bdpbinomial {bayesDP} | R Documentation |
bdpbinomial
is used for estimating posterior samples from a
binomial outcome where an informative prior is used. The prior weight
is determined using a discount function. This code is modeled after
the methodologies developed in Haddad et al. (2017).
bdpbinomial(
y_t = NULL,
N_t = NULL,
y0_t = NULL,
N0_t = NULL,
y_c = NULL,
N_c = NULL,
y0_c = NULL,
N0_c = NULL,
discount_function = "identity",
alpha_max = 1,
fix_alpha = FALSE,
a0 = 1,
b0 = 1,
number_mcmc = 10000,
weibull_scale = 0.135,
weibull_shape = 3,
method = "mc",
compare = TRUE
)
y_t |
scalar. Number of events for the current treatment group. |
N_t |
scalar. Sample size of the current treatment group. |
y0_t |
scalar. Number of events for the historical treatment group. |
N0_t |
scalar. Sample size of the historical treatment group. |
y_c |
scalar. Number of events for the current control group. |
N_c |
scalar. Sample size of the current control group. |
y0_c |
scalar. Number of events for the historical control group. |
N0_c |
scalar. Sample size of the historical control group. |
discount_function |
character. Specify the discount function to use.
Currently supports |
alpha_max |
scalar. Maximum weight the discount function can apply. Default is 1. For a two-arm trial, users may specify a vector of two values where the first value is used to weight the historical treatment group and the second value is used to weight the historical control group. |
fix_alpha |
logical. Fix alpha at alpha_max? Default value is FALSE. |
a0 |
scalar. Prior value for the beta rate. Default is 1. |
b0 |
scalar. Prior value for the beta rate. Default is 1. |
number_mcmc |
scalar. Number of Monte Carlo simulations. Default is 10000. |
weibull_scale |
scalar. Scale parameter of the Weibull discount function
used to compute alpha, the weight parameter of the historical data. Default
value is 0.135. For a two-arm trial, users may specify a vector of two values
where the first value is used to estimate the weight of the historical
treatment group and the second value is used to estimate the weight of the
historical control group. Not used when |
weibull_shape |
scalar. Shape parameter of the Weibull discount function
used to compute alpha, the weight parameter of the historical data. Default
value is 3. For a two-arm trial, users may specify a vector of two values
where the first value is used to estimate the weight of the historical
treatment group and the second value is used to estimate the weight of the
historical control group. Not used when |
method |
character. Analysis method with respect to estimation of the weight
paramter alpha. Default method " |
compare |
logical. Should a comparison object be included in the fit?
For a one-arm analysis, the comparison object is simply the posterior
chain of the treatment group parameter. For a two-arm analysis, the comparison
object is the posterior chain of the treatment effect that compares treatment and
control. If |
bdpbinomial
uses a two-stage approach for determining the
strength of historical data in estimation of a binomial count mean outcome.
In the first stage, a discount function is used that that defines
the maximum strength of the historical data and discounts based on
disagreement with the current data. Disagreement between current and
historical data is determined by stochastically comparing the respective
posterior distributions under noninformative priors. With binomial data,
the comparison is the proability (p
) that the current count is less
than the historical count. The comparison metric p
is then input
into the Weibull discount function and the final strength of the historical
data is returned (alpha).
In the second stage, posterior estimation is performed where the discount
function parameter, alpha
, is used incorporated in all posterior
estimation procedures.
To carry out a single arm (OPC) analysis, data for the current treatment
(y_t
and N_t
) and historical treatment (y0_t
and
N0_t
) must be input. The results are then based on the posterior
distribution of the current data augmented by the historical data.
To carry our a two-arm (RCT) analysis, data for the current treatment and at least one of current or historical control data must be input. The results are then based on the posterior distribution of the difference between current treatment and control, augmented by available historical data.
For more details, see the bdpbinomial
vignette:
vignette("bdpbinomial-vignette", package="bayesDP")
bdpbinomial
returns an object of class "bdpbinomial". The
functions summary
and
print
are used to obtain and
print a summary of the results, including user inputs. The
plot
function displays visual
outputs as well.
An object of class bdpbinomial
is a list containing at least
the following components:
posterior_treatment
list. Entries contain values related to the treatment group:
alpha_discount
numeric. Alpha value, the weighting parameter of the historical data.
p_hat
numeric. The posterior probability of the stochastic comparison
between the current and historical data.
posterior
vector. A vector of length number_mcmc
containing
posterior Monte Carlo samples of the event rate of the treatment
group. If historical treatment data is present, the posterior
incorporates the weighted historical data.
posterior_flat
vector. A vector of length number_mcmc
containing
Monte Carlo samples of the event rate of the current treatment group
under a flat/non-informative prior, i.e., no incorporation of the
historical data.
prior
vector. If historical treatment data is present, a vector of length
number_mcmc
containing Monte Carlo samples of the event rate
of the historical treatment group under a flat/non-informative prior.
posterior_control
list. Similar entries as posterior_treament
. Only present if a
control group is specified.
final
list. Contains the final comparison object, dependent on the analysis type:
One-arm analysis: vector. Posterior chain of binomial proportion.
Two-arm analysis: vector. Posterior chain of binomial proportion difference comparing treatment and control groups.
args1
list. Entries contain user inputs. In addition, the following elements are ouput:
arm2
binary indicator. Used internally to indicate one-arm or two-arm
analysis.
intent
character. Denotes current/historical status of treatment and
control groups.
Haddad, T., Himes, A., Thompson, L., Irony, T., Nair, R. MDIC Computer Modeling and Simulation working group.(2017) Incorporation of stochastic engineering models as prior information in Bayesian medical device trials. Journal of Biopharmaceutical Statistics, 1-15.
summary
,
print
,
and plot
for details of each of the
supported methods.
# One-arm trial (OPC) example
fit <- bdpbinomial(
y_t = 10,
N_t = 500,
y0_t = 25,
N0_t = 250,
method = "fixed"
)
summary(fit)
print(fit)
## Not run:
plot(fit)
## End(Not run)
# Two-arm (RCT) example
fit2 <- bdpbinomial(
y_t = 10,
N_t = 500,
y0_t = 25,
N0_t = 250,
y_c = 8,
N_c = 500,
y0_c = 20,
N0_c = 250,
method = "fixed"
)
summary(fit2)
print(fit2)
## Not run:
plot(fit2)
## End(Not run)