SimEvolEnzCons version 2.0.0 (2021-10-28)

new features about regulation groups
add new functions
- class_group: classifies enzymes in regulation groups
- search_group: gives the group number of an interest enzyme
- group_types: gives the types of all regulation groups
- predict_grp: computes equilibria for different regulation groups
- apparent.activities.Aq: computes the apparent pseudo-activities for the regulation groups
- extract.tabEtot: creates table of all concentration from simulation results
- graph.simul.group: graphics of enzyme concentrations through time for regulation groups
- graph.simul.conc.end: graphics of enzyme concentrations two-by-two at end of simulations
modify existing functions
- compute.beta.from.B: computes regulation matrix beta taking account of the list of regulation groups
- graph.simul.others.by.sim: add possibility of envelope curve for graphics between flux and absolute/relative concentration
- simul.evol.graph.methods (4 first functions): add equilibrium when there are regulation groups
- simul.evol.enz.one: does not compute anymore the equilibrium when there are regulation groups
add data
- 2 new datasets that present different cases with regulation groups
package presentation
- new section about regulation groups

SimEvolEnzCons version 1.0.3 (2021-06-23)

fixed bug which prevents to plot the response coefficients in simul.graph.time.by.enz

replace by in examples
export function RNV.compute.elements() (but please rather use RNV.for.simul())
change condition in graph.simul.triangle.diagram.e to check if eq_th_select is a matrix or a numeric
graph.simul.triangle.diagram.e returns “why_no_lines” which explain why options not passed, rather than printed them in the console
no code line under comments in examples
save user options for par() when needed (in RNV.mean.simul(), RNV.graph.double.at.eq()) or put away (in graph.simul. functions)
use message() rather print() to show current simulations in simul.evol.enz.multiple()

minor corrections
- in simul.evol.enz.one: modification of the predicted equilibrium in simulation when there is some regulation groups (sum(1/B)>1), due to the effective equilibrium not computable in this case

minor adaptation to case regulation plus independence
- in is.B.accurate: check if sum(1/B) is an integer (normally equal to the number of regulation groups), and not just equal to 1
- in flux.shape.from.one.point: add the choice to compute Ejm from alpha computation because computing from tau has no sense when there is regulated and independent enzymes
- in flux.shape.from.one.point: indication of regulation presence to avoid the tau computing
add the graphics of flux in relation to relative concentration in graph.simul.other.by.sim
bug corrections
- correction of equilibrium computing in flux.shape.for.all.points

possibility to change symbol and line sizes in RNV.mean.simul
symbol modifications in the third graphics of RNV.mean.simul (relative concentration = triangle, RNV mean by simul = point, RNV mean = square)
possibility to change symbol sizes in graph.simul.triangle.diagram

possibility to put the graphics legend and choose its position in flux.shape.from.one.point.graphics

possibility to put the graphics legend and choose its position in flux.dome.graphics

possibility to choice the color palette for contour lines in flux.dome.projections
possibility to plot RNV divided by Ei in RNV.size.at.equilibr

possibility to add enzyme names on plots generated by RNV.size.at.equilibr and RNV.graph.double.at.eq