Merge pull request #8 from JoKra1/main

v0.1.24

Author: JoKra1

LICENSE

@@ -2,7 +2,7 @@
 
 ## Description
 
-``mssm`` is a toolbox to estimate Generalized Additive Mixed Models (GAMMs) semi Markov-switching GAMMs (sMs-GAMMs) and sMs Impulse Response GAMMs (sMs-IR-GAMMs). The ``main`` branch is updated frequently to reflect new developments. The ``stable`` branch should reflect the latest releases. if you don't need the newest functionality, you should install from the ``stable`` branch (see below for instructions).
+``mssm`` is a toolbox to estimate Generalized Additive Mixed Models (GAMMs) semi Markov-switching GAMMs (sMs-GAMMs) and sMs Impulse Response GAMMs (sMs-IR-GAMMs). The ``main`` branch is updated frequently to reflect new developments. The ``stable`` branch should reflect the latest releases. If you don't need the newest functionality, you should install from the ``stable`` branch (see below for instructions).
 
 ## Installation
 
@@ -28,8 +28,12 @@ pip install -i https://test.pypi.org/simple/ mssm
 
 ### Building from source
 
-You can also build directly from source. This requires ``conda`` or an installation of [eigen](https://eigen.tuxfamily.org/index.php?title=Main_Page)(``setup.py`` then expects ``eigen`` in "usr/local/include/eigen3". This will probably not work on windows.). Once you have ``conda`` installed,
-[install eigen from conda-forge](https://anaconda.org/conda-forge/eigen). After cloning and navigating into the downloaded repository you can then install via ``pip install . ``.
+You can also build directly from source. This requires ``conda`` or an installation of [eigen](https://eigen.tuxfamily.org/index.php?title=Main_Page) (``setup.py`` then expects ``eigen`` in "usr/local/include/eigen3". This will probably not work on windows - the ``conda`` strategy should.). Once you have ``conda`` installed,
+[install eigen from conda-forge](https://anaconda.org/conda-forge/eigen). After cloning and navigating into the downloaded repository you can then install via:
+
+```
+pip install .
+```
 
 ## To get started
 

README.md

@@ -25,4 +25,6 @@ classifiers = [
 # https://pypi.org/project/setuptools-scm/ - automatic version number based on tag
 dynamic = ["version"]
 
-[tool.setuptools_scm]
+[tool.setuptools_scm]
+# https://github.com/pypa/setuptools_scm/issues/342
+local_scheme = "no-local-version" 

pyproject.toml

@@ -602,7 +602,11 @@ def fit(self,burn_in=100,maxiter_inner=30,m_avg=15,conv_tol=1e-7,extend_lambda=T
                     temp = temp_schedule[iter]
 
                 durs,states,llks = self.__propose_all_states(pool,cov,temp,n_pi,n_TR,s_log_o_probs,dur_log_probs,var_map)
-                states_flat = np.array([st for s in states for st in s],dtype=int)
+
+                if not self.mvar_by is None:
+                    states_flat = np.array([st for s in states for _ in range(len(factor_levels[self.mvar_by])) for st in s],dtype=int)
+                else:
+                    states_flat = np.array([st for s in states for st in s],dtype=int)
 
             ### Convergence control ###
 
@@ -764,7 +768,11 @@ def fit(self,burn_in=100,maxiter_inner=30,m_avg=15,conv_tol=1e-7,extend_lambda=T
         # Now we can decode.
         with mp.Pool(processes=self.cpus) as pool:
             _,states_max,_ = self.__decode_all_states(pool,cov,self.__pi,self.__TR,s_log_o_probs,dur_log_probs,var_map)
-            max_states_flat = np.array([st for s in states_max for st in s],dtype=int)
+
+            if not self.mvar_by is None:
+                max_states_flat = np.array([st for s in states_max for _ in range(len(factor_levels[self.mvar_by])) for st in s],dtype=int)
+            else:
+                max_states_flat = np.array([st for s in states_max for st in s],dtype=int)
 
         return llk_hist,max_states_flat
 

src/mssm/models.py

@@ -28,15 +28,20 @@ def step_fellner_schall_sparse(gInv,emb_SJ,Bps,cCoef,cLam,scale,verbose=False):
   # equal to zero: every coefficient of a term is penalized away. In that
   # case num /denom is not defined so we return directly.
   if denom <= 0: # Prevent overflow
-     return 1e+7
-  nLam = scale * (num / denom) * cLam
-  nLam = max(nLam,1e-7) # Prevent Lambda going to zero
-  nLam = min(nLam,1e+7) # Prevent overflow
+     nLam = 1e+7
+  else:
+     nLam = scale * (num / denom) * cLam
+
+     nLam = max(nLam,1e-7) # Prevent Lambda going to zero
+     nLam = min(nLam,1e+7) # Prevent overflow
 
   if verbose:
    print(f"Num = {(gInv @ emb_SJ).trace()} - {Bps} == {num}\nDenom = {denom}; Lambda = {nLam}")
 
-  return nLam-cLam
+  # Compute lambda delta
+  delta_lam = nLam-cLam
+
+  return delta_lam
 
 def grad_lambda(gInv,emb_SJ,Bps,cCoef,scale):
    # P. Deriv of restricted likelihood with respect to lambda.

src/mssm/src/python/gamm_solvers.py

@@ -218,7 +218,7 @@ def compute_log_probs(n_j,n_obs,has_scale_split,
    if not mvar_by is None:
       # We need to split the s_log_o_probs from every series by the multivariate factor
       # and then sum the log-probs together. This is a strong independence assumption (see Langrock, 2021)
-      n_by_mvar = factor_levels[mvar_by]
+      n_by_mvar = len(factor_levels[mvar_by])
       s_log_o_probs = [s_prob.reshape(n_j,n_by_mvar,-1).sum(axis=1) for s_prob in s_log_o_probs]
 
    return s_log_o_probs,dur_log_probs

src/mssm/src/python/sem.py

@@ -53,7 +53,6 @@ def B_spline_basis(i, cov, state_est, nk, drop_outer_k=False, convolve=False, mi
   # Setup basis with even knot locations.
   # Code based on Eilers, P., & Marx, B. (2010). Splines, knots, and penalties. https://doi.org/10.1002/WICS.125
   # See also: Eilers, P. H. C., & Marx, B. D. (1996). Flexible smoothing with B-splines and penalties. https://doi.org/10.1214/ss/1038425655
-  # However, knot location calculation was adapted to match mgcv (Wood, 2017)
 
   xl = min(cov)
   xr = max(cov)
@@ -64,12 +63,6 @@ def B_spline_basis(i, cov, state_est, nk, drop_outer_k=False, convolve=False, mi
   if not min_c is None:
     xl = min_c
 
-  rg = xr - xl
-
-  # MGCV adjustment.
-  xr += 0.001*rg
-  xl -= 0.001*rg
-
   # ndx is equal to n in Eilers & Marx (2011)
   # So there will be n-1 knots (without expansion)
   # n + 1 + 2*deg knots with expansion