Merge pull request #256 from mach3-software/feature_credits

tidy: Doxygen Credits

Diagnostics/CombineMaCh3Chains.cpp

@@ -11,6 +11,10 @@
 // MaCh3 includes
 #include "manager/manager.h"
 
+/// @file CombineMaCh3Chains
+/// @author Ewan Miller
+/// @author Kamil Skwarczynski
+
 std::string OutFileName = "";
 int targetCompression = 1;
 std::vector<std::string> inpFileList;

covariance/PCAHandler.h

@@ -26,6 +26,7 @@
 
 /// @brief Class responsible for handling Principal Component Analysis (PCA) of covariance matrix
 /// @see For more details, visit the [Wiki](https://github.com/mach3-software/MaCh3/wiki/03.-Eigen-Decomposition-%E2%80%90-PCA).
+/// @author Clarence Wret
 class PCAHandler{
  public:
 

covariance/covarianceXsec.h

@@ -6,6 +6,9 @@
 
 /// @brief Class responsible for handling of systematic error parameters with different types defined in the config. Like spline, normalisation parameters etc.
 /// @see For more details, visit the [Wiki](https://github.com/mach3-software/MaCh3/wiki/02.-Implementation-of-Systematic).
+/// @author Dan Barrow
+/// @author Ed Atkin
+/// @author Kamil Skwarczynski
 class covarianceXsec : public covarianceBase {
   public:
     /// @brief Constructor

manager/MaCh3Modes.h

@@ -30,6 +30,7 @@ struct MaCh3ModeInfo {
 
 /// @brief KS: Class describing MaCh3 modes used in the analysis, it is being initialised from config
 /// @see For more details, visit the [Wiki](https://github.com/mach3-software/MaCh3/wiki/08.-MaCh3-Modes).
+/// @author Kamil Skwarczynski
 class MaCh3Modes {
  public:
   /// @brief KS: Initialise MaCh3 modes

manager/manager.h

@@ -13,6 +13,8 @@ class TFile;
 
 /// @brief The manager class is responsible for managing configurations and settings.
 /// @see For more details, visit the [Wiki](https://github.com/mach3-software/MaCh3/wiki/01.-Manager-and-config-handling).
+/// @author Ed Atkin
+/// @author Kamil Skwarczynski
 class manager {
 public:
   /// @brief Constructs a manager object with the specified file name.

mcmc/MCMCProcessor.h

@@ -60,6 +60,8 @@ enum ParameterEnum {
 /// @brief Class responsible for processing MCMC chains, performing diagnostics, generating plots, and managing Bayesian analysis.
 /// @details This class provides utilities to handle MCMC output generated by mcmc::runMCMC. It is particularly useful for extracting values from previous MCMC runs and initiating new MCMC runs with those values. Inspired by nd280_utils/DrawComp.cpp.
 /// @see For more details and examples, visit the [Wiki](https://github.com/mach3-software/MaCh3/wiki/09.-Bayesian-Analysis,-Plotting-and-MCMC-Processor).
+/// @author Clarence Wret
+/// @author Kamil Skwarczynski
 class MCMCProcessor {
   public:
     /// @brief Constructs an MCMCProcessor object with the specified input file and options.
@@ -80,7 +82,8 @@ class MCMCProcessor {
     /// @param Mute Allow silencing many messages, especially important if we calculate matrix many times
     void MakeCovariance_MP(const bool Mute = false);
     /// @brief Make and Draw SubOptimality
-    /// \cite roberts2009adaptive
+    /// @cite roberts2009adaptive
+    /// @author Henry Wallace
     void MakeSubOptimality(const int NIntervals = 10);
 
