Merge pull request #1255 from borglab/fix/doxygen

INSTALL.md

@@ -50,7 +50,7 @@ will run up to 10x faster in Release mode! See the end of this document for
 additional debugging tips.
 
 3. GTSAM has Doxygen documentation. To generate, run 'make doc' from your
-build directory.
+build directory after setting the `GTSAM_BUILD_DOCS` and `GTSAM_BUILD_[HTML|LATEX]` cmake flags.
 
 4. The instructions below install the library to the default system install path and
 build all components. From a terminal, starting in the root library folder,

doc/CMakeLists.txt

@@ -26,6 +26,7 @@ if (GTSAM_BUILD_DOCS)
         gtsam/basis 
         gtsam/discrete
         gtsam/geometry
+        gtsam/hybrid
         gtsam/inference
         gtsam/linear
         gtsam/navigation
@@ -33,7 +34,6 @@ if (GTSAM_BUILD_DOCS)
         gtsam/sam
         gtsam/sfm
         gtsam/slam
-        gtsam/smart
         gtsam/symbolic
         gtsam
     )
@@ -42,10 +42,12 @@ if (GTSAM_BUILD_DOCS)
     set(gtsam_unstable_doc_subdirs
         gtsam_unstable/base
         gtsam_unstable/discrete
+        gtsam_unstable/dynamics
+        gtsam_unstable/geometry
         gtsam_unstable/linear
-        gtsam_unstable/nonlinear 
-        gtsam_unstable/slam 
-        gtsam_unstable/dynamics 
+        gtsam_unstable/nonlinear
+        gtsam_unstable/partition
+        gtsam_unstable/slam
         gtsam_unstable
     )
     

doc/DoxygenLayout.xml

@@ -18,7 +18,6 @@
       <tab type="files" visible="yes" title="" intro=""/>
       <tab type="globals" visible="yes" title="" intro=""/>
     </tab>
-    <tab type="dirs" visible="yes" title="" intro=""/>
     <tab type="examples" visible="yes" title="" intro=""/>  
   </navindex>
 

gtsam/base/ConcurrentMap.h

@@ -62,7 +62,7 @@ namespace gtsam {
  * convenience to avoid having lengthy types in the code.  Through timing,
  * we've seen that the fast_pool_allocator can lead to speedups of several
  * percent.
- * @addtogroup base
+ * @ingroup base
  */
 template<typename KEY, typename VALUE>
 class ConcurrentMap : public ConcurrentMapBase<KEY,VALUE> {

gtsam/base/DSFMap.h

@@ -28,7 +28,7 @@ namespace gtsam {
 /**
  * Disjoint set forest using an STL map data structure underneath
  * Uses rank compression and union by rank, iterator version
- * @addtogroup base
+ * @ingroup base
  */
 template <class KEY>
 class DSFMap {

gtsam/base/DSFVector.h

@@ -33,7 +33,7 @@ namespace gtsam {
  * A fast implementation of disjoint set forests that uses vector as underly data structure.
  * This is the absolute minimal DSF data structure, and only allows size_t keys
  * Uses rank compression but not union by rank :-(
- * @addtogroup base
+ * @ingroup base
  */
 class GTSAM_EXPORT DSFBase {
 
@@ -59,7 +59,7 @@ public:
 
 /**
  * DSFVector additionally keeps a vector of keys to support more expensive operations
- * @addtogroup base
+ * @ingroup base
  */
 class GTSAM_EXPORT DSFVector: public DSFBase {
 

gtsam/base/FastList.h

@@ -34,7 +34,7 @@ namespace gtsam {
  * convenience to avoid having lengthy types in the code.  Through timing,
  * we've seen that the fast_pool_allocator can lead to speedups of several
  * percent.
-   * @addtogroup base
+   * @ingroup base
  */
 template<typename VALUE>
 class FastList: public std::list<VALUE, typename internal::FastDefaultAllocator<VALUE>::type> {

gtsam/base/FastMap.h

@@ -31,7 +31,7 @@ namespace gtsam {
  * convenience to avoid having lengthy types in the code.  Through timing,
  * we've seen that the fast_pool_allocator can lead to speedups of several
  * percent.
- * @addtogroup base
+ * @ingroup base
  */
 template<typename KEY, typename VALUE>
 class FastMap : public std::map<KEY, VALUE, std::less<KEY>,

gtsam/base/FastSet.h

@@ -43,7 +43,7 @@ namespace gtsam {
  * fast_pool_allocator instead of the default STL allocator.  This is just a
  * convenience to avoid having lengthy types in the code.  Through timing,
  * we've seen that the fast_pool_allocator can lead to speedups of several %.
- * @addtogroup base
+ * @ingroup base
  */
 template<typename VALUE>
 class FastSet: public std::set<VALUE, std::less<VALUE>,

gtsam/base/FastVector.h

@@ -27,7 +27,7 @@ namespace gtsam {
 /**
  * FastVector is a type alias to a std::vector with a custom memory allocator.
  * The particular allocator depends on GTSAM's cmake configuration.
- * @addtogroup base
+ * @ingroup base
  */
 template <typename T>
 using FastVector =

gtsam/base/SymmetricBlockMatrix.h

@@ -47,7 +47,7 @@ namespace gtsam {
   * matrix view.  firstBlock() determines the block that appears to have index 0 for all operations
   * (except re-setting firstBlock()).
   *
-  * @addtogroup base */
+  * @ingroup base */
   class GTSAM_EXPORT SymmetricBlockMatrix
   {
   public:

gtsam/base/Testable.h

@@ -51,7 +51,7 @@ namespace gtsam {
    * tests and in generic algorithms.
    *
    * See macros for details on using this structure
-   * @addtogroup base
+   * @ingroup base
    * @tparam T is the objectype this constrains to be testable - assumes print() and equals()
    */
   template <class T>

gtsam/base/ThreadsafeException.h

@@ -14,7 +14,7 @@
  * @brief    Base exception type that uses tbb_allocator if GTSAM is compiled with TBB
  * @author   Richard Roberts
  * @date     Aug 21, 2010
- * @addtogroup base
+ * @ingroup base
  */
 
