MBNMAtime (version 0.2.4)

mb.write: Write MBNMA time-course models JAGS code

Description

Writes JAGS code for a Bayesian time-course model for model-based network meta-analysis (MBNMA).

Usage

mb.write(
  fun = tpoly(degree = 1),
  link = "identity",
  positive.scale = TRUE,
  intercept = NULL,
  rho = 0,
  covar = "varadj",
  omega = NULL,
  corparam = TRUE,
  sdscale = FALSE,
  class.effect = list(),
  UME = FALSE
)

Value

A single long character string containing the JAGS model generated based on the arguments passed to the function.

Arguments

fun

An object of class "timefun" generated (see Details) using any of tloglin(), tpoly(), titp(), temax(), tfpoly(), tspline() or tuser()

link

Can take either "identity" (the default), "log" (for modelling Ratios of Means friedrich2011MBNMAtime) or "smd" (for modelling Standardised Mean Differences - although this also corresponds to an identity link function).

positive.scale

A boolean object that indicates whether all continuous mean responses (y) are positive and therefore whether the baseline response should be given a prior that constrains it to be positive (e.g. for scales that cannot be <0).

intercept

A boolean object that indicates whether an intercept (written as alpha in the model) is to be included. If left as NULL (the default), an intercept will be included only for studies reporting absolute means, and will be excluded for studies reporting change from baseline (as indicated in network$cfb).

rho

The correlation coefficient when modelling within-study correlation between time points. The default is a string representing a prior distribution in JAGS, indicating that it be estimated from the data (e.g. rho="dunif(0,1)"). rho also be assigned a numeric value (e.g. rho=0.7), which fixes rho in the model to this value (e.g. for use in a deterministic sensitivity analysis). If set to rho=0 (the default) then this implies modelling no correlation between time points.

covar

A character specifying the covariance structure to use for modelling within-study correlation between time-points. This can be done by specifying one of the following:

• "varadj" - a univariate likelihood with a variance adjustment to assume a constant correlation between subsequent time points jansen2015MBNMAtime. This is the default.

• "CS" - a multivariate normal likelihood with a compound symmetry structure

• "AR1" - a multivariate normal likelihood with an autoregressive AR1 structure

omega

DEPRECATED IN VERSION 0.2.3 ONWARDS (~uniform(-1,1) now used for correlation between parameters rather than a Wishart prior). A scale matrix for the inverse-Wishart prior for the covariance matrix used to model the correlation between time-course parameters (see Details for time-course functions). omega must be a symmetric positive definite matrix with dimensions equal to the number of time-course parameters modelled using relative effects (pool="rel"). If left as NULL (the default) a diagonal matrix with elements equal to 1 is used.

corparam

A boolean object that indicates whether correlation should be modeled between relative effect time-course parameters. Default is FALSE and this is automatically set to FALSE if class effects are modeled. Setting it to TRUE models correlation between time-course parameters. This can help identify parameters that are estimated poorly for some treatments by allowing sharing of information between parameters for different treatments in the network, but may also cause some shrinkage.

sdscale

Logical object to indicate whether to write a model that specifies a reference SD for standardising when modelling using Standardised Mean Differences. Specifying sdscale=TRUE will therefore only modify the model if link function is set to SMD (link="smd").

class.effect

A list of named strings that determines which time-course parameters to model with a class effect and what that effect should be ("common" or "random"). For example: list(emax="common", et50="random").

UME

Can take either TRUE or FALSE (for an unrelated mean effects model on all or no time-course parameters respectively) or can be a vector of parameter name strings to model as UME. For example: c("beta.1", "beta.2").

Examples

# Write a linear time-course MBNMA:
# random treatment effects on beta.1
# equal baselines in study arms
model <- mb.write(fun=tpoly(degree=1, pool.1="rel", method.1="random"))

# Write an emax time-course MBNMA with:
# a Hill parameter
# no intercept
model <- mb.write(fun=temax(pool.emax="rel", method.emax="common",
    pool.et50="abs", method.et50="common", pool.hill="abs", method.hill="common"),
  intercept=TRUE)

# Write a log-linear time-course MBNMA with:
# AR1 correlation between time points
model <- mb.write(fun=tloglin(),
  rho="dunif(0,1)", covar="AR1")

# Define a user-defined time-course relationship for the MBNMA JAGS model
userfun <- ~ (exp(beta.1 * time) / (beta.2 * time))
model <- mb.write(fun=tuser(fun=userfun,
    pool.1="rel", method.1="random",
    pool.2="rel", method.2="common"))