From bf875dd4928e0170dba7079388e9373cd828bce7 Mon Sep 17 00:00:00 2001
From: hyunjimoon <mhj1667@gmail.com>
Date: Sat, 4 Sep 2021 02:16:40 -0400
Subject: [PATCH 1/4] backend work for stan supported nonHMC samplers

---
 NAMESPACE                              |  6 ++
 R/backends.R                           | 81 ++++++++++++++++++++++++++
 R/results.R                            |  2 +-
 man/SBC_backend_cmdstan_optimize.Rd    | 18 ++++++
 man/SBC_backend_cmdstan_variational.Rd | 18 ++++++
 man/compute_results.Rd                 |  4 +-
 6 files changed, 126 insertions(+), 3 deletions(-)
 create mode 100644 man/SBC_backend_cmdstan_optimize.Rd
 create mode 100644 man/SBC_backend_cmdstan_variational.Rd

diff --git a/NAMESPACE b/NAMESPACE
index c0b5cae..2750c14 100755
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -3,13 +3,17 @@
 S3method("[",SBC_datasets)
 S3method("[",SBC_results)
 S3method(SBC_fit,SBC_backend_brms)
+S3method(SBC_fit,SBC_backend_cmdstan_optimize)
 S3method(SBC_fit,SBC_backend_cmdstan_sample)
+S3method(SBC_fit,SBC_backend_cmdstan_variational)
 S3method(SBC_fit,SBC_backend_rstan_sample)
 S3method(SBC_fit_to_diagnostics,CmdStanMCMC)
 S3method(SBC_fit_to_diagnostics,brmsfit)
 S3method(SBC_fit_to_diagnostics,default)
 S3method(SBC_fit_to_diagnostics,stanfit)
 S3method(SBC_fit_to_draws_matrix,CmdStanMCMC)
+S3method(SBC_fit_to_draws_matrix,CmdStanMLE)
+S3method(SBC_fit_to_draws_matrix,CmdStanVB)
 S3method(SBC_fit_to_draws_matrix,brmsfit)
 S3method(SBC_fit_to_draws_matrix,default)
 S3method(check_all_SBC_diagnostics,SBC_results)
@@ -33,7 +37,9 @@ S3method(summary,SBC_nuts_diagnostics)
 S3method(summary,SBC_results)
 export(SBC_backend_brms)
 export(SBC_backend_brms_from_generator)
+export(SBC_backend_cmdstan_optimize)
 export(SBC_backend_cmdstan_sample)
+export(SBC_backend_cmdstan_variational)
 export(SBC_backend_rstan_sample)
 export(SBC_datasets)
 export(SBC_diagnostic_messages)
diff --git a/R/backends.R b/R/backends.R
index f2d113a..ce4df9a 100644
--- a/R/backends.R
+++ b/R/backends.R
@@ -267,6 +267,87 @@ SBC_fit_to_diagnostics.CmdStanMCMC <- function(fit, fit_output, fit_messages, fi
   res
 }
 