 #pragma once

gtsam/base/VerticalBlockMatrix.h

@@ -38,7 +38,7 @@ namespace gtsam {
    * row for all operations.  To include all rows, rowEnd() should be set to the number of rows in
    * the matrix (i.e. one after the last true row index).
    *
-   * @addtogroup base */
+   * @ingroup base */
   class GTSAM_EXPORT VerticalBlockMatrix
   {
   public:

gtsam/base/make_shared.h

@@ -26,7 +26,7 @@
 #include <type_traits>
 
 namespace gtsam {
-  /// An shorthand alias for accessing the ::type inside std::enable_if that can be used in a template directly
+  /// An shorthand alias for accessing the \::type inside std::enable_if that can be used in a template directly
   template<bool B, class T = void>
   using enable_if_t = typename std::enable_if<B, T>::type;
 }

gtsam/base/timing.h

@@ -147,7 +147,7 @@ namespace gtsam {
       size_t id_;
       size_t t_;
       size_t tWall_;
-      double t2_ ; ///< cache the \sum t_i^2
+      double t2_ ; ///< cache the \f$ \sum t_i^2 \f$
       size_t tIt_;
       size_t tMax_;
       size_t tMin_;

gtsam/base/types.cpp

@@ -14,7 +14,7 @@
  * @brief    Functions for handling type information
  * @author   Varun Agrawal
  * @date     May 18, 2020
- * @addtogroup base
+ * @ingroup base
  */
 
 #include <gtsam/base/types.h>

gtsam/base/types.h

@@ -14,7 +14,7 @@
  * @brief    Typedefs for easier changing of types
  * @author   Richard Roberts
  * @date     Aug 21, 2010
- * @addtogroup base
+ * @ingroup base
  */
 
 #pragma once

gtsam/basis/Basis.h

@@ -78,6 +78,8 @@ using Weights = Eigen::Matrix<double, 1, -1>; /* 1xN vector */
  * @tparam M Size of the identity matrix.
  * @param w The weights of the polynomial.
  * @return Mx(M*N) kronecker product [w(0)*I, w(1)*I, ..., w(N-1)*I]
+ *
+ * @ingroup basis
  */
 template <size_t M>
 Matrix kroneckerProductIdentity(const Weights& w) {
@@ -90,7 +92,10 @@ Matrix kroneckerProductIdentity(const Weights& w) {
   return result;
 }
 
-/// CRTP Base class for function bases
+/**
+ * CRTP Base class for function bases
+ *  @ingroup basis
+ */
 template <typename DERIVED>
 class Basis {
  public:

gtsam/basis/BasisFactors.h

@@ -32,6 +32,8 @@ namespace gtsam {
  *
  * Example, degree 8 Chebyshev polynomial measured at x=0.5:
  *  EvaluationFactor<Chebyshev2> factor(key, measured, model, 8, 0.5);
+ *
+ * @ingroup basis
  */
 template <class BASIS>
 class EvaluationFactor : public FunctorizedFactor<double, Vector> {
@@ -86,6 +88,8 @@ class EvaluationFactor : public FunctorizedFactor<double, Vector> {
  *
  * @param BASIS: The basis class to use e.g. Chebyshev2
  * @param M: Size of the evaluated state vector.
+ *
+ * @ingroup basis
  */
 template <class BASIS, int M>
 class VectorEvaluationFactor
@@ -149,6 +153,8 @@ class VectorEvaluationFactor
  *  VectorComponentFactor<BASIS, P> controlPrior(key, measured, model,
  *                                               N, i, t, a, b);
  *  where N is the degree and i is the component index.
+ *
+ * @ingroup basis
  */
 template <class BASIS, size_t P>
 class VectorComponentFactor

gtsam/basis/ParameterMatrix.h

@@ -10,7 +10,7 @@
  * -------------------------------------------------------------------------- */
 
 /**
- * @file ParamaterMatrix.h
+ * @file ParameterMatrix.h
  * @brief Define ParameterMatrix class which is used to store values at
  * interpolation points.
  * @author Varun Agrawal, Frank Dellaert

gtsam/discrete/AlgebraicDecisionTree.h

@@ -31,6 +31,8 @@ namespace gtsam {
    * Algebraic Decision Trees fix the range to double
    * Just has some nice constructors and some syntactic sugar
    * TODO: consider eliminating this class altogether?
+   *
+   * @ingroup discrete
    */
   template <typename L>
   class GTSAM_EXPORT AlgebraicDecisionTree : public DecisionTree<L, double> {

gtsam/discrete/Assignment.h

@@ -31,6 +31,7 @@ namespace gtsam {
  * An assignment from labels to value index (size_t).
  * Assigns to each label a value. Implemented as a simple map.
  * A discrete factor takes an Assignment and returns a value.
+ * @ingroup discrete
  */
 template <class L>
 class Assignment : public std::map<L, size_t> {

gtsam/discrete/DecisionTree.h

@@ -38,6 +38,8 @@ namespace gtsam {
    * Decision Tree
    * L = label for variables
    * Y = function range (any algebra), e.g., bool, int, double
+   *
+   * @ingroup discrete
    */
   template<typename L, typename Y>
   class DecisionTree {

gtsam/discrete/DecisionTreeFactor.h

@@ -36,7 +36,9 @@ namespace gtsam {
   class DiscreteConditional;
 
   /**
-   * A discrete probabilistic factor
+   * A discrete probabilistic factor.
+   *
+   * @ingroup discrete
    */
   class GTSAM_EXPORT DecisionTreeFactor : public DiscreteFactor,
                                           public AlgebraicDecisionTree<Key> {

gtsam/discrete/DiscreteBayesNet.h

@@ -33,7 +33,7 @@ namespace gtsam {
 
 /** 
  * A Bayes net made from discrete conditional distributions. 
- * @addtogroup discrete
+ * @ingroup discrete
  */
 class GTSAM_EXPORT DiscreteBayesNet: public BayesNet<DiscreteConditional> {
  public:

gtsam/discrete/DiscreteBayesTree.h

@@ -62,7 +62,10 @@ class GTSAM_EXPORT DiscreteBayesTreeClique
 };
 
