write.likelihood {MBNMAtime}

Adds sections of JAGS code for an MBNMA model that correspond to the likelihood

Description

Adds sections of JAGS code for an MBNMA model that correspond to the likelihood

Usage

write.likelihood(
  model,
  timecourse,
  rho = 0,
  covar = "varadj",
  link = "identity",
  sdscale = FALSE,
  fun
)

Arguments

model

A character object of JAGS MBNMA model code

timecourse

A character object representing the time-course used in the MBNMA model

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 (Jansen et al. 2015). This is the default.

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

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

link

Can take either "identity" (the default), "log" (for modelling Ratios of Means (Friedrich et al. 2011)) or "smd" (for modelling Standardised Mean Differences - although this also corresponds to an identity link function).

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").

fun

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

Value

A character vector of JAGS MBNMA model code that includes likelihood components of the model