From 520bcefa98e8b858c144d179dbc2dc5832ef4a07 Mon Sep 17 00:00:00 2001 From: Torkel Date: Sat, 13 Jul 2024 17:55:50 -0400 Subject: [PATCH] add reference for added stuff, remvoe for stuff that has not been added. --- docs/src/model_creation/network_analysis.md | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/docs/src/model_creation/network_analysis.md b/docs/src/model_creation/network_analysis.md index 68f3ccd033..786e104f7d 100644 --- a/docs/src/model_creation/network_analysis.md +++ b/docs/src/model_creation/network_analysis.md @@ -530,7 +530,7 @@ we note that it essentially generates the same equation twice (i.e. $\frac{dX₁ \frac{dX₁(t)}{dt} = - k₁X₁(t) + k₂(-X₁(t) + Γ) \\ X₂(t) = -X₁(t) + Γ ``` -Using Catalyst, it is possible to detect any such conserved quantities and eliminate them from the system. Here, when we convert our [`ReactionSystem` to an `ODESystem`](@ref ref), we provide the `remove_conserved = true` argument to instruct Catalyst to perform this elimination: +Using Catalyst, it is possible to detect any such conserved quantities and eliminate them from the system. Here, when we convert our `ReactionSystem` to an `ODESystem`, we provide the `remove_conserved = true` argument to instruct Catalyst to perform this elimination: ```@example network_analysis_conservation_laws osys = convert(ODESystem, rs; remove_conserved = true) ``` @@ -538,7 +538,7 @@ We note that the output system only contains a single (differential) equation. T ```@example network_analysis_conservation_laws observed(osys) ``` -Using the [`unknowns` function](@ref ref) we can confirm that the ODE only have a single unknown variable: +Using the `unknowns` function we can confirm that the ODE only have a single unknown variable: ```@example network_analysis_conservation_laws unknowns(osys) ``` @@ -565,9 +565,9 @@ plot(sol) Any species eliminated using `remove_conserved = true` will not be plotted by default. However, it can be added to the plot using [the `idxs` plotting option](@ref simulation_plotting_options). E.g. here we would use `plot(sol; idxs = [:X₁, :X₂])` to plot both species. !!! danger - Currently, there is a bug where the values associated with conservation laws are not updated properly in response to [`remake`](@ref ref) (or [other problem-updating functions, such as `getu`](@ref ref)). Hence, problems created using the `remove_conserved = true` *should not* be modified. + Currently, there is a bug where the values associated with conservation laws are not updated properly in response to [`remake`](@ref simulation_structure_interfacing_problems_remake) (or [other problem-updating functions, such as `getu`](@ref simulation_structure_interfacing_functions)). Hence, problems created using the `remove_conserved = true` *should not* be modified. -While `X₂` is an observable (and not unknown) of the ODE, we can [access it](@ref ref) just like if `remove_conserved = true` has not been used: +While `X₂` is an observable (and not unknown) of the ODE, we can [access it](@ref simulation_structure_interfacing_problems) just like if `remove_conserved = true` has not been used: ```@example network_analysis_conservation_laws sol[:X₂] ```