 /* ************************************************************************* */
-/** A Bayes tree representing a Discrete density */
+/**
+ * @brief A Bayes tree representing a Discrete density.
+ * @ingroup discrete
+ */
 class GTSAM_EXPORT DiscreteBayesTree
     : public BayesTree<DiscreteBayesTreeClique> {
  private:

gtsam/discrete/DiscreteConditional.h

@@ -32,6 +32,8 @@ namespace gtsam {
 /**
  * Discrete Conditional Density
  * Derives from DecisionTreeFactor
+ *
+ * @ingroup discrete
  */
 class GTSAM_EXPORT DiscreteConditional
     : public DecisionTreeFactor,

gtsam/discrete/DiscreteDistribution.h

@@ -27,6 +27,8 @@ namespace gtsam {
 /**
  * A prior probability on a set of discrete variables.
  * Derives from DiscreteConditional
+ *
+ * @ingroup discrete
  */
 class GTSAM_EXPORT DiscreteDistribution : public DiscreteConditional {
  public:

gtsam/discrete/DiscreteEliminationTree.h

@@ -24,6 +24,10 @@
 
 namespace gtsam {
 
+  /**
+   * @brief Elimination tree for discrete factors.
+   * @ingroup discrete
+   */
   class GTSAM_EXPORT DiscreteEliminationTree :
     public EliminationTree<DiscreteBayesNet, DiscreteFactorGraph>
   {

gtsam/discrete/DiscreteFactor.h

@@ -31,6 +31,8 @@ class DiscreteConditional;
 /**
  * Base class for discrete probabilistic factors
  * The most general one is the derived DecisionTreeFactor
+ *
+ * @ingroup discrete
  */
 class GTSAM_EXPORT DiscreteFactor: public Factor {
 

gtsam/discrete/DiscreteFactorGraph.h

@@ -40,7 +40,14 @@ class DiscreteEliminationTree;
 class DiscreteBayesTree;
 class DiscreteJunctionTree;
 
-/** Main elimination function for DiscreteFactorGraph */
+/**
+ * @brief Main elimination function for DiscreteFactorGraph.
+ * 
+ * @param factors 
+ * @param keys 
+ * @return GTSAM_EXPORT
+ * @ingroup discrete
+ */
 GTSAM_EXPORT std::pair<boost::shared_ptr<DiscreteConditional>, DecisionTreeFactor::shared_ptr>
 EliminateDiscrete(const DiscreteFactorGraph& factors, const Ordering& keys);
 
@@ -64,6 +71,7 @@ template<> struct EliminationTraits<DiscreteFactorGraph>
 /**
  * A Discrete Factor Graph is a factor graph where all factors are Discrete, i.e.
  *   Factor == DiscreteFactor
+ * @ingroup discrete
  */
 class GTSAM_EXPORT DiscreteFactorGraph
     : public FactorGraph<DiscreteFactor>,

gtsam/discrete/DiscreteJunctionTree.h

@@ -44,7 +44,8 @@ namespace gtsam {
    * The tree structure and elimination method are exactly analogous to the EliminationTree,
    * except that in the JunctionTree, at each node multiple variables are eliminated at a time.
    *
-   * \addtogroup Multifrontal
+   * \ingroup Multifrontal
+   * @ingroup discrete
    * \nosubgrouping
    */
   class GTSAM_EXPORT DiscreteJunctionTree :

gtsam/discrete/DiscreteKey.h

@@ -31,6 +31,7 @@ namespace gtsam {
   /**
    * Key type for discrete variables.
    * Includes Key and cardinality.
+   * @ingroup discrete
    */
   using DiscreteKey = std::pair<Key,size_t>;
 

gtsam/discrete/DiscreteLookupDAG.h

@@ -32,6 +32,7 @@ class DiscreteBayesNet;
 
 /**
  * @brief DiscreteLookupTable table for max-product
+ * @ingroup discrete
  *
  * Inherits from discrete conditional for convenience, but is not normalized.
  * Is used in the max-product algorithm.

gtsam/discrete/DiscreteMarginals.h

@@ -28,6 +28,7 @@ namespace gtsam {
 
   /**
    * A class for computing marginals of variables in a DiscreteFactorGraph
+   * @ingroup discrete
    */
 class DiscreteMarginals {
 

gtsam/discrete/DiscreteValues.h

@@ -36,6 +36,7 @@ namespace gtsam {
  * Another good thing is we don't need to have the special DiscreteKey which
  * stores cardinality of a Discrete variable. It should be handled naturally in
  * the new class DiscreteValue, as the variable's type (domain)
+ * @ingroup discrete
  */
 class GTSAM_EXPORT DiscreteValues : public Assignment<Key> {
  public:

gtsam/discrete/Signature.h

@@ -48,6 +48,8 @@ namespace gtsam {
    *   (E|T,L) = "F F F 1"
    *   X|E = "95/5 2/98"
    *   (D|E,B) = "9/1 2/8 3/7 1/9"
+   *
+   * @ingroup discrete
    */
   class GTSAM_EXPORT Signature {
 

gtsam/geometry/Cal3.h

@@ -16,7 +16,7 @@
  */
 
 /**
- * @addtogroup geometry
+ * @ingroup geometry
  */
 
 #pragma once
@@ -63,7 +63,7 @@ void calibrateJacobians(const Cal& calibration, const Point2& pn,
 
 /**
  * @brief Common base class for all calibration models.
- * @addtogroup geometry
+ * @ingroup geometry
  * \nosubgrouping
  */
 class GTSAM_EXPORT Cal3 {

gtsam/geometry/Cal3Bundler.h

@@ -26,7 +26,7 @@ namespace gtsam {
 
 /**
  * @brief Calibration used by Bundler
- * @addtogroup geometry
+ * @ingroup geometry
  * \nosubgrouping
  */
 class GTSAM_EXPORT Cal3Bundler : public Cal3 {

gtsam/geometry/Cal3DS2.h

@@ -29,7 +29,7 @@ namespace gtsam {
  * @brief Calibration of a camera with radial distortion that also supports
  * Lie-group behaviors for optimization.
  * \sa Cal3DS2_Base
- * @addtogroup geometry
+ * @ingroup geometry
  * \nosubgrouping
  */
 class GTSAM_EXPORT Cal3DS2 : public Cal3DS2_Base {

gtsam/geometry/Cal3DS2_Base.h

@@ -27,7 +27,7 @@ namespace gtsam {
 
 /**
  * @brief Calibration of a camera with radial distortion
- * @addtogroup geometry
+ * @ingroup geometry
  * \nosubgrouping
  *
  * Uses same distortionmodel as OpenCV, with

gtsam/geometry/Cal3Fisheye.h

@@ -30,7 +30,7 @@ namespace gtsam {
 
 /**
  * @brief Calibration of a fisheye camera
- * @addtogroup geometry
+ * @ingroup geometry
  * \nosubgrouping
  *
  * Uses same distortionmodel as OpenCV, with

gtsam/geometry/Cal3Unified.h

@@ -18,7 +18,7 @@
  */
 
 /**
- * @addtogroup geometry
+ * @ingroup geometry
  */
 
 #pragma once
@@ -30,7 +30,7 @@ namespace gtsam {
 /**
  * @brief Calibration of a omni-directional camera with mirror + lens radial
  * distortion
- * @addtogroup geometry
+ * @ingroup geometry
  * \nosubgrouping
  *
  * Similar to Cal3DS2, does distortion but has additional mirror parameter xi