+#' Backend based on variational approximation via `cmdstanr`.
+#'
+#' @param model an object of class `CmdStanModel` (as created by `cmdstanr::cmdstan_model`)
+#' @param ... other arguments passed to the `$variational()` method of the model. The `data` and
+#'   `parallel_chains` arguments cannot be set this way as they need to be controlled by the SBC
+#'   package.
+#' @export
+SBC_backend_cmdstan_variational <- function(model, ...) {
+  stopifnot(inherits(model, "CmdStanModel"))
+  if(length(model$exe_file()) == 0) {
+    stop("The model has to be already compiled, call $compile() first.")
+  }
+  args <- list(...)
+  unacceptable_params <- c("data", "parallel_chains ", "cores", "num_cores")
+  if(any(names(args) %in% unacceptable_params)) {
+    stop(paste0("Parameters ", paste0("'", unacceptable_params, "'", collapse = ", "),
+                " cannot be provided when defining a backend as they need to be set ",
+                "by the SBC package"))
+  }
+  structure(list(model = model, args = args), class = "SBC_backend_cmdstan_variational")
+}
+
+#' @export
+SBC_fit.SBC_backend_cmdstan_variational <- function(backend, generated, cores) {
+  fit <- do.call(backend$model$variational,
+                 combine_args(backend$args,
+                              list(
+                                data = generated,
+                                parallel_chains = cores)))
+
+  if(all(fit$return_codes() != 0)) {
+    stop("No chains finished succesfully")
+  }
+
+  fit
+}
+
+#' @export
+SBC_fit_to_draws_matrix.CmdStanVB <- function(fit) {
+  fit$draws(format = "draws_matrix")
+}
+
+#' Backend based on optimize approximation via `cmdstanr`.
+#'
+#' @param model an object of class `CmdStanModel` (as created by `cmdstanr::cmdstan_model`)
+#' @param ... other arguments passed to the `$optimize()` method of the model. The `data` and
+#'   `parallel_chains` arguments cannot be set this way as they need to be controlled by the SBC
+#'   package.
+#' @export
+SBC_backend_cmdstan_optimize <- function(model, ...) {
+  stopifnot(inherits(model, "CmdStanModel"))
+  if(length(model$exe_file()) == 0) {
+    stop("The model has to be already compiled, call $compile() first.")
+  }
+  args <- list(...)
+  unacceptable_params <- c("data")
+  if(any(names(args) %in% unacceptable_params)) {
+    stop(paste0("Parameters ", paste0("'", unacceptable_params, "'", collapse = ", "),
+                " cannot be provided when defining a backend as they need to be set ",
+                "by the SBC package"))
+  }
+  structure(list(model = model, args = args), class = "SBC_backend_cmdstan_optimize")
+}
+#' @export
+SBC_fit.SBC_backend_cmdstan_optimize <- function(backend, generated, cores) {
+  fit <- do.call(backend$model$optimize,
+                 combine_args(backend$args,
+                              list(
+                                data = generated)))
+
+                 if(all(fit$return_codes() != 0)) {
+                   stop("Point optimization failed!")
+                 }
+
+                 fit
+}
+#' @export
+SBC_fit_to_draws_matrix.CmdStanMLE <- function(fit) {
+  fit$draws(format = "draws_matrix")
+}
+
 # For internal use, creates brms backend.
 new_SBC_backend_brms <- function(compiled_model,
   args
diff --git a/R/results.R b/R/results.R
index 2d94a68..aec1bb1 100644
--- a/R/results.R
+++ b/R/results.R
@@ -217,7 +217,7 @@ length.SBC_results <- function(x) {
 #'
 #' @param datasets an object of class `SBC_datasets`
 #' @param backend the model + sampling algorithm. The built-in backends can be constructed
-#'   using `SBC_backend_cmdstan_sample()`, `SBC_backend_rstan_sample()` and `SBC_backend_brms()`.
+#'   using `SBC_backend_cmdstan_sample()`, `SBC_backend_cmdstan_variational()`,`SBC_backend_cmdstan_optimize()`, `SBC_backend_rstan_sample()` and `SBC_backend_brms()`.
 #'   (more to come). The backend is an S3 class supporting at least the `SBC_fit`,
 #'   `SBC_fit_to_draws_matrix` methods.
 #' @param cores_per_fit how many cores should the backend be allowed to use for a single fit?
diff --git a/man/SBC_backend_cmdstan_optimize.Rd b/man/SBC_backend_cmdstan_optimize.Rd
new file mode 100644
index 0000000..6731809
--- /dev/null
+++ b/man/SBC_backend_cmdstan_optimize.Rd
@@ -0,0 +1,18 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/backends.R
+\name{SBC_backend_cmdstan_optimize}
+\alias{SBC_backend_cmdstan_optimize}
+\title{Backend based on optimize approximation via \code{cmdstanr}.}
+\usage{
+SBC_backend_cmdstan_optimize(model, ...)
+}
+\arguments{
+\item{model}{an object of class \code{CmdStanModel} (as created by \code{cmdstanr::cmdstan_model})}
+
+\item{...}{other arguments passed to the \verb{$variational()} method of the model. The \code{data} and
+\code{parallel_chains} arguments cannot be set this way as they need to be controlled by the SBC
+package.}
+}
+\description{
+Backend based on optimize approximation via \code{cmdstanr}.
+}
diff --git a/man/SBC_backend_cmdstan_variational.Rd b/man/SBC_backend_cmdstan_variational.Rd
new file mode 100644
index 0000000..ad07463
--- /dev/null
+++ b/man/SBC_backend_cmdstan_variational.Rd
@@ -0,0 +1,18 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/backends.R
+\name{SBC_backend_cmdstan_variational}
+\alias{SBC_backend_cmdstan_variational}
+\title{Backend based on variational approximation via \code{cmdstanr}.}
+\usage{
+SBC_backend_cmdstan_variational(model, ...)
+}
+\arguments{
+\item{model}{an object of class \code{CmdStanModel} (as created by \code{cmdstanr::cmdstan_model})}
+
+\item{...}{other arguments passed to the \verb{$variational()} method of the model. The \code{data} and
+\code{parallel_chains} arguments cannot be set this way as they need to be controlled by the SBC
+package.}
+}
+\description{
+Backend based on variational approximation via \code{cmdstanr}.
+}
diff --git a/man/compute_results.Rd b/man/compute_results.Rd
index af6a5ca..8ebe0a8 100644
--- a/man/compute_results.Rd
+++ b/man/compute_results.Rd
@@ -18,7 +18,7 @@ compute_results(
 \item{datasets}{an object of class \code{SBC_datasets}}
 
