From c94f2d649b762a8f2d97fdefb1cd29e10e3f03c5 Mon Sep 17 00:00:00 2001
From: Jouni Helske <jouni.helske@utu.fi>
Date: Sun, 1 Sep 2024 21:44:18 +0300
Subject: [PATCH] update docs

---
 NAMESPACE                      |  2 --
 R/seqHMM-package.R             |  1 -
 man/average_marginal_effect.Rd |  2 +-
 man/estimate_mnhmm.Rd          | 11 ++++++++++-
 man/estimate_nhmm.Rd           | 11 ++++++++++-
 man/forward_backward.Rd        |  7 ++++---
 6 files changed, 25 insertions(+), 9 deletions(-)

diff --git a/NAMESPACE b/NAMESPACE
index ed06c54c..b290bc32 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -114,8 +114,6 @@ importFrom(graphics,strwidth)
 importFrom(graphics,text)
 importFrom(methods,hasArg)
 importFrom(numDeriv,jacobian)
-importFrom(posterior,as_draws_rvars)
-importFrom(posterior,draws_of)
 importFrom(rstan,optimizing)
 importFrom(rstantools,rstan_config)
 importFrom(stats,BIC)
diff --git a/R/seqHMM-package.R b/R/seqHMM-package.R
index 3e11d059..4142e6de 100644
--- a/R/seqHMM-package.R
+++ b/R/seqHMM-package.R
@@ -25,7 +25,6 @@
 #' @import Rcpp
 #' @importFrom future plan sequential multisession
 #' @importFrom future.apply future_lapply
-#' @importFrom posterior as_draws_rvars draws_of
 #' @importFrom rstan optimizing
 #' @importFrom rstantools rstan_config
 #' @importFrom RcppParallel RcppParallelLibs CxxFlags
diff --git a/man/average_marginal_effect.Rd b/man/average_marginal_effect.Rd
index 81a23259..eb7cf5c3 100644
--- a/man/average_marginal_effect.Rd
+++ b/man/average_marginal_effect.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/ame.R
+% Please edit documentation in R/average_marginal_effect.R
 \name{average_marginal_effect}
 \alias{average_marginal_effect}
 \title{Average Marginal Effects of Covariates of Non-homogenous Hidden Markov Models}
diff --git a/man/estimate_mnhmm.Rd b/man/estimate_mnhmm.Rd
index 653a072c..681a7c93 100644
--- a/man/estimate_mnhmm.Rd
+++ b/man/estimate_mnhmm.Rd
@@ -23,6 +23,7 @@ estimate_mnhmm(
   restarts = 1L,
   threads = 1L,
   store_data = TRUE,
+  verbose = TRUE,
   ...
 )
 }
@@ -84,7 +85,15 @@ is stored to the model object. For large datasets, this can be set to
 \code{FALSE}, in which case you might need to pass the data separately to some
 post-prosessing functions.}
 
-\item{...}{Additional arguments to \code{\link[rstan:stanmodel-method-optimizing]{rstan::optimizing()}}.}
+\item{verbose}{If \code{TRUE} (default), print progress messages during the final
+optimization (after restarts). Note that due to the design of \code{rstan}, the
+reason for the termination of optimization (e.g., reached the maximum number
+of iterations) is only available by the final message show with
+\code{verbose = TRUE}.}
+
+\item{...}{Additional arguments to \code{\link[rstan:stanmodel-method-optimizing]{rstan::optimizing()}}. Most importantly,
+argument \code{iter} defines the maximum number of iterations for optimization.
+The default is \code{2000}.}
 }
 \value{
 Object of class \code{mnhmm}.
diff --git a/man/estimate_nhmm.Rd b/man/estimate_nhmm.Rd
index d97fa334..558993bb 100644
--- a/man/estimate_nhmm.Rd
+++ b/man/estimate_nhmm.Rd
@@ -20,6 +20,7 @@ estimate_nhmm(
   restarts = 1L,
   threads = 1L,
   store_data = TRUE,
+  verbose = TRUE,
   ...
 )
 }
@@ -72,7 +73,15 @@ is stored to the model object. For large datasets, this can be set to
 \code{FALSE}, in which case you might need to pass the data separately to some
 post-prosessing functions.}
 
-\item{...}{Additional arguments to \code{\link[rstan:stanmodel-method-optimizing]{rstan::optimizing()}}.}
+\item{verbose}{If \code{TRUE} (default), print progress messages during the final
+optimization (after restarts). Note that due to the design of \code{rstan}, the
+reason for the termination of optimization (e.g., reached the maximum number
+of iterations) is only available by the final message show with
+\code{verbose = TRUE}.}
+
+\item{...}{Additional arguments to \code{\link[rstan:stanmodel-method-optimizing]{rstan::optimizing()}}. Most importantly,
+argument \code{iter} defines the maximum number of iterations for optimization.
+The default is \code{2000}.}
 }
 \value{
 Object of class \code{nhmm}.
diff --git a/man/forward_backward.Rd b/man/forward_backward.Rd
index b265cbd8..5aaa1584 100644
--- a/man/forward_backward.Rd
+++ b/man/forward_backward.Rd
@@ -47,12 +47,13 @@ computed and returned in logarithmic scale for numerical stability. If
 is \code{1}. Not used for \code{nhmm} and \code{mnhmm} objects.}
 
 \item{as_data_frame}{If \code{TRUE} (default), the output is returned as a
-data.frame. Otherwise, a list of array(s) is returned.}
+data.frame. Otherwise, a list of array(s) is returned. Ignored if
+\code{log_space} is \code{FALSE}, in which case list of arrays is always returned.}
 }
 \value{
 If \code{as_data_frame} is \code{TRUE} a \code{data.frame} with
-log-values of forward and backward probabilities. If \code{FALSE}, a list with
-components
+log-values of forward and backward probabilities. If \code{FALSE} or
+\code{log_space = FALSE}, a list with components
 \itemize{
 \item forward_probs\cr If \code{log_space = FALSE}, scaled forward probabilities,
 i.e. probability of state given observations up to that time point.