gtsam/geometry/Cal3_S2.h

@@ -16,7 +16,7 @@
  */
 
 /**
- * @addtogroup geometry
+ * @ingroup geometry
  */
 
 #pragma once
@@ -28,7 +28,7 @@ namespace gtsam {
 
 /**
  * @brief The most common 5DOF 3D->2D calibration
- * @addtogroup geometry
+ * @ingroup geometry
  * \nosubgrouping
  */
 class GTSAM_EXPORT Cal3_S2 : public Cal3 {

gtsam/geometry/Cal3_S2Stereo.h

@@ -24,7 +24,7 @@ namespace gtsam {
 
 /**
  * @brief The most common 5DOF 3D->2D calibration, stereo version
- * @addtogroup geometry
+ * @ingroup geometry
  * \nosubgrouping
  */
 class GTSAM_EXPORT Cal3_S2Stereo : public Cal3_S2 {
@@ -38,7 +38,7 @@ class GTSAM_EXPORT Cal3_S2Stereo : public Cal3_S2 {
   using shared_ptr = boost::shared_ptr<Cal3_S2Stereo>;
 
   /// @name Standard Constructors
-  /// @
+  /// @{
 
   /// default calibration leaves coordinates unchanged
   Cal3_S2Stereo() = default;
@@ -55,6 +55,8 @@ class GTSAM_EXPORT Cal3_S2Stereo : public Cal3_S2 {
   Cal3_S2Stereo(double fov, int w, int h, double b)
       : Cal3_S2(fov, w, h), b_(b) {}
 
+  /// @}
+
   /**
    * Convert intrinsic coordinates xy to image coordinates uv, fixed derivaitves
    * @param p point in intrinsic coordinates
@@ -82,7 +84,6 @@ class GTSAM_EXPORT Cal3_S2Stereo : public Cal3_S2 {
    */
   Vector3 calibrate(const Vector3& p) const { return Cal3_S2::calibrate(p); }
 
-  /// @}
   /// @name Testable
   /// @{
 

gtsam/geometry/CalibratedCamera.h

@@ -46,7 +46,7 @@ private:
 
 /**
  * A pinhole camera class that has a Pose3, functions as base class for all pinhole cameras
- * @addtogroup geometry
+ * @ingroup geometry
  * \nosubgrouping
  */
 class GTSAM_EXPORT PinholeBase {
@@ -241,7 +241,7 @@ private:
  * A Calibrated camera class [R|-R't], calibration K=I.
  * If calibration is known, it is more computationally efficient
  * to calibrate the measurements rather than try to predict in pixels.
- * @addtogroup geometry
+ * @ingroup geometry
  * \nosubgrouping
  */
 class GTSAM_EXPORT CalibratedCamera: public PinholeBase {

gtsam/geometry/Line3.h

@@ -38,7 +38,7 @@ GTSAM_EXPORT Line3 transformTo(const Pose3 &wTc, const Line3 &wL,
 
 /**
  * A 3D line (R,a,b) : (Rot3,Scalar,Scalar)
- * @addtogroup geometry
+ * @ingroup geometry
  * \nosubgrouping
  */
 class GTSAM_EXPORT Line3 {

gtsam/geometry/OrientedPlane3.h

@@ -133,8 +133,6 @@ public:
   inline double distance() const {
     return d_;
   }
-
-  /// @}
 };
 
 template<> struct traits<OrientedPlane3> : public internal::Manifold<

gtsam/geometry/PinholeCamera.h

@@ -26,7 +26,7 @@ namespace gtsam {
 /**
  * A pinhole camera class that has a Pose3 and a Calibration.
  * Use PinholePose if you will not be optimizing for Calibration
- * @addtogroup geometry
+ * @ingroup geometry
  * \nosubgrouping
  */
 template<typename Calibration>

gtsam/geometry/PinholePose.h

@@ -27,7 +27,7 @@ namespace gtsam {
 
 /**
  * A pinhole camera class that has a Pose3 and a *fixed* Calibration.
- * @addtogroup geometry
+ * @ingroup geometry
  * \nosubgrouping
  */
 template<typename CALIBRATION>
@@ -236,7 +236,7 @@ public:
  * A pinhole camera class that has a Pose3 and a *fixed* Calibration.
  * Instead of using this class, one might consider calibrating the measurements
  * and using CalibratedCamera, which would then be faster.
- * @addtogroup geometry
+ * @ingroup geometry
  * \nosubgrouping
  */
 template<typename CALIBRATION>

gtsam/geometry/Pose2.h

@@ -30,7 +30,7 @@ namespace gtsam {
 
 /**
  * A 2D pose (Point2,Rot2)
- * @addtogroup geometry
+ * @ingroup geometry
  * \nosubgrouping
  */
 class Pose2: public LieGroup<Pose2, 3> {

gtsam/geometry/Pose3.cpp

@@ -27,7 +27,6 @@
 namespace gtsam {
 
 using std::vector;
-using Point3Pairs = vector<Point3Pair>;
 
 /** instantiate concept checks */
 GTSAM_CONCEPT_POSE_INST(Pose3)

gtsam/geometry/Pose3.h

@@ -31,7 +31,7 @@ class Pose2;
 
 /**
  * A 3D pose (R,t) : (Rot3,Point3)
- * @addtogroup geometry
+ * @ingroup geometry
  * \nosubgrouping
  */
 class GTSAM_EXPORT Pose3: public LieGroup<Pose3, 6> {
@@ -83,7 +83,7 @@ public:
    *  A pose aTb is estimated between pairs (a_point, b_point) such that a_point = aTb * b_point
    *  Note this allows for noise on the points but in that case the mapping will not be exact.
    */
-  static boost::optional<Pose3> Align(const std::vector<Point3Pair>& abPointPairs);
+  static boost::optional<Pose3> Align(const Point3Pairs& abPointPairs);
 
   // Version of Pose3::Align that takes 2 matrices.
   static boost::optional<Pose3> Align(const Matrix& a, const Matrix& b);

gtsam/geometry/Rot2.h

@@ -30,7 +30,7 @@ namespace gtsam {
   /**
    * Rotation matrix
    * NOTE: the angle theta is in radians unless explicitly stated
-   * @addtogroup geometry
+   * @ingroup geometry
    * \nosubgrouping
    */
   class GTSAM_EXPORT Rot2 : public LieGroup<Rot2, 1> {
@@ -86,7 +86,7 @@ namespace gtsam {
     static Rot2 atan2(double y, double x);
 
