Merge pull request #347 from LCSB-BioCore/mk-doc-fixes

documentation fixes and formatting, ...

docs/src/tutorials/2_analysis.md

@@ -7,7 +7,8 @@ exploring the biological models. The currently supported methods include
 
 - Flux balance analysis (FBA), in function [`flux_balance_analysis`](@ref)
 - Flux variability analysis (FVA), in [`flux_variability_analysis`](@ref)
-- Flux sampling by hit-and-run algorithm, in [`hit_and_run`](@ref)
+- Flux sampling by linearized hit-and-run algorithm, in
+  [`affine_hit_and_run`](@ref)
 - Parsimonious flux balance analysis (pFBA), in
   [`parsimonious_flux_balance_analysis`](@ref)
 
@@ -149,15 +150,15 @@ Otherwise, the function behaves just like [`flux_balance_analysis`](@ref):
 
 ## Flux sampling
 
-For the [`hit_and_run`](@ref), you need a previously optimized and constrained
+For the [`affine_hit_and_run`](@ref), you need a previously optimized and constrained
 model from another analysis function, such as [`flux_balance_analysis`](@ref),
 or created by [`make_optimization_model`](@ref). You may need to carefully
 choose the number of iterations and sample sizes to match your model; see the
-documentation of [`hit_and_run`](@ref) for details.
+documentation of [`affine_hit_and_run`](@ref) for details.
 
 As an example, you can run the sampling for 100 thousand iterations with:
 ```
-hit_and_run(100_000, make_optimization_model(m, GLPK.Optimizer))
+affine_hit_and_run(100_000, make_optimization_model(m, GLPK.Optimizer))
 ```
 
 You should receive a matching flux sample with the (default) 1000 samples in a

src/reconstruction/community.jl

@@ -70,11 +70,12 @@ end
 
 Add `model` to `community`, which is a pre-existing community model with
 `exchange_rxn_ids` and `exchange_met_ids`. The `model_name` is appended to
-each reaction and metabolite, see [`join`](@ref). If `biomass_id` is specified
-then a biomass metabolite for `model` is also added to the resulting model. The
-column corresponding to the `biomass_id` reaction then produces this new biomass
-metabolite with unit coefficient. Note, `exchange_rxn_ids` and
-`exchange_met_ids` must already exist in the `community` model.
+each reaction and metabolite, see [`join_with_exchanges`](@ref). If
+`biomass_id` is specified then a biomass metabolite for `model` is also added
+to the resulting model. The column corresponding to the `biomass_id` reaction
+then produces this new biomass metabolite with unit coefficient. Note,
+`exchange_rxn_ids` and `exchange_met_ids` must already exist in the `community`
+model.
 
 # Example
 ```

src/reconstruction/modifications/generic.jl

@@ -20,7 +20,7 @@ with_removed_metabolites(args...; kwargs...) =
     with_added_reactions(args...; kwargs...) 
 
 Specifies a model variant with reactions added. Forwards the arguments to
-[`add_Reactions`](@ref). Intended to be used with [`screen`](@ref).
+[`add_reactions`](@ref). Intended to be used with [`screen`](@ref).
 """
 with_added_reactions(args...; kwargs...) = m -> add_reactions(m, args...; kwargs...)