Add robust evaluation of the relative risk function (#54)

* add absolute value to robustify the log relative risk evaluation

* update license and installation

LICENSE

@@ -1,6 +1,6 @@
 BSD 2-Clause License
 
-Copyright (c) 2020, IHME Math Sciences
+Copyright (c) 2023, IHME Math Sciences
 All rights reserved.
 
 Redistribution and use in source and binary forms, with or without

pyproject.toml

@@ -1,3 +1,22 @@
 [build-system]
 requires = ["setuptools"]
-build-backend = "setuptools.build_meta"
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "mrtool"
+version = "0.1.3"
+description = "Featured nonlinear mixed effects model"
+readme = "README.rst"
+requires-python = ">=3.10"
+license = { file = "LICENSE" }
+authors = [
+    { name = "IHME Math Sciences", email = "[email protected]" },
+]
+dependencies = ["numpy", "pandas", "scipy", "xspline", "xarray", "limetr==0.0.6"]
+
+[project.optional-dependencies]
+dev = ["pytest", "pytest-mock"]
+doc = ["sphinx", "sphinx-autodoc-typehints", "furo"]
+
+[project.urls]
+github = "https://github.com/ihmeuw-msca/mrtool"

src/mrtool/core/utils.py

@@ -463,14 +463,16 @@ def mat_to_log_fun(alt_mat, ref_mat=None, add_one=True):
     else:
         if ref_mat is None or ref_mat.size == 0:
             def fun(beta):
-                return np.log(shift + alt_mat.dot(beta))
+                alt_val = np.abs(shift + alt_mat.dot(beta))
+                return np.log(alt_val)
 
             def jac_fun(beta):
                 return alt_mat/(shift + alt_mat.dot(beta)[:, None])
         else:
             def fun(beta):
-                return np.log(shift + alt_mat.dot(beta)) - \
-                       np.log(shift + ref_mat.dot(beta))
+                alt_val = np.abs(shift + alt_mat.dot(beta))
+                ref_val = np.abs(shift + ref_mat.dot(beta))
+                return np.log(alt_val) - np.log(ref_val)
 
             def jac_fun(beta):
                 return alt_mat/(shift + alt_mat.dot(beta)[:, None]) - \