     /**
-     * Random, generates random angle \in [-p,pi]
+     * Random, generates random angle \f$\in\f$ [-pi,pi]
      * Example:
      *   std::mt19937 engine(42);
      *   Unit3 unit = Unit3::Random(engine);

gtsam/geometry/Rot3.h

@@ -53,7 +53,7 @@ namespace gtsam {
  * @brief Rot3 is a 3D rotation represented as a rotation matrix if the
  * preprocessor symbol GTSAM_USE_QUATERNIONS is not defined, or as a quaternion
  * if it is defined.
- * @addtogroup geometry
+ * @ingroup geometry
  */
 class GTSAM_EXPORT Rot3 : public LieGroup<Rot3, 3> {
  private:
@@ -129,7 +129,7 @@ class GTSAM_EXPORT Rot3 : public LieGroup<Rot3, 3> {
     Rot3(double w, double x, double y, double z) : Rot3(Quaternion(w, x, y, z)) {}
 
     /**
-     * Random, generates a random axis, then random angle \in [-p,pi]
+     * Random, generates a random axis, then random angle \f$\in\f$ [-pi,pi]
      * Example:
      *   std::mt19937 engine(42);
      *   Unit3 unit = Unit3::Random(engine);

gtsam/geometry/SO4.h

@@ -74,7 +74,7 @@ GTSAM_EXPORT Matrix3 topLeft(const SO4 &Q, OptionalJacobian<9, 6> H = boost::non
 
 /**
  * Project to Stiefel manifold of 4*3 orthonormal 3-frames in R^4, i.e., pi(Q)
- * -> S \in St(3,4).
+ * -> \f$ S \in St(3,4) \f$.
  */
 GTSAM_EXPORT Matrix43 stiefel(const SO4 &Q, OptionalJacobian<12, 6> H = boost::none);
 

gtsam/geometry/SOn.h

@@ -121,7 +121,8 @@ class SO : public LieGroup<SO<N>, internal::DimensionSO(N)> {
   /// currently only defined for SO3.
   static SO ClosestTo(const MatrixNN& M);
 
-  /// Named constructor that finds chordal mean = argmin_R \sum sqr(|R-R_i|_F),
+  /// Named constructor that finds chordal mean
+  /// \f$ mu = argmin_R \sum sqr(|R-R_i|_F) \f$,
   /// currently only defined for SO3.
   static SO ChordalMean(const std::vector<SO>& rotations);
 

gtsam/geometry/Similarity2.h

@@ -132,7 +132,7 @@ class GTSAM_EXPORT Similarity2 : public LieGroup<Similarity2, 4> {
    * using the algorithm described here:
    * http://www5.informatik.uni-erlangen.de/Forschung/Publikationen/2005/Zinsser05-PSR.pdf
    */
-  static Similarity2 Align(const std::vector<Pose2Pair>& abPosePairs);
+  static Similarity2 Align(const Pose2Pairs& abPosePairs);
 
   /// @}
   /// @name Lie Group

gtsam/geometry/Similarity3.h

@@ -120,7 +120,7 @@ class GTSAM_EXPORT Similarity3 : public LieGroup<Similarity3, 7> {
   /**
    *  Create Similarity3 by aligning at least three point pairs
    */
-  static Similarity3 Align(const std::vector<Point3Pair>& abPointPairs);
+  static Similarity3 Align(const Point3Pairs& abPointPairs);
 
   /**
    * Create the Similarity3 object that aligns at least two pose pairs.

gtsam/geometry/SphericalCamera.h

@@ -34,7 +34,7 @@ namespace gtsam {
  * Empty calibration. Only needed to play well with other cameras
  * (e.g., when templating functions wrt cameras), since other cameras
  * have constuctors in the form ‘camera(pose,calibration)’
- * @addtogroup geometry
+ * @ingroup geometry
  * \nosubgrouping
  */
 class GTSAM_EXPORT EmptyCal {
@@ -64,7 +64,7 @@ class GTSAM_EXPORT EmptyCal {
 /**
  * A spherical camera class that has a Pose3 and measures bearing vectors.
  * The camera has an ‘Empty’ calibration and the only 6 dof are the pose
- * @addtogroup geometry
+ * @ingroup geometry
  * \nosubgrouping
  */
 class GTSAM_EXPORT SphericalCamera {
@@ -82,7 +82,6 @@ class GTSAM_EXPORT SphericalCamera {
   EmptyCal::shared_ptr emptyCal_;
 
  public:
-  /// @}
   /// @name Standard Constructors
   /// @{
 

gtsam/geometry/StereoCamera.h

@@ -42,7 +42,7 @@ private:
 
 /**
  * A stereo camera class, parameterize by left camera pose and stereo calibration
- * @addtogroup geometry
+ * @ingroup geometry
  */
 class GTSAM_EXPORT StereoCamera {
 

gtsam/geometry/StereoPoint2.h

@@ -26,7 +26,7 @@ namespace gtsam {
 
 /**
  * A 2D stereo point, v will be same for rectified images
- * @addtogroup geometry
+ * @ingroup geometry
  * \nosubgrouping
  */
 class GTSAM_EXPORT StereoPoint2 {

gtsam/global_includes.h

@@ -13,7 +13,7 @@
  * @file     global_includes.h
  * @brief    Included from all GTSAM files
  * @author   Richard Roberts
- * @addtogroup base
+ * @ingroup base
  */
 
 #pragma once

gtsam/groups.dox

@@ -1,7 +1,7 @@
 /**
 
 \defgroup LinearSolving Solving of sparse linear systems with least-squares
-@{
+@{ @}
 
 \defgroup Multifrontal Solving by multifrontal variable elimination (QR and Cholesky)
 @{ @}
@@ -9,9 +9,48 @@
 \defgroup Sequential Solving by sequential variable elimination (QR and Cholesky)
 @{ @}
 
