Update

Author: jchristopherson

examples/CMakeLists.txt

@@ -53,3 +53,9 @@ target_include_directories(lowess_example PUBLIC ${fplot_INCLUDE_DIR})
 add_executable(bootstrap_example bootstrap_example.f90)
 target_link_libraries(bootstrap_example fstats ${fplot_LIBRARY})
 target_include_directories(bootstrap_example PUBLIC ${fplot_INCLUDE_DIR})
+
+# MCMC Example
+add_executable(mcmc_example mcmc_example.f90)
+target_link_libraries(mcmc_example fstats)
+target_link_libraries(mcmc_example ${fplot_LIBRARY})
+target_include_directories(mcmc_example PUBLIC ${fplot_INCLUDE_DIR})

examples/mcmc_example.f90

@@ -0,0 +1,152 @@
+module nl_example
+    use iso_fortran_env
+contains
+    subroutine exfun(x, p, f, stop)
+        ! Arguments
+        real(real64), intent(in) :: x(:), p(:)
+        real(real64), intent(out) :: f(:)
+        logical, intent(out) :: stop
+
+        ! Function
+        f = p(4) * x**3 + p(3) * x**2 + p(2) * x + p(1)
+
+        ! No need to stop
+        stop = .false.
+    end subroutine
+end module
+
+program example
+    use iso_fortran_env
+    use fstats
+    use fplot_core
+    use nl_example
+    implicit none
+
+    ! Local Variables
+    logical :: check
+    integer(int32) :: i, n
+    procedure(regression_function), pointer :: fcn
+    real(real64) :: xp(21), yp(21), mdl(4), ym(21)
+    real(real64), allocatable, dimension(:,:) :: chain
+    type(metropolis_hastings) :: mcmc
+
+    ! Plot Variables
+    type(multiplot) :: plt, pplt
+    class(terminal), pointer :: term
+    type(plot_2d) :: plt1, plt2, plt3, plt4, xyplt
+    type(plot_data_histogram) :: pdh
+    type(plot_data_2d) :: pd
+
+    ! Initialization
+    fcn => exfun
+
+    ! Data to fit
+    xp = [0.0d0, 0.1d0, 0.2d0, 0.3d0, 0.4d0, 0.5d0, 0.6d0, 0.7d0, 0.8d0, &
+        0.9d0, 1.0d0, 1.1d0, 1.2d0, 1.3d0, 1.4d0, 1.5d0, 1.6d0, 1.7d0, &
+        1.8d0, 1.9d0, 2.0d0]
+    yp = [1.216737514d0, 1.250032542d0, 1.305579195d0, 1.040182335d0, &
+        1.751867738d0, 1.109716707d0, 2.018141531d0, 1.992418729d0, &
+        1.807916923d0, 2.078806005d0, 2.698801324d0, 2.644662712d0, &
+        3.412756702d0, 4.406137221d0, 4.567156645d0, 4.999550779d0, &
+        5.652854194d0, 6.784320119d0, 8.307936836d0, 8.395126494d0, &
+        10.30252404d0]
+
+    ! Generate an initial estimate - based upon prior knowledge of the problem
+    mdl = [1.186d0, 0.447d0, -0.12d0, 1.06d0]
+    call random_number(mdl)
+
+    ! Initialize the MH object
+    call mcmc%initialize(fcn, xp, yp, mdl)
+
+    ! Form the Markov chain
+    call mcmc%evaluate(fcn, xp, yp)
+
+    ! Extract the chain and plot
+    chain = mcmc%get_chain()
+    n = mcmc%get_chain_length()
+    print "(AI0)", "Chain Length: ", n
+
+    ! Update the model using the means of each parameter
+    mdl = chain(n,:)
+    call fcn(xp, mdl, ym, check)
+
+    ! Report out the results
+    do i = 1, size(mdl)
+        print "(AI0)", "Parameter ", i
+        print "(AAF10.7)", achar(9), "Value: ", chain(n, i)
+        print "(AAF10.7)", achar(9), "Mean: ", mean(chain(:,i))
+        print "(AAF10.7)", achar(9), "Std. Dev.: ", standard_deviation(chain(:,i))
+    end do
+
+    ! Plot the histograms for each parameter
+    call plt%initialize(2, 2)
+    term => plt%get_terminal()
+    call term%set_window_height(800)
+    call term%set_window_width(1200)
+    call plt1%initialize()
+    call plt2%initialize()
+    call plt3%initialize()
+    call plt4%initialize()
+
+    call plt1%set_title("p_1")
+    call pdh%define_data(chain(:,1))
+    call pdh%set_transparency(0.5)
+    call plt1%push(pdh)
+
+    call plt2%set_title("p_2")
+    call pdh%define_data(chain(:,2))
+    call plt2%push(pdh)
+
+    call plt3%set_title("p_3")
+    call pdh%define_data(chain(:,3))
+    call plt3%push(pdh)
+
+    call plt4%set_title("p_4")
+    call pdh%define_data(chain(:,4))
+    call plt4%push(pdh)
+
+    call plt%set(1, 1, plt1)
+    call plt%set(2, 1, plt2)
+    call plt%set(1, 2, plt3)
+    call plt%set(2, 2, plt4)
+    call plt%draw()
+
+    ! Generate a parameter plot
+    call pplt%initialize(2, 2)
+    term => pplt%get_terminal()
+    call term%set_window_height(800)
+    call term%set_window_width(1200)
+    call plt1%clear_all()
+    call plt2%clear_all()
+    call plt3%clear_all()
+    call plt4%clear_all()
+
+    call pd%define_data(chain(:,1))
+    call plt1%push(pd)
+
+    call pd%define_data(chain(:,2))
+    call plt2%push(pd)
+
+    call pd%define_data(chain(:,3))
+    call plt3%push(pd)
+
+    call pd%define_data(chain(:,4))
+    call plt4%push(pd)
+
+    call pplt%set(1, 1, plt1)
+    call pplt%set(2, 1, plt2)
+    call pplt%set(1, 2, plt3)
+    call pplt%set(2, 2, plt4)
+    call pplt%draw()
+
+    ! Generate an X-Y plot based upon the means of each parameter set
+    call xyplt%initialize()
+    call pd%define_data(xp, ym)
+    call pd%set_line_width(2.0)
+    call xyplt%push(pd)
+    call pd%define_data(xp, yp)
+    call pd%set_draw_line(.false.)
+    call pd%set_draw_markers(.true.)
+    call xyplt%push(pd)
+    call xyplt%draw()
+end program

src/fstats.f90

@@ -15,6 +15,7 @@ module fstats
     use fstats_bootstrap
     use fstats_sampling
     use fstats_smoothing
+    use fstats_mcmc
     implicit none
     private
     public :: distribution
@@ -88,5 +89,8 @@ module fstats
     public :: doe_fit_model
     public :: doe_evaluate_model
     public :: doe_model
+
+    ! FSTATS_MCMC.F90
+    public :: metropolis_hastings
 
 end module

src/fstats_distributions.f90

@@ -908,8 +908,8 @@ pure function mvnd_get_cholesky(this) result(rst)
     ! Process
     integer(int32) :: n
     if (allocated(this%m_cholesky)) then
-        n = size(this%m_cholesky)
-        allocate(rst(n, n), source = this%m_cov)
+        n = size(this%m_cholesky, 1)
+        allocate(rst(n, n), source = this%m_cholesky)
     else
         allocate(rst(0, 0))
     end if