diff --git a/R/sparse.R b/R/sparse.R index 92b45d3..d588e30 100644 --- a/R/sparse.R +++ b/R/sparse.R @@ -2,6 +2,13 @@ #' @param obj The TMB object with random effects turned on and #' optimized #' @param iter Total iterations to run (warmup + sampling) +#' @param init Either 'last.par.best' (default) or 'random'. The +#' former starts from the joint mode and the latter draws from +#' a multivariate t distribution with df=1 centered at the mode +#' using the inverse joint precision matrix as a covariance +#' matrix. Note that StanEstimators only allows for the same +#' init vector for all chains currently. If a seed is specified +#' it will be set and thus the inits used will be reproducible. #' @param warmup Total warmup iterations #' @param chains Number of chains #' @param cores Number of parallel cores to use diff --git a/man/pairs_admb.Rd b/man/pairs_admb.Rd index 4fa1d45..c53c9dd 100644 --- a/man/pairs_admb.Rd +++ b/man/pairs_admb.Rd @@ -8,6 +8,7 @@ confidence ellipses.} pairs_admb( fit, order = NULL, + inc_warmup = FALSE, diag = c("trace", "acf", "hist"), acf.ylim = c(-1, 1), ymult = NULL, @@ -30,6 +31,9 @@ NULL (default) to use the order declared in the model, or sizes ordered by slowest or fastest mixing respectively. See example for usage.} +\item{inc_warmup}{Whether to include the warmup samples or not +(default).} + \item{diag}{What type of plot to include on the diagonal, options are 'acf' which plots the autocorrelation function \code{acf}, 'hist' shows marginal posterior histograms, and diff --git a/man/sample_sparse_tmb.Rd b/man/sample_sparse_tmb.Rd index 0dd8ad9..a790142 100644 --- a/man/sample_sparse_tmb.Rd +++ b/man/sample_sparse_tmb.Rd @@ -11,7 +11,9 @@ sample_sparse_tmb( cores, chains, control = NULL, - seed = NULL + seed = NULL, + init = c("last.par.best", "random"), + metric = c("sparse", "dense", "diag", "unit") ) } \arguments{ @@ -29,6 +31,14 @@ optimized} \item{control}{NUTS control list} \item{seed}{Random number seed} + +\item{init}{Either 'last.par.best' (default) or 'random'. The +former starts from the joint mode and the latter draws from +a multivariate t distribution with df=1 centered at the mode +using the inverse joint precision matrix as a covariance +matrix. Note that StanEstimators only allows for the same +init vector for all chains currently. If a seed is specified +it will be set and thus the inits used will be reproducible.} } \value{ A fitted MCMC object of class 'adfit'