-@}
-
-\defgroup SLAM Useful SLAM components
+\defgroup base Base
 @{ @}
 
-*/
+\defgroup basis Basis
+@{ @}
+
+\defgroup discrete Discrete
+@{ @}
+
+\defgroup geometry Geometry
+@{
+  Geometric primitives.
+@}
+
+\defgroup hybrid Hybrid
+@{ @}
+
+\defgroup inference Inference
+@{ @}
+
+\defgroup linear Linear
+@{ @}
+
+\defgroup navigation Navigation
+@{ @}
+
+\defgroup nonlinear Nonlinear
+@{ @}
+
+\defgroup sam SAM
+@{ @}
+
+\defgroup sfm SFM
+@{ @}
+
+\defgroup slam SLAM
+@{ Useful SLAM components @}
+
+\defgroup symbolic Symbolic
+@{ @}
+
+\defgroup isam2 ISAM2
+@{ @}
+
+*/ 

gtsam/hybrid/GaussianMixture.h

@@ -45,6 +45,7 @@ namespace gtsam {
  * where i indexes the components and k_i is a component-wise normalization
  * constant.
  *
+ * @ingroup hybrid
  */
 class GTSAM_EXPORT GaussianMixture
     : public HybridFactor,

gtsam/hybrid/GaussianMixtureFactor.h

@@ -40,6 +40,7 @@ using GaussianFactorVector = std::vector<gtsam::GaussianFactor::shared_ptr>;
  * Represents the underlying Gaussian Mixture as a Decision Tree, where the set
  * of discrete variables indexes to the continuous gaussian distribution.
  *
+ * @ingroup hybrid
  */
 class GTSAM_EXPORT GaussianMixtureFactor : public HybridFactor {
  public:

gtsam/hybrid/HybridBayesNet.h

@@ -29,6 +29,8 @@ namespace gtsam {
 /**
  * A hybrid Bayes net is a collection of HybridConditionals, which can have
  * discrete conditionals, Gaussian mixtures, or pure Gaussian conditionals.
+ *
+ * @ingroup hybrid
  */
 class GTSAM_EXPORT HybridBayesNet : public BayesNet<HybridConditional> {
  public:

gtsam/hybrid/HybridBayesTree.h

@@ -34,8 +34,11 @@ class HybridConditional;
 class VectorValues;
 
 /* ************************************************************************* */
-/** A clique in a HybridBayesTree
+/**
+ * @brief A clique in a HybridBayesTree
  * which is a HybridConditional internally.
+ *
+ * @ingroup hybrid
  */
 class GTSAM_EXPORT HybridBayesTreeClique
     : public BayesTreeCliqueBase<HybridBayesTreeClique,

gtsam/hybrid/HybridConditional.h

@@ -54,6 +54,8 @@ namespace gtsam {
  *
  * A great reference to the type-erasure pattern is Eduaado Madrid's CppCon
  * talk (https://www.youtube.com/watch?v=s082Qmd_nHs).
+ *
+ * @ingroup hybrid
  */
 class GTSAM_EXPORT HybridConditional
     : public HybridFactor,

gtsam/hybrid/HybridDiscreteFactor.h

@@ -28,6 +28,8 @@ namespace gtsam {
  * A HybridDiscreteFactor is a thin container for DiscreteFactor, which allows
  * us to hide the implementation of DiscreteFactor and thus avoid diamond
  * inheritance.
+ *
+ * @ingroup hybrid
  */
 class GTSAM_EXPORT HybridDiscreteFactor : public HybridFactor {
  private:

gtsam/hybrid/HybridEliminationTree.h

@@ -25,6 +25,8 @@ namespace gtsam {
 
 /**
  * Elimination Tree type for Hybrid
+ *
+ * @ingroup hybrid
  */
 class GTSAM_EXPORT HybridEliminationTree
     : public EliminationTree<HybridBayesNet, HybridGaussianFactorGraph> {

gtsam/hybrid/HybridFactor.h

@@ -40,6 +40,8 @@ DiscreteKeys CollectDiscreteKeys(const DiscreteKeys &key1,
  *  - HybridDiscreteFactor
  *  - GaussianMixtureFactor
  *  - GaussianMixture
+ *
+ * @ingroup hybrid
  */
 class GTSAM_EXPORT HybridFactor : public Factor {
  private:

gtsam/hybrid/HybridGaussianFactor.h

@@ -27,6 +27,8 @@ namespace gtsam {
  * A HybridGaussianFactor is a layer over GaussianFactor so that we do not have
  * a diamond inheritance i.e. an extra factor type that inherits from both
  * HybridFactor and GaussianFactor.
+ *
+ * @ingroup hybrid
  */
 class GTSAM_EXPORT HybridGaussianFactor : public HybridFactor {
  private:

gtsam/hybrid/HybridGaussianFactorGraph.h

@@ -39,7 +39,14 @@ class DecisionTreeFactor;
 
 class JacobianFactor;
 
-/** Main elimination function for HybridGaussianFactorGraph */
+/**
+ * @brief Main elimination function for HybridGaussianFactorGraph.
+ * 
+ * @param factors The factor graph to eliminate.
+ * @param keys The elimination ordering.
+ * @return The conditional on the ordering keys and the remaining factors.
+ * @ingroup hybrid
+ */
 GTSAM_EXPORT
 std::pair<boost::shared_ptr<HybridConditional>, HybridFactor::shared_ptr>
 EliminateHybrid(const HybridGaussianFactorGraph& factors, const Ordering& keys);
@@ -68,10 +75,12 @@ struct EliminationTraits<HybridGaussianFactorGraph> {
 };
 
 /**
- * Gaussian Hybrid Factor Graph
+ * Hybrid Gaussian Factor Graph
  * -----------------------
  * This is the linearized version of a hybrid factor graph.
  * Everything inside needs to be hybrid factor or hybrid conditional.
+ *
+ * @ingroup hybrid
  */
 class GTSAM_EXPORT HybridGaussianFactorGraph
     : public HybridFactorGraph,
@@ -120,13 +129,13 @@ class GTSAM_EXPORT HybridGaussianFactorGraph
   void add(JacobianFactor&& factor);
 
   /// Add a Jacobian factor as a shared ptr.
-  void add(boost::shared_ptr<JacobianFactor> factor);
+  void add(JacobianFactor::shared_ptr factor);
 
   /// Add a DecisionTreeFactor to the factor graph.
   void add(DecisionTreeFactor&& factor);
 
   /// Add a DecisionTreeFactor as a shared ptr.
-  void add(boost::shared_ptr<DecisionTreeFactor> factor);
+  void add(DecisionTreeFactor::shared_ptr factor);
 
   /**
    * Add a gaussian factor *pointer* to the internal gaussian factor graph

gtsam/hybrid/HybridGaussianISAM.h

@@ -26,6 +26,11 @@
 
 namespace gtsam {
 
+/**
+ * @brief 
+ *
+ * @ingroup hybrid
+ */
 class GTSAM_EXPORT HybridGaussianISAM : public ISAM<HybridBayesTree> {
  public:
   typedef ISAM<HybridBayesTree> Base;

gtsam/hybrid/HybridJunctionTree.h

@@ -45,7 +45,8 @@ class HybridEliminationTree;
  * EliminationTree, except that in the JunctionTree, at each node multiple
  * variables are eliminated at a time.
  *
- * \addtogroup Multifrontal
+ * \ingroup Multifrontal
+ * \ingroup hybrid
  * \nosubgrouping
  */
 class GTSAM_EXPORT HybridJunctionTree

gtsam/inference/BayesNet.h

@@ -27,7 +27,7 @@ namespace gtsam {
 
 /**
  * A BayesNet is a tree of conditionals, stored in elimination order.
- * @addtogroup inference
+ * @ingroup inference
  */
 template <class CONDITIONAL>
 class BayesNet : public FactorGraph<CONDITIONAL> {

gtsam/inference/BayesTree-inst.h

@@ -10,7 +10,7 @@
  * -------------------------------------------------------------------------- */
 
