docs ready, release

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: bssm
 Type: Package
 Title: Bayesian Inference of State Space Models
-Version: 0.0.74
-Date: 2017-02-24
+Version: 0.0.75
+Date: 2017-05-10
 Author: Jouni Helske, Matti Vihola
 Maintainer: Jouni Helske <jouni.helske@jyu.fi>
 Description: Efficient methods for Bayesian inference of state space models. 

R/particle_smoother.R

@@ -5,7 +5,7 @@
 #'
 #' @param object Model.
 #' @param nsim Number of samples.
-#' @param filter Choice of particle filter algorithm. For Gaussian models, 
+#' @param filter_type Choice of particle filter algorithm. For Gaussian models, 
 #' possible choices are \code{"bsf"} (bootstrap particle filter) and 
 #' \code{"apf"} (auxiliary particle filter). In addition, for non-Gaussian or 
 #' non-linear models, \code{"psi"} uses psi-particle filter, and 
@@ -160,7 +160,7 @@ particle_smoother.svm <- function(object, nsim,
   out$alpha <- aperm(out$alpha, c(2, 1, 3))
   out
 }
-
+#' @rdname particle_smoother
 #' @method particle_smoother nlg_ssm
 #' @export
 particle_smoother.nlg_ssm <- function(object, nsim, 

R/run_mcmc.R

@@ -216,7 +216,7 @@ run_mcmc.ngssm <- function(object, n_iter, nsim_states, type = "full",
   delayed_acceptance = TRUE, n_burnin = floor(n_iter/2),
   n_thin = 1, gamma = 2/3, target_acceptance = 0.234, S, end_adaptive_phase = TRUE,
   local_approx  = TRUE, n_threads = 1,
-  seed = sample(.Machine$integer.max, size = 1), ...) {
+  seed = sample(.Machine$integer.max, size = 1), max_iter = 100, conv_tol = 1e-8, ...) {
 
   a <- proc.time()
   check_target(target_acceptance)
@@ -474,7 +474,7 @@ run_mcmc.nlg_ssm <-  function(object, n_iter, nsim_states, type = "full",
   delayed_acceptance = TRUE, n_burnin = floor(n_iter/2), n_thin = 1,
   gamma = 2/3, target_acceptance = 0.234, S, end_adaptive_phase = TRUE,
   n_threads = 1, seed = sample(.Machine$integer.max, size = 1), max_iter = 100, 
-  conv_tol = 1e-8, iekf_iter = 0, ...) {
+  conv_tol = 1e-4, iekf_iter = 0, ...) {
 
   a <- proc.time()
   check_target(target_acceptance)