 \item{backend}{the model + sampling algorithm. The built-in backends can be constructed
-using \code{SBC_backend_cmdstan_sample()}, \code{SBC_backend_rstan_sample()} and \code{SBC_backend_brms()}.
+using \code{SBC_backend_cmdstan_sample()}, \code{SBC_backend_cmdstan_optimize()}, \code{SBC_backend_rstan_sample()} and \code{SBC_backend_brms()}.
 (more to come). The backend is an S3 class supporting at least the \code{SBC_fit},
 \code{SBC_fit_to_draws_matrix} methods.}
 
@@ -44,7 +44,7 @@ the work may be distributed less equally across workers. We recommend setting th
 enough that a single batch takes at least several seconds, i.e. for small models,
 you can often reduce computation time noticeably by increasing this value.
 You can use \code{options(SBC.min_chunk_size = value)} to set a minimum chunk size globally.
-See documentation of \code{future.chunk.size} argument for \code{future_lapply()} for more details.}
+See documentation of \code{future.chunk.size} argument for \code{future.apply::future_lapply()} for more details.}
 }
 \value{
 An object of class \code{SBC_results} that holds:

From b31ea60611708061ba8dd53ee3b882ce98b9cdf8 Mon Sep 17 00:00:00 2001
From: Dashadower <tttllshin@gmail.com>
Date: Mon, 6 Sep 2021 10:13:00 +0900
Subject: [PATCH 2/4] Support variational, disable optimize for now

---
 R/backends.R                        | 16 ++++++++--------
 R/results.R                         |  7 +++++--
 man/SBC_backend_cmdstan_optimize.Rd |  2 +-
 man/compute_results.Rd              |  2 +-
 4 files changed, 15 insertions(+), 12 deletions(-)

diff --git a/R/backends.R b/R/backends.R
index ce4df9a..450b3c7 100644
--- a/R/backends.R
+++ b/R/backends.R
@@ -294,8 +294,7 @@ SBC_fit.SBC_backend_cmdstan_variational <- function(backend, generated, cores) {
   fit <- do.call(backend$model$variational,
                  combine_args(backend$args,
                               list(
-                                data = generated,
-                                parallel_chains = cores)))
+                                data = generated)))
 
   if(all(fit$return_codes() != 0)) {
     stop("No chains finished succesfully")
@@ -307,6 +306,7 @@ SBC_fit.SBC_backend_cmdstan_variational <- function(backend, generated, cores) {
 #' @export
 SBC_fit_to_draws_matrix.CmdStanVB <- function(fit) {
   fit$draws(format = "draws_matrix")
+
 }
 
