final changes for readme

Author: mjowen

README.md

@@ -2,29 +2,25 @@
 Using limit cycle continuation methods to speed up evaluation of ion channel cell models
 
 # Using the code
-The code should be cloned from GitHub, or downloaded from Zenodo.
+The code can be cloned from GitHub (most recent version), or downloaded from Zenodo (version of record).
 
 # Setting up the Julia project
 For up to date versions of the dependent packages, run the *packages.jl* file.
 
 To use the same package versions as used in the paper, refer to the *Project.toml* and *Manifest.toml* and use *Pkg.instantiate()*.
 
+Note the figures were generated under a different environment to the one given in the *Project.toml* and *Manifest.toml* files, which were only used to generated the results/data.
+
 # Running the analysis
-The analysis from the paper can be run by running the scripts *simulationTimings.jl* and *mhmcmc.jl*.
+The analysis from the paper can be run by running the scripts *simulationTimings.jl*, *mcmcSetup.jl* and *mhmcmc.jl*.
 
 Note that running the scripts will override the previously recorded results.
 
 When running *mhmcmc.jl*, there are a handful of changes you may wish to make. 
-The number of samples to run the MCMC algorithm for can be changed from the default of 50,000.
-The "converger" can be chosen by setting the variables *use_continuation* and *use_fast_ODE*. 
+The number of samples to run the MCMC algorithm for can be changed from the default of 40,000.
+The "converger" can be chosen by setting the variables *use_continuation* and *use_tracking_ODE*. 
 If `use_continuation=true`, then the continuation converger will be used.
-Otherwise, the ODE solver will be used to converge, running for 10,000ms if `use_fast_ODE=true` or 50,000ms otherwise.
+Otherwise, the ODE solver will be used to converge, running from a previous limit cycle if `use_tracking_ODE=true` or from standard initial conditions otherwise.
 
 # Reproducing the figures from the pre-generated data
-The figures for the benchmark results can be loaded built from the *.json* files.
-The files can be loaded into a Julia workspace using:
-```
-using BenchmarkTools, Plots, BenchmarkPlots, StatsPlots
-t = BenchmarkTools.load("simulation_timings.json")[1]
-```
-Then, the plotting code from the end of the *simulationTimings.jl* can be run.
+The figures can be regenerated using *figures.jl* (for results figures) and *diagrams.jl* for the phase plane diagrams.