post_RA_3bm {ra4bayesmeta} | R Documentation |
Posterior reference analysis based on a data frame using 3 benchmarks
Description
Computes a table of Hellinger distances between marginal posterior distributions
for different parameters in the NNHM
induced by the actual heterogeneity priors specified in tau.prior
and
posterior benchmarks proposed in the Supplementary Material of Ott et al. (2021).
Usage
post_RA_3bm(df, tau.prior=list(function(x) dhalfnormal(x, scale=1)),
H.dist.method = "integral",
m_inf=NA, M_inf=NA, rlmc0=0.0001, rlmc1=0.9999,
mu.mean=0, mu.sd=4)
Arguments
df |
data frame with one column "y" containing the (transformed) effect estimates for the individual studies and one column "sigma" containing the standard errors of these estimates. |
tau.prior |
list of prior specifications, which are either functions returning the probability densities of the actual priors of interest for the heterogeneity parameter tau or character strings specifying priors implemented in the |
H.dist.method |
method for computation of Hellinger distances between marginal posterior densities. Either |
m_inf |
parameter value |
M_inf |
parameter value |
rlmc0 |
RLMC target value for the SGC( |
rlmc1 |
RLMC target value for the SIGC( |
mu.mean |
mean of the normal prior for the effect mu. |
mu.sd |
standard deviation of the normal prior for the effect mu. |
Details
The three posterior benchmarks used are
introduced in the Supplementary Material of Ott et al. (2021, Sections 2.2.1 and 2.5, see also Section 3.4 in Ott at al. (2021) for Jeffreys reference prior),
where they are denoted by
po_{m_{inf}}(\Psi)
, po_{J}(\Psi)
and po_{M_{inf}}(\Psi)
.
Here, \Psi \in \{ \mu, \tau, \theta_1, ..., \theta_k, \theta_{new} \}
denotes the parameter of interest in the NNHM,
where \theta_{i}
is the random effect in the i
th study and
\theta_{new}
the predicted effect for a new study.
Note that Jeffreys reference posterior po_{J}
is proper if
there are at least two studies in the meta-analysis data set.
It is based on the improper Jeffreys reference prior,
which is minimally informative given the data.
If integral-based computation (H.dist.method = "integral"
) of Hellinger distances is selected (the default), numerical integration is applied to obtain the Hellinger distance between the two marginal posterior densities (by using the function H
).
If moment-based computation (H.dist.method = "moment"
) is selected, the marginal densities are first approximated by normal densities with the same means and standard deviations and then the Hellinger distance between these normal densities can be obtained by an analytical formula (implemented in the function H_normal
).
The default values for mu.mean
and mu.sd
are suitable for effects mu on the log odds (ratio) scale.
Value
A list with two elements:
The first element named "table" is a matrix containing the Hellinger distance estimates and the
second element called "par" is a named vector giving the parameter values
of the benchmark priors.
The vector "par" has the following three components:
m_inf
, M_inf
and C
.
The matrix "table" contains the Hellinger distance estimates between marginal posteriors
and has 3
columns and n*(k+3)
rows,
where n
=length(tau.prior
) is the number of actual heterogeneity priors specified
and k
is the number of studies in the meta-analysis data set
(so that there are k+3
parameters of interest).
The columns of the matrix give the following Hellinger distance estimates
between two marginal posteriors (for the parameter of interest \Psi
varying with rows)
induced by the following two heterogeneity priors
(from left to right):
H(po_{m_inf}, po_act)
:benchmark prior SGC(m_inf) and actual prior
H(po_J, po_act)
:Jeffreys reference prior
\pi_J
and actual priorH(po_{M_inf}, po_act)
:benchmark prior SIGC(M_inf) and actual prior
The actual heterogenity prior and the parameter of interest \Psi
vary
with the rows in the following order:
mu, pri_act_1
:-
\Psi=\mu
and first actual prior intau.prior
mu, pri_act_2
:-
\Psi=\mu
and second actual prior intau.prior
- ...
mu, pri_act_n
:-
\Psi=\mu
and nth actual prior intau.prior
tau, pri_act_1
:-
\Psi=\tau
and first actual prior intau.prior
- ...
tau, pri_act_n
:-
\Psi=\tau
and nth actual prior theta_1, pri_act_1
:-
\Psi=\theta_1
and first actual prior - ...
theta_k, pri_act_n
:-
\Psi=\theta_k
and nth actual prior theta_new, pri_act_1
:-
\Psi=\theta_{new}
and first actual prior - ...
theta_new, pri_act_n
:-
\Psi=\theta_{new}
and nth actual prior
Warnings
A warning message will be displayed if one of the parameters m_inf
or M_inf
has a value larger than 5*10^6, since this may lead to numerical problems
in the bayesmeta
function
used for computation of the marginal posteriors.
If the integral-based method is used to compute Hellinger distances (H.dist.method = "integral"
),
numerical problems may occur in some cases, which may lead to implausible outputs.
Therefore, we generally recommend to double-check the results of the integral-based method using the moment-based method (H.dist.method = "moment"
) - especially if the former results are implausibe. If large differences between the two methods are observed, we recommend to rely on the moment-based method unless a normal approximation of the involved densities is inappropriate.
References
Ott, M., Plummer, M., Roos, M. (2021). Supplementary Material: How vague is vague? How informative is informative? Reference analysis for Bayesian meta-analysis. Statistics in Medicine. doi:10.1002/sim.9076
Ott, M., Plummer, M., Roos, M. (2021). How vague is vague? How informative is informative? Reference analysis for Bayesian meta-analysis. Statistics in Medicine 40, 4505–4521. doi:10.1002/sim.9076
See Also
Examples
# for aurigular acupuncture (AA) data set with two
# actual half-normal heterogeneity priors
data(aa)
# it takes several seconds to run this function
post_RA_3bm(df=aa, tau.prior=list(function(t)dhalfnormal(t, scale=0.5),
function(t)dhalfnormal(t, scale=1)))