactions and ``M`` species, labelled by the unknown vector
 ```math
 \mathbf{x}(t) = \begin{pmatrix} x_1(t) \\ \vdots \\ x_M(t)) \end{pmatrix}.
 ```
@@ -384,7 +384,7 @@ Recall that in the matrix-vector representation for the RRE ODEs, the entries,
 ``N_{m k}``, of the stoichiometry matrix, ``N``, give the net change in species
 ``m`` due to reaction ``k``. If we let ``\mathbf{N}_k`` denote the ``k``th
 column of this matrix, this vector corresponds to the change in the species
-state vector, ``\mathbf{x}(t)``, due to reaction ``k``, i.e. when reaction ``k``
+unknown vector, ``\mathbf{x}(t)``, due to reaction ``k``, i.e. when reaction ``k``
 occurs ``\mathbf{x}(t) \to \mathbf{x}(t) + \mathbf{N}_k``. Moreover, by
 integrating the ODE
 ```math

src/networkapi.jl

@@ -1402,7 +1402,7 @@ Notes:
 - `disablechecks` will disable checking for whether the passed in variable is
   already defined, which is useful when adding many new variables to the system.
   *Do not disable checks* unless you are sure the passed in variable is a new
-  variable, as this will potentially leave the system in an undefined state.
+  variable, as this will potentially leave the system in an undefined unknown.
 """
 function addspecies!(network::ReactionSystem, s::Symbolic; disablechecks = false)
     reset_networkproperties!(network)
@@ -1434,7 +1434,7 @@ integer id of the species within the system.
 - `disablechecks` will disable checking for whether the passed in variable is
   already defined, which is useful when adding many new variables to the system.
   *Do not disable checks* unless you are sure the passed in variable is a new
-  variable, as this will potentially leave the system in an undefined state.
+  variable, as this will potentially leave the system in an undefined unknown.
 """
 function addspecies!(network::ReactionSystem, s::Num; disablechecks = false)
     addspecies!(network, value(s), disablechecks = disablechecks)
@@ -1450,7 +1450,7 @@ id of the parameter within the system.
 - `disablechecks` will disable checking for whether the passed in variable is
   already defined, which is useful when adding many new variables to the system.
   *Do not disable checks* unless you are sure the passed in variable is a new
-  variable, as this will potentially leave the system in an undefined state.
+  variable, as this will potentially leave the system in an undefined unknown.
 """
 function addparam!(network::ReactionSystem, p::Symbolic; disablechecks = false)
     reset_networkproperties!(network)
@@ -1479,7 +1479,7 @@ integer id of the parameter within the system.
 - `disablechecks` will disable checking for whether the passed in variable is
   already defined, which is useful when adding many new variables to the system.
   *Do not disable checks* unless you are sure the passed in variable is a new
-  variable, as this will potentially leave the system in an undefined state.
+  variable, as this will potentially leave the system in an undefined unknown.
 """
 function addparam!(network::ReactionSystem, p::Num; disablechecks = false)
     addparam!(network, value(p); disablechecks = disablechecks)