ddepn-package	ddepn-package
addstimuli	addstimuli
bestgam	bestgam
bin2dec	propagate.effect
calcpr	prior
center_ddepn	center_ddepn
cls	run_checks
compare.graphs.tc	compare.graphs
coord	coord
create_signetwork	create_signetwork
create_signetwork_cv	create_signetwork
crossover	crossover
ddepn	ddepn
detailed.to.simple.regulations	internal.functions
draw_segments	create_signetwork
esub	bestgam
expand.gamma	expand.gamma
format_ddepn	format_ddepn
gelman_diag	gelman_diag
get.aic	modelcomparison
get.arrowhead	plotdetailed
get.arrowtail	plotdetailed
get.bic	modelcomparison
get.data	internal.functions
get.gammashifted	internal.functions
get.labels	plotdetailed
get.partitions	internal.functions
get.phi.final	get.phi.final
get.phi.final.mcmc	get.phi.final
getE	perform.hmmsearch
getfirstphi	getfirstphi
get_theta_consensus	plot_profiles
hcc1954	hcc1954
hcc1954fcf	hcc1954
hcc1954fcfmedian	hcc1954
hcc1954raw	hcc1954
initialphi	samplephi
internal.functions	internal.functions
kegggraph.to.detailed.adjacency	kegggraph.to.detailed.adjacency
kegggraphs	kegggraphs
likl	likl
makedata	makedata
make_edge_df	plot_edgeconfidences
mcmc_accept	mcmc_accept
mcmc_ddepn	mcmc_ddepn
mcmc_move	mcmc_move
mcmc_performance	mcmc_performance
netga	netga
perform.hmmsearch	perform.hmmsearch
perform_edge_test	create_signetwork
perform_network_tests	create_signetwork
pgs	posterior
plotdetailed	plotdetailed
plotmatrix	internal.functions
plotrepresult	plotrepresult
plot_edgeconfidences	plot_edgeconfidences
plot_mcmctraces	plot_mcmctraces
plot_profiles	plot_profiles
posterior	posterior
pri	posterior
prior	prior
propagate.effect.set	propagate.effect
propagate.effect.simple	propagate.effect
random.gammaprime	random.gammaprime
replicatecolumns	perform.hmmsearch
resume_ddepn	ddepn
reverse.direction	internal.functions
runmcmc	mcmc_ddepn
run_checks	run_checks
samplephi	samplephi
signalnetwork	signalnetwork
simulatedata	simulatedata
tp.median	internal.functions
transitive.closure	internal.functions
transitive.reduction	internal.functions
trapezoid	mcmc_performance
uniquegamma	uniquegamma
uniquegammaposs	uniquegamma
wrapddepn	run_checks
zlambda	zlambda