 #' Backend based on optimize approximation via `cmdstanr`.
@@ -317,6 +317,7 @@ SBC_fit_to_draws_matrix.CmdStanVB <- function(fit) {
 #'   package.
 #' @export
 SBC_backend_cmdstan_optimize <- function(model, ...) {
+  stop("The optimize method is currently not supported.")
   stopifnot(inherits(model, "CmdStanModel"))
   if(length(model$exe_file()) == 0) {
     stop("The model has to be already compiled, call $compile() first.")
@@ -334,14 +335,13 @@ SBC_backend_cmdstan_optimize <- function(model, ...) {
 SBC_fit.SBC_backend_cmdstan_optimize <- function(backend, generated, cores) {
   fit <- do.call(backend$model$optimize,
                  combine_args(backend$args,
-                              list(
-                                data = generated)))
+                              list(data = generated)))
 
-                 if(all(fit$return_codes() != 0)) {
-                   stop("Point optimization failed!")
-                 }
+   if(all(fit$return_codes() != 0)) {
+     stop("Point optimization failed!")
+   }
 
-                 fit
+   fit
 }
 #' @export
 SBC_fit_to_draws_matrix.CmdStanMLE <- function(fit) {
diff --git a/R/results.R b/R/results.R
index aec1bb1..3527957 100644
--- a/R/results.R
+++ b/R/results.R
@@ -271,7 +271,6 @@ compute_results <- function(datasets, backend,
       generated = datasets$generated[[i]]
     )
   }
-
   if(is.null(gen_quants)) {
     future.globals <- FALSE
   } else {
@@ -288,6 +287,7 @@ compute_results <- function(datasets, backend,
     future.globals = future.globals,
     future.chunk.size = chunk_size)
 
+  print("reached1")
 
   # Combine, check and summarise
   fits <- rep(list(NULL), length(datasets))
@@ -306,8 +306,11 @@ compute_results <- function(datasets, backend,
     if(is.null(results_raw[[i]]$error)) {
       stats_list[[i]] <- results_raw[[i]]$stats
       stats_list[[i]]$dataset_id <- i
+      print(results_raw[[i]]$backend_diagnostics)
       backend_diagnostics_list[[i]] <- results_raw[[i]]$backend_diagnostics
-      backend_diagnostics_list[[i]]$dataset_id <- i
+      if(!is.null(results_raw[[i]]$backend_diagnostics)){
+        backend_diagnostics_list[[i]]$dataset_id <- i
+      }
     }
     else {
       if(n_errors < max_errors_to_show) {
diff --git a/man/SBC_backend_cmdstan_optimize.Rd b/man/SBC_backend_cmdstan_optimize.Rd
index 6731809..6f4d16c 100644
--- a/man/SBC_backend_cmdstan_optimize.Rd
+++ b/man/SBC_backend_cmdstan_optimize.Rd
@@ -9,7 +9,7 @@ SBC_backend_cmdstan_optimize(model, ...)
 \arguments{
 \item{model}{an object of class \code{CmdStanModel} (as created by \code{cmdstanr::cmdstan_model})}
 
-\item{...}{other arguments passed to the \verb{$variational()} method of the model. The \code{data} and
+\item{...}{other arguments passed to the \verb{$optimize()} method of the model. The \code{data} and
 \code{parallel_chains} arguments cannot be set this way as they need to be controlled by the SBC
 package.}
 }
diff --git a/man/compute_results.Rd b/man/compute_results.Rd
index 8ebe0a8..5a6aab0 100644
--- a/man/compute_results.Rd
+++ b/man/compute_results.Rd
@@ -18,7 +18,7 @@ compute_results(
 \item{datasets}{an object of class \code{SBC_datasets}}
 