     /// @brief Reset 2D posteriors, in case we would like to calculate in again with different BurnInCut
@@ -307,6 +310,7 @@ class MCMCProcessor {
     /// @brief KS: Calculate autocorrelations supports both OpenMP and CUDA :)
     inline void AutoCorrelation();
     /// @brief MJR: Autocorrelation function using FFT algorithm for extra speed
+    /// @author Michael Reh
     inline void AutoCorrelation_FFT();
     /// @brief KS: calc Effective Sample Size
     /// @param nLags Should be the same nLags as used in AutoCorrelation()
@@ -315,24 +319,25 @@ class MCMCProcessor {
     /// This function computes the Effective Sample Size (ESS) using the autocorrelations
     /// calculated by AutoCorrelation(). Ensure that the parameter nLags here matches
     /// the number of lags used in AutoCorrelation() to obtain accurate results.
-    /// \cite StanManual
-    /// \cite hanson2008mcmc
-    /// \cite gabry2024visual
+    /// @cite StanManual
+    /// @cite hanson2008mcmc
+    /// @cite gabry2024visual
     inline void CalculateESS(const int nLags, const std::vector<std::vector<double>>& LagL);
     /// @brief Get the batched means variance estimation and variable indicating if number of batches is sensible
-    /// \cite chakraborty2019estimating
-    /// \cite rossetti2024batch
+    /// @cite chakraborty2019estimating
+    /// @cite rossetti2024batch
     inline void BatchedAnalysis();
     /// @brief CW: Batched means, literally read from an array and chuck into TH1D
     inline void BatchedMeans();
     /// @brief Geweke Diagnostic based on the methods described by Fang (2014) and Karlsbakk (2011).
-    /// \cite Fang2014GewekeDiagnostics
-    /// \cite karlsbakk2011
+    /// @cite Fang2014GewekeDiagnostics
+    /// @cite karlsbakk2011
     inline void GewekeDiagnostic();
     /// @brief Acceptance Probability
     inline void AcceptanceProbabilities();
     /// @brief RC: Perform spectral analysis of MCMC
-    /// \cite Dunkley:2004sv
+    /// @cite Dunkley:2004sv
+    /// @author Richard Calland
     inline void PowerSpectrumAnalysis();
 
     /// Name of MCMC file

mcmc/MinuitFit.h

@@ -9,7 +9,8 @@
 #include "Math/Functor.h"
 
 /// @brief Implementation of Minuit fitting algorithm
-/// \cite James:2004xla
+/// @cite James:2004xla
+/// @author Kamil Skwarczynski
 class MinuitFit : public LikelihoodFit {
  public:
   /// @brief Constructor

mcmc/PSO.h

@@ -11,7 +11,9 @@
 
 /// @brief Class particle - stores the position, velocity and personal best
 /// With functions which move particle and update velocity
-/// @note Created by Emily Ip on 24/2/2023.
+/// @author Emily Ip
+/// @author Mark Scott
+/// @date 24/2/2023
 class particle{
   public:
       particle(){};
@@ -69,7 +71,9 @@ class particle{
  /// @brief Class PSO, consist of a vector of object Class Particle and global best
  /// Takes in the size (number of particle) and number of iteration
  /// functions includes: finding global best, updating velocity, actual minimisation function
-/// @note Created by Emily Ip on 24/2/2023.
+/// @author Emily Ip
+/// @author Mark Scott
+/// @date 24/2/2023
 class PSO : public LikelihoodFit {
   public:
     /// @brief constructor

mcmc/SampleSummary.h

@@ -20,6 +20,8 @@ namespace M3 {
 // *******************
 /// @brief Class to calculate pvalue produce posterior predictive and many fancy Bayesian stuff \cite gelman1996posterior
 /// @details For more information, visit the [Wiki](https://github.com/mach3-software/MaCh3/wiki/10.-Posterior-Predictive,-p%E2%80%90value-etc.).
+/// @author Clarence Wret
+/// @author Kamil Skwarczynski
 class SampleSummary {
 // *******************
   public:

mcmc/StatisticalUtils.h

@@ -14,6 +14,7 @@
 
 /// @file StatisticalUtils.h
 /// @brief Utility functions for statistical interpretations in MaCh3
+/// @author Kamil Skwarczynski
 
 // **************************
 /// @brief  KS: Following H. Jeffreys \cite jeffreys1998theory

mcmc/gpuMCMCProcessorUtils.cuh

@@ -9,6 +9,9 @@
 
 #include "manager/gpuUtils.cuh"
 
