View source: R/run.functions.R
pDcalc | R Documentation |
Uses results from MBNMA JAGS models to calculate pD via the plugin method \insertCitespiegelhalter2002MBNMAtime. Can only be used for models with known standard errors or covariance matrices (typically univariate).
pDcalc(
obs1,
obs2,
fups = NULL,
narm,
NS,
theta.result,
resdev.result,
likelihood = "normal",
type = "time"
)
obs1 |
A matrix (study x arm) or array (study x arm x time point) containing
observed data for |
obs2 |
A matrix (study x arm) or array (study x arm x time point) containing
observed data for |
fups |
A numeric vector of length equal to the number of studies,
containing the number of follow-up mean responses reported in each study. Required for
time-course MBNMA models (if |
narm |
A numeric vector of length equal to the number of studies, containing the number of arms in each study. |
NS |
A single number equal to the number of studies in the dataset. |
theta.result |
A matrix (study x arm) or array (study x arm x time point) containing the posterior mean predicted means/probabilities/rate in each arm of each study. This will be estimated by the JAGS model. |
resdev.result |
A matrix (study x arm) or array (study x arm x time point) containing the posterior mean residual deviance contributions in each arm of each study. This will be estimated by the JAGS model. |
likelihood |
A character object of any of the following likelihoods:
|
type |
The type of MBNMA model fitted. Can be either |
Method for calculating pD via the plugin method proposed by \insertCitespiegelhalter2002MBNMAtime. Standard errors / covariance matrices must be assumed to be known. To obtain values for theta.result and resdev.result these parameters must be monitored when running the JAGS model.
For non-linear time-course MBNMA models residual deviance contributions may be skewed, which
can lead to non-sensical results when calculating pD via the plugin method.
Alternative approaches are to use pV (pv
) as an approximation \insertCiteplummer2008MBNMAtime or
pD calculated by Kullback–Leibler divergence (pd.kl
) or using an optimism adjustment (popt
) \insertCiteplummer2008MBNMAtime.
A numeric value for the effective number of parameters, pD, calculated via the plugin method
TO ADD pV REF
# Using the alogliptin dataset
network <- mb.network(alog_pcfb)
# Run Emax model saving predicted means and residual deviance contributions
emax <- mb.run(network, fun=temax(),
parameters.to.save=c("theta", "resdev"), intercept=FALSE)
# Get matrices of observed data
jagsdat <- getjagsdata(network$data.ab)
# Plugin estimation of pD is problematic with non-linear models as it often leads to
#negative values, hence use of pV, pd.kl and popt as other measures for the effective
#number of parameters
pDcalc(obs1=jagsdat$y, obs2=jagsdat$se,
fups=jagsdat$fups, narm=jagsdat$narm, NS=jagsdat$NS,
theta.result = emax$BUGSoutput$mean$theta,
resdev.result = emax$BUGSoutput$mean$resdev
)
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