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A
abcRun()
(in
Meld
)
add_salt()
(in
Meld
)
asciihist
(in
trunk.BIP.Viz
)
add_data()
(in
_BayesVar
)
ascii
(in
trunk.BIP.Viz
)
B
basicfit()
(in
trunk.BIP.Bayes.Melding
)
Bernoulli()
(in
trunk.BIP.Bayes.like
)
BIP
(in trunk)
Bayes
(in
trunk.BIP
)
Beta()
(in
trunk.BIP.Bayes.like
)
bvariables
(in
trunk.BIP.Bayes.general
)
BayesVar()
(in
trunk.BIP.Bayes.general.bvariables
)
Binomial()
(in
trunk.BIP.Bayes.like
)
C
calculateBaseWeights()
(in
Condensation
)
CM
(in
trunk.BIP.SDE.example
)
continuous_conjugate_priors
(in
trunk.BIP.Bayes.general.bvariables
)
Categor()
(in
trunk.BIP.Bayes.like
)
condensation
(in
trunk.BIP.SMC
)
ct
(in
trunk.BIP.SDE.example
)
clearFig()
(in
RTplot
)
Condensation
(in
trunk.BIP.SMC.condensation
)
D
dimensions()
(in
_Sampler
)
display()
(in
Model
)
dtplot
(in
trunk.BIP.Bayes.Melding
)
discrete_conjugate_priors
(in
trunk.BIP.Bayes.general.bvariables
)
do_inference()
(in
FitModel
)
dispatch()
(in
trunk.BIP.SDE.gillespie
)
Dream
(in
trunk.BIP.Bayes.Samplers.MCMC
)
E
enumRun()
(in
trunk.BIP.Bayes.Melding
)
evaluateObservationDensity()
(in
Model
)
evaluate_gaussian()
(in
trunk.BIP.SMC.condensation
)
example
(in
trunk.BIP.SDE
)
F
f1()
(in
trunk.BIP.SDE.example
)
f4()
(in
trunk.BIP.SDE.example
)
find_best_tau()
(in
trunk.BIP.Bayes.like
)
f2()
(in
trunk.BIP.SDE.example
)
f5()
(in
trunk.BIP.SDE.example
)
FitModel
(in
trunk.BIP.Bayes.Melding
)
f3()
(in
trunk.BIP.SDE.example
)
filtM()
(in
Meld
)
G
Gamma()
(in
trunk.BIP.Bayes.like
)
get_prior_sample()
(in
_BayesVar
)
GlobalData
(in
trunk.BIP.SMC.condensation
)
general
(in
trunk.BIP.Bayes
)
getPosteriors()
(in
Meld
)
gr_convergence()
(in
_Sampler
)
get_posterior_sample()
(in
_BayesVar
)
getStats()
(in
Model
)
gr_R()
(in
_Sampler
)
get_prior_dist()
(in
_BayesVar
)
gillespie
(in
trunk.BIP.SDE
)
GSSA()
(in
Model
)
H
Histogram
(in
trunk.BIP.Viz.ascii
)
horizontal()
(in
Histogram
)
Histogram
(in
trunk.BIP.Viz.asciihist
)
horizontal()
(in
Histogram
)
I
imp_sample()
(in
Meld
)
iterate()
(in
Model
)
ini
(in
trunk.BIP.SDE.example
)
IterationData
(in
trunk.BIP.SMC.condensation
)
L
lhs
(in
trunk.BIP.Bayes
)
lhsFromSample()
(in
trunk.BIP.Bayes.lhs
)
logPooling()
(in
Meld
)
lhs()
(in
trunk.BIP.Bayes.lhs
)
like
(in
trunk.BIP.Bayes
)
lhsFromDensity()
(in
trunk.BIP.Bayes.lhs
)
Lognormal()
(in
trunk.BIP.Bayes.like
)
M
M
(in
trunk.BIP.SDE.example
)
Meld
(in
trunk.BIP.Bayes.Melding
)
Model
(in
trunk.BIP.SMC.condensation
)
main()
(in
trunk.BIP.SDE.gillespie
)
Melding
(in
trunk.BIP.Bayes
)
model()
(in
trunk.BIP.Bayes.Melding
)
main2()
(in
trunk.BIP.Bayes.Melding
)
Metropolis
(in
trunk.BIP.Bayes.Samplers.MCMC
)
model_as_ra()
(in
Meld
)
MCMC
(in
trunk.BIP.Bayes.Samplers
)
mh_test()
(in
trunk.BIP.Bayes.Melding
)
mcmc_run()
(in
Meld
)
Model
(in
trunk.BIP.SDE.gillespie
)
N
Negbin()
(in
trunk.BIP.Bayes.like
)
Normal()
(in
trunk.BIP.Bayes.like
)
O
obtainObservations()
(in
Model
)
optimize()
(in
FitModel
)
P
p1()
(in
trunk.BIP.SDE.gillespie
)
plot_series()
(in
trunk.BIP.Bayes.PlotMeld
)
Poisson()
(in
trunk.BIP.Bayes.like
)
p2()
(in
trunk.BIP.SDE.gillespie
)
plot_series2()
(in
trunk.BIP.Bayes.PlotMeld
)
pred_new_cases()
(in
trunk.BIP.Bayes.PlotMeld
)
phiplot
(in
trunk.BIP.Bayes.Melding
)
plothist()
(in
RTplot
)
predictNewBases()
(in
Condensation
)
pickBaseSample()
(in
Condensation
)
plotlines()
(in
RTplot
)
predictSamplePosition()
(in
Model
)
plot_par_series()
(in
trunk.BIP.Bayes.PlotMeld
)
plotlines()
(in
RTpyplot
)
prior_sample()
(in
FitModel
)
plot_par_violin()
(in
trunk.BIP.Bayes.PlotMeld
)
PlotMeld
(in
trunk.BIP.Bayes
)
propf
(in
trunk.BIP.SDE.example
)
plot_pred()
(in
trunk.BIP.Bayes.PlotMeld
)
plotRaHist()
(in
trunk.BIP.Bayes.Melding
)
pt
(in
trunk.BIP.SDE.example
)
plot_results()
(in
FitModel
)
po()
(in
_Sampler
)
R
r
(in
trunk.BIP.SDE.example
)
RTpyplot
(in
trunk.BIP.Viz.realtime
)
runFilter()
(in
Condensation
)
rank_restr()
(in
trunk.BIP.Bayes.lhs
)
run()
(in
FitModel
)
runModel()
(in
Meld
)
realtime
(in
trunk.BIP.Viz
)
run()
(in
Meld
)
RTplot
(in
trunk.BIP.Viz.realtime
)
run()
(in
Model
)
S
Samplers
(in
trunk.BIP.Bayes
)
setPhi()
(in
Meld
)
Simple()
(in
trunk.BIP.Bayes.like
)
scatter()
(in
RTplot
)
setPhiFromData()
(in
Meld
)
sir()
(in
Meld
)
SDE
(in
trunk.BIP
)
setTheta()
(in
Meld
)
SMC
(in
trunk.BIP
)
ser
(in
trunk.BIP.SDE.gillespie
)
setThetaFromData()
(in
Meld
)
step()
(in
Dream
)
set_priors()
(in
FitModel
)
setupPriorConditions()
(in
Model
)
step()
(in
Metropolis
)
T
t0
(in
trunk.BIP.SDE.example
)
thplot
(in
trunk.BIP.Bayes.Melding
)
trace_acceptance
(in
_Sampler
)
term_pool()
(in
_Sampler
)
tmat
(in
trunk.BIP.SDE.example
)
trace_convergence
(in
_Sampler
)
U
Uniform()
(in
trunk.BIP.Bayes.like
)
updateAfterIterating()
(in
Condensation
)
V
vertical()
(in
Histogram
)
violin_plot()
(in
trunk.BIP.Bayes.PlotMeld
)
Viz
(in
trunk.BIP
)
vertical()
(in
Histogram
)
Viz
(in
trunk.BIP.Bayes.Melding
)
vnames
(in
trunk.BIP.SDE.example
)
W
watch_chain()
(in
Metropolis
)
Weibull()
(in
trunk.BIP.Bayes.like
)
_
__BayesC
(in
trunk.BIP.Bayes.general.bvariables
)
__init__()
(in
Histogram
)
_linesFromRA()
(in
RTplot
)
__BayesD
(in
trunk.BIP.Bayes.general.bvariables
)
__init__()
(in
RTplot
)
_monitor_plot()
(in
FitModel
)
__init()
(in
Dream
)
__init__()
(in
RTpyplot
)
_monitor_setup()
(in
FitModel
)
__init__()
(in
FitModel
)
__licence__
(in
trunk.BIP.Viz.asciihist
)
_output_loglike()
(in
Meld
)
__init__()
(in
Meld
)
__str__()
(in
_BayesVar
)
_po
(in
_Sampler
)
__init__()
(in
Metropolis
)
_accept()
(in
Metropolis
)
_post_from_conjugate()
(in
_BayesVar
)
__init__()
(in
_Sampler
)
_add_salt()
(in
Metropolis
)
_propose()
(in
Dream
)
__init__()
(in
_BayesVar
)
_BayesVar
(in
trunk.BIP.Bayes.general.bvariables
)
_propose()
(in
Metropolis
)
__init__()
(in
__BayesC
)
_dimensions
(in
_Sampler
)
_R
(in
_Sampler
)
__init__()
(in
__BayesD
)
_flavorize()
(in
_BayesVar
)
_read_results()
(in
FitModel
)
__init__()
(in
Model
)
_get95_bands()
(in
FitModel
)
_rms_error()
(in
FitModel
)
__init__()
(in
Condensation
)
_get_likelihoods()
(in
Dream
)
_rms_fit()
(in
Metropolis
)
__init__()
(in
GlobalData
)
_histFromRA()
(in
RTplot
)
_Sampler
(in
trunk.BIP.Bayes.Samplers.MCMC
)
__init__()
(in
IterationData
)
_imp_sample()
(in
Metropolis
)
_setup()
(in
RTpyplot
)
__init__()
(in
Model
)
_init_priors()
(in
FitModel
)
_update()
(in
_BayesVar
)
__init__()
(in
Histogram
)
_likelihood()
(in
_BayesVar
)
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