 /**
- * @file    BayesTree-inl.h
+ * @file    BayesTree-inst.h
  * @brief   Bayes Tree is a tree of cliques of a Bayes Chain
  * @author  Frank Dellaert
  * @author  Michael Kaess

gtsam/inference/BayesTree.h

@@ -59,7 +59,7 @@ namespace gtsam {
    * @tparam CLIQUE The type of the clique data structure, defaults to BayesTreeClique, normally do not change this
    * as it is only used when developing special versions of BayesTree, e.g. for ISAM2.
    *
-   * \addtogroup Multifrontal
+   * \ingroup Multifrontal
    * \nosubgrouping
    */
   template<class CLIQUE>

gtsam/inference/ClusterTree-inst.h

@@ -1,5 +1,5 @@
 /**
- * @file EliminatableClusterTree-inst.h
+ * @file ClusterTree-inst.h
  * @date Oct 8, 2013
  * @author Kai Ni
  * @author Richard Roberts

gtsam/inference/ClusterTree.h

@@ -1,5 +1,5 @@
 /**
- * @file EliminatableClusterTree.h
+ * @file ClusterTree.h
  * @date Oct 8, 2013
  * @author Kai Ni
  * @author Richard Roberts
@@ -139,7 +139,6 @@ class ClusterTree {
              const KeyFormatter& keyFormatter = DefaultKeyFormatter) const;
 
   /// @}
-
   /// @name Advanced Interface
   /// @{
 
@@ -169,6 +168,7 @@ class ClusterTree {
 
  protected:
   /// @name Details
+  /// @{
 
   /// Assignment operator - makes a deep copy of the tree structure, but only pointers to factors
   /// are copied, factors are not cloned.
@@ -236,6 +236,7 @@ class EliminatableClusterTree : public ClusterTree<GRAPH> {
 
  protected:
   /// @name Details
+  /// @{
 
   /// Assignment operator - makes a deep copy of the tree structure, but only pointers to factors
   /// are copied, factors are not cloned.

gtsam/inference/DotWriter.h

@@ -30,7 +30,7 @@ namespace gtsam {
 
 /**
  * @brief DotWriter is a helper class for writing graphviz .dot files.
- * @addtogroup inference
+ * @ingroup inference
  */
 struct GTSAM_EXPORT DotWriter {
   double figureWidthInches;   ///< The figure width on paper in inches

gtsam/inference/EliminationTree-inst.h

@@ -10,7 +10,7 @@
 * -------------------------------------------------------------------------- */
 
 /**
-* @file    EliminationTree-inl.h
+* @file    EliminationTree-inst.h
 * @author  Frank Dellaert
 * @author  Richard Roberts
 * @date    Oct 13, 2010

gtsam/inference/FactorGraph-inst.h

@@ -10,7 +10,7 @@
  * -------------------------------------------------------------------------- */
 
 /**
- * @file   FactorGraph-inl.h
+ * @file   FactorGraph-inst.h
  * @brief  Factor Graph Base Class
  * @author Carlos Nieto
  * @author Frank Dellaert

gtsam/inference/ISAM-inst.h

@@ -10,7 +10,7 @@
  * -------------------------------------------------------------------------- */
 
 /**
- * @file    ISAM-inl.h
+ * @file    ISAM-inst.h
  * @brief   Incremental update functionality (iSAM) for BayesTree.
  * @author  Michael Kaess
  */

gtsam/inference/JunctionTree.h

@@ -43,7 +43,7 @@ namespace gtsam {
    * The tree structure and elimination method are exactly analagous to the EliminationTree,
    * except that in the JunctionTree, at each node multiple variables are eliminated at a time.
    *
-   * \addtogroup Multifrontal
+   * \ingroup Multifrontal
    * \nosubgrouping
    */
   template<class BAYESTREE, class GRAPH>

gtsam/inference/Ordering.h

@@ -89,7 +89,8 @@ public:
    */
   FastMap<Key, size_t> invert() const;
 
-  /// @name Fill-reducing Orderings @{
+  /// @name Fill-reducing Orderings
+  /// @{
 
   /// Compute a fill-reducing ordering using COLAMD from a factor graph (see details for note on
   /// performance). This internally builds a VariableIndex so if you already have a VariableIndex,
@@ -215,7 +216,8 @@ public:
 
   /// @}
 
-  /// @name Named Constructors @{
+  /// @name Named Constructors
+  /// @{
 
   template<class FACTOR_GRAPH>
   static Ordering Create(OrderingType orderingType,
@@ -241,7 +243,8 @@ public:
 
   /// @}
 
-  /// @name Testable @{
+  /// @name Testable
+  /// @{
 
   GTSAM_EXPORT
   void print(const std::string& str = "", const KeyFormatter& keyFormatter =

gtsam/linear/AcceleratedPowerMethod.h

@@ -74,8 +74,8 @@ class AcceleratedPowerMethod : public PowerMethod<Operator> {
 
   /**
    * Run accelerated power iteration to get ritzVector with beta and previous
-   * two ritzVector x0 and x00, and return y = (A * x0 - \beta * x00) / || A * x0
-   * - \beta * x00 ||
+   * two ritzVector x0 and x00, and return 
+   *   \f$y = (A * x0 - \beta * x00) / || A * x0 - \beta * x00 ||\f$
    */
   Vector acceleratedPowerIteration (const Vector &x1, const Vector &x0,
                         const double beta) const {
@@ -86,8 +86,8 @@ class AcceleratedPowerMethod : public PowerMethod<Operator> {
 