 \item{backend}{the model + sampling algorithm. The built-in backends can be constructed
-using \code{SBC_backend_cmdstan_sample()}, \code{SBC_backend_cmdstan_optimize()}, \code{SBC_backend_rstan_sample()} and \code{SBC_backend_brms()}.
+using \code{SBC_backend_cmdstan_sample()}, \code{SBC_backend_cmdstan_variational()},\code{SBC_backend_cmdstan_optimize()}, \code{SBC_backend_rstan_sample()} and \code{SBC_backend_brms()}.
 (more to come). The backend is an S3 class supporting at least the \code{SBC_fit},
 \code{SBC_fit_to_draws_matrix} methods.}
 

From b26c87f8a543c483bcf083ffdad0734a01e33100 Mon Sep 17 00:00:00 2001
From: Dashadower <tttllshin@gmail.com>
Date: Mon, 6 Sep 2021 10:16:37 +0900
Subject: [PATCH 3/4] Remove debug code

---
 R/results.R | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/R/results.R b/R/results.R
index 3527957..0b4ac80 100644
--- a/R/results.R
+++ b/R/results.R
@@ -287,8 +287,6 @@ compute_results <- function(datasets, backend,
     future.globals = future.globals,
     future.chunk.size = chunk_size)
 
-  print("reached1")
-
   # Combine, check and summarise
   fits <- rep(list(NULL), length(datasets))
   outputs <- rep(list(NULL), length(datasets))
@@ -306,7 +304,6 @@ compute_results <- function(datasets, backend,
     if(is.null(results_raw[[i]]$error)) {
       stats_list[[i]] <- results_raw[[i]]$stats
       stats_list[[i]]$dataset_id <- i
-      print(results_raw[[i]]$backend_diagnostics)
       backend_diagnostics_list[[i]] <- results_raw[[i]]$backend_diagnostics
       if(!is.null(results_raw[[i]]$backend_diagnostics)){
         backend_diagnostics_list[[i]]$dataset_id <- i

From 5d5b3410e580f19e7eaa119ba9974f517b303e00 Mon Sep 17 00:00:00 2001
From: hyunjimoon <mhj1667@gmail.com>
Date: Tue, 7 Sep 2021 05:27:05 -0400
Subject: [PATCH 4/4] address variational backend issue 35

---
 NAMESPACE                           |  3 --
 R/.Rapp.history                     |  0
 R/backends.R                        | 43 ++---------------------------
 R/results.R                         |  6 ++--
 man/SBC_backend_cmdstan_optimize.Rd | 18 ------------
 man/compute_results.Rd              |  6 ++--
 6 files changed, 8 insertions(+), 68 deletions(-)
 create mode 100644 R/.Rapp.history
 delete mode 100644 man/SBC_backend_cmdstan_optimize.Rd

diff --git a/NAMESPACE b/NAMESPACE
index 2750c14..6e6d874 100755
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -3,7 +3,6 @@
 S3method("[",SBC_datasets)
 S3method("[",SBC_results)
 S3method(SBC_fit,SBC_backend_brms)
-S3method(SBC_fit,SBC_backend_cmdstan_optimize)
 S3method(SBC_fit,SBC_backend_cmdstan_sample)
 S3method(SBC_fit,SBC_backend_cmdstan_variational)
 S3method(SBC_fit,SBC_backend_rstan_sample)
@@ -12,7 +11,6 @@ S3method(SBC_fit_to_diagnostics,brmsfit)
 S3method(SBC_fit_to_diagnostics,default)
 S3method(SBC_fit_to_diagnostics,stanfit)
 S3method(SBC_fit_to_draws_matrix,CmdStanMCMC)
-S3method(SBC_fit_to_draws_matrix,CmdStanMLE)
 S3method(SBC_fit_to_draws_matrix,CmdStanVB)
 S3method(SBC_fit_to_draws_matrix,brmsfit)
 S3method(SBC_fit_to_draws_matrix,default)
@@ -37,7 +35,6 @@ S3method(summary,SBC_nuts_diagnostics)
 S3method(summary,SBC_results)
 export(SBC_backend_brms)
 export(SBC_backend_brms_from_generator)
-export(SBC_backend_cmdstan_optimize)
 export(SBC_backend_cmdstan_sample)
 export(SBC_backend_cmdstan_variational)
 export(SBC_backend_rstan_sample)
diff --git a/R/.Rapp.history b/R/.Rapp.history
new file mode 100644
index 0000000..e69de29
diff --git a/R/backends.R b/R/backends.R
index 450b3c7..7366dbb 100644
--- a/R/backends.R
+++ b/R/backends.R
@@ -280,7 +280,7 @@ SBC_backend_cmdstan_variational <- function(model, ...) {
     stop("The model has to be already compiled, call $compile() first.")
   }
   args <- list(...)
-  unacceptable_params <- c("data", "parallel_chains ", "cores", "num_cores")
+  unacceptable_params <- c("data")
   if(any(names(args) %in% unacceptable_params)) {
     stop(paste0("Parameters ", paste0("'", unacceptable_params, "'", collapse = ", "),
                 " cannot be provided when defining a backend as they need to be set ",
@@ -297,7 +297,7 @@ SBC_fit.SBC_backend_cmdstan_variational <- function(backend, generated, cores) {
                                 data = generated)))
 
   if(all(fit$return_codes() != 0)) {
-    stop("No chains finished succesfully")
+    stop("Variational inference did not finish succesfully")
   }
 
   fit
@@ -309,45 +309,6 @@ SBC_fit_to_draws_matrix.CmdStanVB <- function(fit) {
 
 }
 
-#' Backend based on optimize approximation via `cmdstanr`.
-#'
-#' @param model an object of class `CmdStanModel` (as created by `cmdstanr::cmdstan_model`)
-#' @param ... other arguments passed to the `$optimize()` method of the model. The `data` and
-#'   `parallel_chains` arguments cannot be set this way as they need to be controlled by the SBC
-#'   package.
-#' @export
-SBC_backend_cmdstan_optimize <- function(model, ...) {
-  stop("The optimize method is currently not supported.")
-  stopifnot(inherits(model, "CmdStanModel"))
-  if(length(model$exe_file()) == 0) {
-    stop("The model has to be already compiled, call $compile() first.")
-  }
-  args <- list(...)
-  unacceptable_params <- c("data")
-  if(any(names(args) %in% unacceptable_params)) {
-    stop(paste0("Parameters ", paste0("'", unacceptable_params, "'", collapse = ", "),
-                " cannot be provided when defining a backend as they need to be set ",
-                "by the SBC package"))
-  }
-  structure(list(model = model, args = args), class = "SBC_backend_cmdstan_optimize")
-}
-#' @export
-SBC_fit.SBC_backend_cmdstan_optimize <- function(backend, generated, cores) {
-  fit <- do.call(backend$model$optimize,
-                 combine_args(backend$args,
-                              list(data = generated)))
-
-   if(all(fit$return_codes() != 0)) {
-     stop("Point optimization failed!")
-   }
-
-   fit
-}
-#' @export
-SBC_fit_to_draws_matrix.CmdStanMLE <- function(fit) {
-  fit$draws(format = "draws_matrix")
-}
-
 # For internal use, creates brms backend.
 new_SBC_backend_brms <- function(compiled_model,
   args
diff --git a/R/results.R b/R/results.R
index 0b4ac80..385121b 100644
--- a/R/results.R
+++ b/R/results.R
@@ -212,13 +212,13 @@ length.SBC_results <- function(x) {
 #'
 #' Parallel processing is supported via the `future` package, for most uses, it is most sensible
 #'  to just call `plan(multisession)` once in your R session and  all
-#'  cores your computer has will be used. For more details refer to the documentation
+#'  cores your computer will be used. For more details refer to the documentation
 #'  of the `future` package.
 #'
 #' @param datasets an object of class `SBC_datasets`
 #' @param backend the model + sampling algorithm. The built-in backends can be constructed
-#'   using `SBC_backend_cmdstan_sample()`, `SBC_backend_cmdstan_variational()`,`SBC_backend_cmdstan_optimize()`, `SBC_backend_rstan_sample()` and `SBC_backend_brms()`.
-#'   (more to come). The backend is an S3 class supporting at least the `SBC_fit`,
+#'   using `SBC_backend_cmdstan_sample()`, `SBC_backend_cmdstan_variational()`, `SBC_backend_rstan_sample()` and `SBC_backend_brms()`.
+#'   (more to come: issue 31, 38, 39). The backend is an S3 class supporting at least the `SBC_fit`,
 #'   `SBC_fit_to_draws_matrix` methods.
 #' @param cores_per_fit how many cores should the backend be allowed to use for a single fit?
 #'    Defaults to the maximum number that does not produce more parallel chains
diff --git a/man/SBC_backend_cmdstan_optimize.Rd b/man/SBC_backend_cmdstan_optimize.Rd
deleted file mode 100644
index 6f4d16c..0000000
--- a/man/SBC_backend_cmdstan_optimize.Rd
+++ /dev/null
@@ -1,18 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/backends.R
-\name{SBC_backend_cmdstan_optimize}
-\alias{SBC_backend_cmdstan_optimize}
-\title{Backend based on optimize approximation via \code{cmdstanr}.}
-\usage{
-SBC_backend_cmdstan_optimize(model, ...)
-}
-\arguments{
-\item{model}{an object of class \code{CmdStanModel} (as created by \code{cmdstanr::cmdstan_model})}
-
-\item{...}{other arguments passed to the \verb{$optimize()} method of the model. The \code{data} and
-\code{parallel_chains} arguments cannot be set this way as they need to be controlled by the SBC
-package.}
-}
-\description{
-Backend based on optimize approximation via \code{cmdstanr}.
-}
diff --git a/man/compute_results.Rd b/man/compute_results.Rd
index 5a6aab0..18cffab 100644
--- a/man/compute_results.Rd
+++ b/man/compute_results.Rd
@@ -18,8 +18,8 @@ compute_results(
 \item{datasets}{an object of class \code{SBC_datasets}}
 
 \item{backend}{the model + sampling algorithm. The built-in backends can be constructed
-using \code{SBC_backend_cmdstan_sample()}, \code{SBC_backend_cmdstan_variational()},\code{SBC_backend_cmdstan_optimize()}, \code{SBC_backend_rstan_sample()} and \code{SBC_backend_brms()}.
-(more to come). The backend is an S3 class supporting at least the \code{SBC_fit},
+using \code{SBC_backend_cmdstan_sample()}, \code{SBC_backend_cmdstan_variational()}, \code{SBC_backend_rstan_sample()} and \code{SBC_backend_brms()}.
+(more to come: issue 31, 38, 39). The backend is an S3 class supporting at least the \code{SBC_fit},
 \code{SBC_fit_to_draws_matrix} methods.}
 
 \item{cores_per_fit}{how many cores should the backend be allowed to use for a single fit?
@@ -60,6 +60,6 @@ An object of class \code{SBC_results} that holds:
 \description{
 Parallel processing is supported via the \code{future} package, for most uses, it is most sensible
 to just call \code{plan(multisession)} once in your R session and  all
-cores your computer has will be used. For more details refer to the documentation
+cores your computer will be used. For more details refer to the documentation
 of the \code{future} package.
 }