Appendix A.

R code for stability analysis of qualitative systems, simulation and stability analysis of
quantitative systems and tables of predictions.
library(LoopAnalyst)
library(pracma)
library(RConics)

CM<-make.cm(3) #creates the system matrix with 3 variables

Fn<-function(n,CM) {(-1)*charpoly(CM)[[n+1]]}
##function that calculates feedback levels from the coefficients of
the characteristic polynomial of the matrix

RH2<-(F1*F2) + F3 #calculates second Hurwitz determinant

#Simulations with quantitative matrices

set.seed(1)
A<-array(NA,c(3,3,10000))
Fb<-matrix(NA,nrow=10000,ncol=ncol(CM))
S1<-rep(NA,10000)
S2<-rep(NA,10000)
S<-rep(NA,10000)

for (s in 1:10000) {
A[,,s]<-matrix(runif(9,0,1),nrow=3,ncol=3)
for (i in 1:nrow(A[,,s])) {
for (j in 1:ncol(A[,,s])) {
if (CM[i,j]!=0) {A[i,j,s]<-(CM[i,j]*A[i,j,s])}
else {A[i,j,s]<-0}
}}
Fb[s,1]<-Fn(1,A[,,s])
Fb[s,2]<-Fn(2,A[,,s])
Fb[s,3]<-Fn(3,A[,,s])
 if (Fb[s,1]<0 & Fb[s,2]<0 & Fb[s,3]<0)
{S1[s]<-"pass"}
else {S1[s]<-"fail"}
if (S1[s]=="pass") {S2[s]<-((Fb[s,1])*(Fb[s,2])+(Fb[s,3]))}
else {S2[s]<-0}
if (S2[s]>0) {S[s]<-"stable"}
else {S[s]<-"unstable"}}

prop.table(table(S=="stable"))
#calculates proportion of stable systems (potential for stability)

########Predictions#########

CR.adj<-make.adjoint(CM) #table of predictions

CR.wp<-weighted.predictions(CM) #weighted predictions

#predictions for simulated quantitative systems

Adjs<-array(NA,c(3,3,10000))

for (s in 1:10000) {
Adjs[,,s]<-adjoint(-A[,,s])}