   /**
    * Run accelerated power iteration to get ritzVector with beta and previous
-   * two ritzVector x0 and x00, and return y = (A * x0 - \beta * x00) / || A * x0
-   * - \beta * x00 ||
+   * two ritzVector x0 and x00, and return
+   *  \f$y = (A * x0 - \beta * x00) / || A * x0 - \beta * x00 ||\f$
    */
   Vector acceleratedPowerIteration () const {
     Vector y = acceleratedPowerIteration(this->ritzVector_, previousVector_, beta_);

gtsam/linear/GaussianBayesNet.h

@@ -30,7 +30,7 @@ namespace gtsam {
 
   /** 
    * GaussianBayesNet is a Bayes net made from linear-Gaussian conditionals.
-   * @addtogroup linear
+   * @ingroup linear
    */
   class GTSAM_EXPORT GaussianBayesNet: public BayesNet<GaussianConditional>
   {

gtsam/linear/GaussianConditional.h

@@ -35,7 +35,7 @@ namespace gtsam {
   * A GaussianConditional functions as the node in a Bayes network.
   * It has a set of parents y,z, etc. and implements a probability density on x.
   * The negative log-probability is given by \f$ \frac{1}{2} |Rx - (d - Sy - Tz - ...)|^2 \f$
-  * @addtogroup linear
+  * @ingroup linear
   */
   class GTSAM_EXPORT GaussianConditional :
     public JacobianFactor,

gtsam/linear/GaussianDensity.h

@@ -27,7 +27,7 @@ namespace gtsam {
   * A GaussianDensity is a GaussianConditional without parents.
   * The negative log-probability is given by \f$ |Rx - d|^2 \f$
   * with \f$ \Lambda = \Sigma^{-1} = R^T R \f$ and \f$ \mu = R^{-1} d \f$
-  * @addtogroup linear
+  * @ingroup linear
   */
   class GTSAM_EXPORT GaussianDensity : public GaussianConditional {
 

gtsam/linear/GaussianJunctionTree.h

@@ -32,7 +32,7 @@ namespace gtsam {
    * factors stored in each cluster. It can be eliminated into a Gaussian Bayes tree with the same
    * structure, which is essentially doing multifrontal sparse matrix factorization.
    *
-   * \addtogroup Multifrontal
+   * \ingroup Multifrontal
    * \nosubgrouping
    */
   class GTSAM_EXPORT GaussianJunctionTree :

gtsam/linear/HessianFactor.h

@@ -338,7 +338,7 @@ namespace gtsam {
 
     /**
      * Compute the gradient at a key:
-     *      \grad f(x_i) = \sum_j G_ij*x_j - g_i
+     *  \f$ \grad f(x_i) = \sum_j G_ij*x_j - g_i \f$
      */
     Vector gradient(Key key, const VectorValues& x) const override;
 
@@ -385,7 +385,7 @@ namespace gtsam {
 *   @param keys The variables to eliminate and their elimination ordering
 *   @return The conditional and remaining factor
 *
-*   \addtogroup LinearSolving */
+*   \ingroup LinearSolving */
 GTSAM_EXPORT std::pair<boost::shared_ptr<GaussianConditional>, boost::shared_ptr<HessianFactor> >
   EliminateCholesky(const GaussianFactorGraph& factors, const Ordering& keys);
 
@@ -403,7 +403,7 @@ GTSAM_EXPORT std::pair<boost::shared_ptr<GaussianConditional>, boost::shared_ptr
 *   @param keys The variables to eliminate and their elimination ordering
 *   @return The conditional and remaining factor
 *
-*   \addtogroup LinearSolving */
+*   \ingroup LinearSolving */
 GTSAM_EXPORT std::pair<boost::shared_ptr<GaussianConditional>, boost::shared_ptr<GaussianFactor> >
   EliminatePreferCholesky(const GaussianFactorGraph& factors, const Ordering& keys);
 

gtsam/linear/JacobianFactor.h

@@ -365,7 +365,7 @@ namespace gtsam {
      * @param keys The variables to eliminate in the order as specified here in \c keys
      * @return The conditional and remaining factor
      *
-     * \addtogroup LinearSolving */
+     * \ingroup LinearSolving */
     friend GTSAM_EXPORT std::pair<boost::shared_ptr<GaussianConditional>, shared_ptr>
       EliminateQR(const GaussianFactorGraph& factors, const Ordering& keys);
 

gtsam/linear/VectorValues.h

@@ -69,7 +69,7 @@ namespace gtsam {
    * which is a view on the underlying data structure.
    *
    * This class is additionally used in gradient descent and dog leg to store the gradient.
-   * @addtogroup linear
+   * @ingroup linear
    */
   class GTSAM_EXPORT VectorValues {
    protected:

gtsam/mainpage.dox

@@ -5,6 +5,12 @@ namespace gtsam {
 
 \mainpage GTSAM
 
+\subpage GTSAM
+
+\subpage GTSAM_UNSTABLE
+
+\page GTSAM
+
 \section new_factor_variable_types Creating new factor and variable types
 
 GTSAM comes with a set of variable and factor types typically used in SFM and

gtsam/navigation/AttitudeFactor.h

@@ -10,7 +10,7 @@
  * -------------------------------------------------------------------------- */
 
 /**
- *  @file   Pose3AttitudeFactor.h
+ *  @file   AttitudeFactor.h
  *  @author Frank Dellaert
  *  @brief  Header file for Attitude factor
  *  @date   January 28, 2014
@@ -29,7 +29,7 @@ namespace gtsam {
  * - measurement is direction of gravity in body frame bF
  * - reference is direction of gravity in navigation frame nG
  * This factor will give zero error if nRb * bF == nG
- * @addtogroup Navigation
+ * @ingroup navigation
  */
 class AttitudeFactor {
 
@@ -74,7 +74,7 @@ public:
 
 /**
  * Version of AttitudeFactor for Rot3
- * @addtogroup Navigation
+ * @ingroup navigation
  */
 class GTSAM_EXPORT Rot3AttitudeFactor: public NoiseModelFactor1<Rot3>, public AttitudeFactor {
 
@@ -147,7 +147,7 @@ template<> struct traits<Rot3AttitudeFactor> : public Testable<Rot3AttitudeFacto
 
 /**
  * Version of AttitudeFactor for Pose3
- * @addtogroup Navigation
+ * @ingroup navigation
  */
 class GTSAM_EXPORT Pose3AttitudeFactor: public NoiseModelFactor1<Pose3>,
     public AttitudeFactor {

gtsam/navigation/BarometricFactor.h

@@ -29,7 +29,7 @@ namespace gtsam {
  * Model with a slowly moving bias to capture differences
  * between the height and the standard atmosphere
  * https://www.grc.nasa.gov/www/k-12/airplane/atmosmet.html
- * @addtogroup Navigation
+ * @ingroup navigation
  */
 class GTSAM_EXPORT BarometricFactor : public NoiseModelFactor2<Pose3, double> {
    private: