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this should fix the braces warnings from r-devel
stan-dev · Jan 22, 2024 · bfb0358 · bfb0358
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diff --git a/rstan/rstan/man/stan_plot_diagnostics.Rd b/rstan/rstan/man/stan_plot_diagnostics.Rd
@@ -65,19 +65,19 @@
   plots \code{stan_diag} should generate:
 
   \itemize{
-    \item{\code{information='sample'}}{Histograms of \code{lp__} 
+    \item \code{information='sample'} Histograms of \code{lp__} 
       and \code{accept_stat}, as well as a scatterplot showing their 
-      joint distribution.}
-    \item{\code{information='stepsize'}}{Violin plots showing the 
+      joint distribution.
+    \item \code{information='stepsize'} Violin plots showing the 
       distributions of \code{lp__} and \code{accept_stat} at each of the sampled
-      step sizes (one per chain).}
-    \item{\code{information='treedepth'}}{Histogram of \code{treedepth} and 
+      step sizes (one per chain).
+    \item \code{information='treedepth'} Histogram of \code{treedepth} and 
       violin plots showing the distributions of \code{lp__} and 
-      \code{accept_stat} for each value of \code{treedepth}.}
-    \item{\code{information='divergence'}}{Violin plots showing the 
+      \code{accept_stat} for each value of \code{treedepth}.
+    \item \code{information='divergence'} Violin plots showing the 
       distributions of \code{lp__} and \code{accept_stat} for iterations that
       encountered divergent transitions (\code{divergent=1}) and those that
-      did not (\code{divergent=0}).}
+      did not (\code{divergent=0}).
     }
   }
 }

diff --git a/rstan/rstan/man/stanfit-method-extract.Rd b/rstan/rstan/man/stanfit-method-extract.Rd
@@ -15,7 +15,7 @@
 
 \section{Methods}{
   \describe{
-    \item{extract}{\code{signature(object = "stanfit")}}{
+    \item{extract}{\code{signature(object = "stanfit")}
     Extract samples from a fitted model represented by an instance of class 
     \code{\linkS4class{stanfit}}.  
     }

diff --git a/rstan/rstan/man/stanfit-method-logprob.Rd b/rstan/rstan/man/stanfit-method-logprob.Rd
@@ -37,24 +37,24 @@
 
 \section{Methods}{
   \describe{
-    \item{log_prob}{\code{signature(object = "stanfit")}}{
+    \item{log_prob}{\code{signature(object = "stanfit")}
       Compute \code{lp__}, the log posterior (up to an additive constant)
       for the model represented by a \code{stanfit} object. Note that,
       by default, \code{log_prob} returns the log posterior in the 
       \emph{unconstrained} space Stan works in internally.
       set \code{adjust_transform = FALSE} to make the values match Stan's output.
     }
-    \item{grad_log_prob}{\code{signature(object = "stanfit")}}{Compute the gradients
+    \item{grad_log_prob}{\code{signature(object = "stanfit")} Compute the gradients
       for \code{log_prob} as well as the log posterior. The latter is returned as 
       an attribute. 
     }
-    \item{get_num_upars}{\code{signature(object = "stanfit")}}{Get the number
+    \item{get_num_upars}{\code{signature(object = "stanfit")} Get the number
       of unconstrained parameters.
     } 
-    \item{constrain_pars}{\code{signature(object = "stanfit")}}{Convert values
+    \item{constrain_pars}{\code{signature(object = "stanfit")} Convert values
       of the parameter from unconstrained space (given as a vector) to their
       constrained space (returned as a named list).}
-    \item{unconstrain_pars}{\code{signature(object = "stanfit")}}{Contrary to
+    \item{unconstrain_pars}{\code{signature(object = "stanfit")} Contrary to
       \code{constrained}, conert values of the parameters from constrained
       to unconstrained space.
     }

diff --git a/rstan/rstan/man/stanfit-method-traceplot.Rd b/rstan/rstan/man/stanfit-method-traceplot.Rd
@@ -16,7 +16,7 @@
 
 \section{Methods}{
   \describe{
-    \item{traceplot}{\code{signature(object = "stanfit")}}{Plot the sampling paths for all chains.}
+    \item{traceplot}{\code{signature(object = "stanfit")} Plot the sampling paths for all chains.}
   }
 }
 

diff --git a/rstan/rstan/man/stanmodel-method-gqs.Rd b/rstan/rstan/man/stanmodel-method-gqs.Rd
@@ -16,7 +16,7 @@
 
 \section{Methods}{
   \describe{
-    \item{\code{object}}{\code{signature(object = "stanmodel")}}{
+    \item{\code{object}}{\code{signature(object = "stanmodel")} 
       Evaluate the generated quantities block of a Stan program
       by supplying \code{data} and the \code{draws} output from a
       previous Stan program.

diff --git a/rstan/rstan/man/stanmodel-method-optimizing.Rd b/rstan/rstan/man/stanmodel-method-optimizing.Rd
@@ -21,8 +21,7 @@
 
 \section{Methods}{
   \describe{
-    \item{optimizing}{\code{signature(object = "stanmodel")}}{
-      %%  ~~describe this method here~~
+    \item{optimizing}{\code{signature(object = "stanmodel")}
       Call Stan's optimization methods to obtain a point estimate 
       for the model defined by S4 class \code{stanmodel} 
       given the data, initial values, etc. 

diff --git a/rstan/rstan/man/stanmodel-method-sampling.Rd b/rstan/rstan/man/stanmodel-method-sampling.Rd
@@ -25,8 +25,7 @@
 
 \section{Methods}{
   \describe{
-    \item{\code{sampling}}{\code{signature(object = "stanmodel")}}{
-      %%  ~~describe this method here~~
+    \item{\code{sampling}}{\code{signature(object = "stanmodel")}
       Call a sampler (NUTS, HMC, or Fixed_param depending on parameters) 
       to draw samples from the model defined by S4 class \code{stanmodel} 
       given the data, initial values, etc. 

diff --git a/rstan/rstan/man/stanmodel-method-vb.Rd b/rstan/rstan/man/stanmodel-method-vb.Rd
@@ -26,8 +26,7 @@
 
 \section{Methods}{
   \describe{
-    \item{vb}{\code{signature(object = "stanmodel")}}{
-      %%  ~~describe this method here~~
+    \item{vb}{\code{signature(object = "stanmodel")}
       Call Stan's variational Bayes methods
       for the model defined by S4 class \code{stanmodel} 
       given the data, initial values, etc.