changes per code review

Author: mitzimorris

src/stan/analyze/mcmc/compute_effective_sample_size.hpp

@@ -31,11 +31,6 @@ namespace analyze {
  * @param sizes stores sizes of chains
  * @return effective sample size for the specified parameter
  */
-#if defined(__GNUC__) || defined(__clang__)
-__attribute__((deprecated))
-#elif defined(_MSC_VER)
-__declspec(deprecated)
-#endif
 inline double
 compute_effective_sample_size(std::vector<const double*> draws,
                               std::vector<size_t> sizes) {
@@ -166,11 +161,6 @@ compute_effective_sample_size(std::vector<const double*> draws,
  * @param size size of chains
  * @return effective sample size for the specified parameter
  */
-#if defined(__GNUC__) || defined(__clang__)
-__attribute__((deprecated))
-#elif defined(_MSC_VER)
-__declspec(deprecated)
-#endif
 inline double
 compute_effective_sample_size(std::vector<const double*> draws, size_t size) {
   int num_chains = draws.size();
@@ -199,11 +189,6 @@ compute_effective_sample_size(std::vector<const double*> draws, size_t size) {
  * @param sizes stores sizes of chains
  * @return effective sample size for the specified parameter
  */
-#if defined(__GNUC__) || defined(__clang__)
-__attribute__((deprecated))
-#elif defined(_MSC_VER)
-__declspec(deprecated)
-#endif
 inline double
 compute_split_effective_sample_size(std::vector<const double*> draws,
                                     std::vector<size_t> sizes) {
@@ -243,11 +228,6 @@ compute_split_effective_sample_size(std::vector<const double*> draws,
  * @param size size of chains
  * @return effective sample size for the specified parameter
  */
-#if defined(__GNUC__) || defined(__clang__)
-__attribute__((deprecated))
-#elif defined(_MSC_VER)
-__declspec(deprecated)
-#endif
 inline double
 compute_split_effective_sample_size(std::vector<const double*> draws,
                                     size_t size) {

src/stan/analyze/mcmc/compute_potential_scale_reduction.hpp

@@ -18,7 +18,7 @@ namespace stan {
 namespace analyze {
 
 /**
- * DEPRECATED - re-implemented as function `rhat`.
+ * \deprecated use `rhat` instead
  *
  * Computes the potential scale reduction (Rhat) for the specified
  * parameter across all kept samples.
@@ -34,11 +34,6 @@ namespace analyze {
  * @param sizes stores sizes of chains
  * @return potential scale reduction for the specified parameter
  */
-#if defined(__GNUC__) || defined(__clang__)
-__attribute__((deprecated))
-#elif defined(_MSC_VER)
-__declspec(deprecated)
-#endif
 inline double
 compute_potential_scale_reduction(std::vector<const double*> draws,
                                   std::vector<size_t> sizes) {
@@ -127,11 +122,6 @@ compute_potential_scale_reduction(std::vector<const double*> draws,
  * @param size stores sizes of chains
  * @return potential scale reduction for the specified parameter
  */
-#if defined(__GNUC__) || defined(__clang__)
-__attribute__((deprecated))
-#elif defined(_MSC_VER)
-__declspec(deprecated)
-#endif
 inline double
 compute_potential_scale_reduction(std::vector<const double*> draws,
                                   size_t size) {
@@ -158,11 +148,6 @@ compute_potential_scale_reduction(std::vector<const double*> draws,
  * @param sizes stores sizes of chains
  * @return potential scale reduction for the specified parameter
  */
-#if defined(__GNUC__) || defined(__clang__)
-__attribute__((deprecated))
-#elif defined(_MSC_VER)
-__declspec(deprecated)
-#endif
 inline double
 compute_split_potential_scale_reduction(std::vector<const double*> draws,
                                         std::vector<size_t> sizes) {
@@ -199,11 +184,6 @@ compute_split_potential_scale_reduction(std::vector<const double*> draws,
  * @param size stores sizes of chains
  * @return potential scale reduction for the specified parameter
  */
-#if defined(__GNUC__) || defined(__clang__)
-__attribute__((deprecated))
-#elif defined(_MSC_VER)
-__declspec(deprecated)
-#endif
 inline double
 compute_split_potential_scale_reduction(std::vector<const double*> draws,
                                         size_t size) {

src/stan/analyze/mcmc/mcse.hpp

@@ -25,9 +25,9 @@ inline double mcse_mean(const Eigen::MatrixXd& chains) {
   if (chains.rows() < 4 || !is_finite_and_varies(chains))
     return std::numeric_limits<double>::quiet_NaN();
 
-  double sd
+  double sample_var
       = (chains.array() - chains.mean()).square().sum() / (chains.size() - 1);
-  return std::sqrt(sd / ess(chains));
+  return std::sqrt(sample_var / ess(chains));
 }
 
 /**