+/// @file gpuMCMCProcessorUtils
+/// @author Kamil Skwarczynski
+
 /// @brief KS: Initialiser, here we allocate memory for variables and copy constants
 /// @param ParStep_gpu Parameter value at each step
 /// @param NumeratorSum_gpu Sum used for nominator of autocorrelation calculations

mcmc/mcmc.h

@@ -3,6 +3,7 @@
 #include "mcmc/FitterBase.h"
 
 /// @brief Implementation of MR2T2 algorithm
+/// @author Asher Kaboth
 class mcmc : public FitterBase {
  public:
    /// @brief Constructor

plotting/GetPostfitParamPlots.cpp

@@ -23,6 +23,7 @@
 #include "plottingUtils/plottingUtils.h"
 #include "plottingUtils/plottingManager.h"
 
+/// @file GetPostfitParamPlots
 /// This script generates post-fit parameter plots. The central postfit value is
 /// taken as the Highest Posterior Density (HPD), but can be easily changed to
 /// another method such as Gaussian. Be cautious as parameter names and the number
@@ -34,7 +35,10 @@
 /// ./GetPostfitParamPlots ProcessMCMC_Output1.root <ProcessMCMC_Output2.root> <ProcessMCMC_Output3.root>
 /// ```
 ///
-/// @note Originally written by Clarence, with changes by Will, updates by Kamil, and converted to a generic plotter by Ewan.
+/// @author Clarence Wret
+/// @author Will Parker
+/// @author Kamil Skwarczynski
+/// @author Ewan Miller
 
 //this file has lots of usage of the ROOT plotting interface that only takes floats, turn this warning off for this CU for now
 #pragma GCC diagnostic ignored "-Wfloat-conversion"

plotting/PlotLLH.cpp

@@ -9,6 +9,9 @@
 #pragma GCC diagnostic ignored "-Wfloat-conversion"
 #pragma GCC diagnostic ignored "-Wconversion"
 
+/// @file PlotLLH
+/// @author Ewan Miller
+
 // some options for the plots
 double ratioPlotSplit;
 double yTitleOffset;

plotting/plottingUtils/plottingManager.h

@@ -34,6 +34,7 @@ namespace MaCh3Plotting {
 /// any style options you like from the StyleManager. Also a hopefully not too distant dream is to
 /// wrap this up in python so it is usable in .py scripts to take advantage of nice existing
 /// plotting libraries for e.g. MCMC plotting.
+/// @author Ewan Miller
 class PlottingManager {
 public:
   // EM: cant make these static as std::getenv("MACH3") not known at compile time

plotting/plottingUtils/styleManager.h

@@ -11,6 +11,7 @@
 #include "TStyle.h"
 
 namespace MaCh3Plotting {
+/// @author Ewan Miller
 class StyleManager {
 public:
   /// @brief Constructor

samplePDF/samplePDFFDBase.h

@@ -13,6 +13,8 @@
 class OscillatorBase;
 
 /// @brief Class responsible for handling implementation of samples used in analysis, reweighting and returning LLH
+/// @author Dan Barrow
+/// @author Ed Atkin
 class samplePDFFDBase :  public samplePDFBase
 {
 public:

splines/SplineMonolith.h

@@ -7,6 +7,8 @@ class SMonolithGPU;
 
 /// @brief Even-by-event class calculating response for spline parameters. It is possible to use GPU acceleration
 /// @see For more details, visit the [Wiki](https://github.com/mach3-software/MaCh3/wiki/05.-Splines).
+/// @author Clarence Wret
+/// @author Kamil Skwarczynski
 class SMonolith : public SplineBase {
   public:
     /// @brief Constructor

splines/splineFDBase.h

@@ -9,6 +9,9 @@
 
 /// @brief Bin-by-bin class calculating response for spline parameters.
 /// @see For more details, visit the [Wiki](https://github.com/mach3-software/MaCh3/wiki/05.-Splines).
+/// @author Dan Barrow
+/// @author Ed Atkin
+/// @author Henry Wallace
 class splineFDBase : public SplineBase {
   /// @todo ETA - do all of these functions and members actually need to be public?
   public: