hpvsim 2.2.1__tar.gz → 2.2.6__tar.gz

hpvsim-2.2.6/.github/workflows/pypi_release.yaml

@@ -0,0 +1,38 @@
+name: Publish HPVsim to PyPI (manual)
+
+on:
+  workflow_dispatch:
+  push:
+    tags:
+      - 'v*'
+
+jobs:
+  build-and-publish:
+    name: Build and publish
+    runs-on: ubuntu-latest
+
+    permissions:
+      id-token: write
+      contents: read
+
+    environment:
+      name: pypi
+      url: https://pypi.org/project/hpvsim/
+
+    steps:
+      - name: Check out repository
+        uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.x'
+
+      - name: Install build backend
+        run: python -m pip install build
+
+      - name: Build sdist and wheel
+        run: python -m build
+
+      - name: Publish
+        uses: pypa/gh-action-pypi-publish@release/v1

{hpvsim-2.2.1 → hpvsim-2.2.6}/.github/workflows/tests.yaml

@@ -1,5 +1,7 @@
 name: HPVsim CI tests
 on:
+  workflow_call:
+  workflow_dispatch:
   pull_request:
   schedule:
     - cron: "0 0 * * *"
@@ -12,7 +14,7 @@ jobs:
       fail-fast: false
       max-parallel: 8
       matrix:
-        python-version: [ '3.12' ]
+        python-version: [ '3.13' ]
     name: Install and test
     steps:
       - name: Checkout sources
@@ -23,6 +25,8 @@ jobs:
           architecture: x64
       - name: Install HPVsim
         run:  pip install -e .
+      - name: Download data on first load
+        run: hpvsim-download-data
       - name: Install tests
         working-directory: ./tests
         run: pip install -r requirements.txt

{hpvsim-2.2.1 → hpvsim-2.2.6}/.readthedocs.yaml

@@ -7,9 +7,12 @@ version: 2
 
 # Set the version of Python and other tools you might need
 build:
-  os: ubuntu-20.04
+  os: ubuntu-24.04
   tools:
-    python: "3.9"
+    python: "3.13"
+  jobs:
+    post_install:
+      - hpvsim-download-data
 
 # Build documentation in the docs/ directory with Sphinx
 sphinx:

{hpvsim-2.2.1 → hpvsim-2.2.6}/CHANGELOG.rst

@@ -9,6 +9,36 @@ All notable changes to the codebase are documented in this file. Changes that ma
    :depth: 1
 
 
+Version 2.2.6 (2026-04-17)
+---------------------------
+- Reconcile different copies of repository
+- *Github info* PR `75 <https://github.com/starsimhub/hpvsim/pull/75>`__
+
+
+Version 2.2.5 (2025-10-27)
+---------------------------
+- Small bugfix for campaign vaccination
+- *Github info* PR `689 <https://github.com/starsimhub/hpvsim_orig/pull/689>`__
+
+
+Version 2.2.4 (2025-08-20)
+---------------------------
+- Fixes a bug in analyzer results for cancer by age and HIV status
+- *Github info* PR `687 <https://github.com/starsimhub/hpvsim_orig/pull/687>`__
+
+
+Version 2.2.3 (2025-06-27)
+---------------------------
+- Small bugfixes and changes to HIV module parameterization
+- *Github info* PR `685 <https://github.com/starsimhub/hpvsim_orig/pull/685>`__
+
+
+Version 2.2.2 (2025-06-20)
+---------------------------
+- Bugfix to allow running simulations beyond 2100
+- *Github info* PR `681 <https://github.com/starsimhub/hpvsim_orig/pull/681>`__
+
+
 Version 2.2.1 (2025-05-29)
 ---------------------------
 - Bugfix for running calibrations to prevent interventions being reinitialized

{hpvsim-2.2.1 → hpvsim-2.2.6}/LICENSE

@@ -1,6 +1,6 @@
 MIT License
 
-Copyright (c) 2023-2025 Bill & Melinda Gates Foundation
+Copyright (c) 2023-2026 Gates Foundation
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

{hpvsim-2.2.1/hpvsim.egg-info → hpvsim-2.2.6}/PKG-INFO

@@ -1,12 +1,12 @@
 Metadata-Version: 2.4
 Name: hpvsim
-Version: 2.2.1
+Version: 2.2.6
 Summary: HPVsim: Human Papillomavirus Simulator
 Author: Robyn Stuart, Jamie Cohen, Cliff Kerr, Romesh Abeysuriya, Mariah Boudreau, Daniel Klein, Hao Hu
 Maintainer-email: HPVsim Team <info@hpvsim.org>
 License-Expression: MIT
 Project-URL: Website, https://hpvsim.org
-Project-URL: Source, https://github.com/institutefordiseasemodeling/hpvsim/
+Project-URL: Source, https://github.com/starsimhub/hpvsim/
 Keywords: HPV,human papillomavirus,cervical cancer,agent-based model,disease modeling,simulation
 Classifier: Intended Audience :: Science/Research
 Classifier: Operating System :: OS Independent
@@ -31,6 +31,9 @@ Dynamic: license-file
 Human papillomavirus simulator (HPVsim)
 =======================================
 
+.. image:: https://badgen.net/pypi/v/hpvsim/?color=blue
+ :target: https://pypi.org/project/hpvsim
+
 .. image:: https://github.com/institutefordiseasemodeling/hpvsim/actions/workflows/tests.yaml/badge.svg
     :target: https://github.com/institutefordiseasemodeling/hpvsim/actions/workflows/tests.yaml
     :alt: pipeline status
@@ -62,7 +65,7 @@ HPVsim has been used for analyses in several countries. Academic papers that hav
 Installation
 ------------
 
-The easiest way to install is simply via pip: ``pip install hpvsim``. Alternatively, you can clone this repository, then run ``pip install -e .`` (don't forget the dot!) in this folder to install ``hpvsim`` and its dependencies. This will make ``hpvsim`` available on the Python path. The first time HPVsim is imported, it will automatically download the required data files (~30 MB).
+The easiest way to install is simply via pip: ``pip install hpvsim``. Alternatively, you can clone this repository, then run ``pip install -e .`` (don't forget the dot!) in this folder to install ``hpvsim`` and its dependencies. This will make ``hpvsim`` available on the Python path. The first time HPVsim is imported, it will automatically download the required data files (~30 MB). You can also download the data manually by running ``hpvsim-download-data`` from the terminal.
 
 
 Usage and documentation
@@ -74,7 +77,7 @@ Documentation is available at https://docs.hpvsim.org. Additional usage examples
 Contributing
 ------------
 
-If you wish to contribute, please follow the Starsim style guide at: https://github.com/amath-idm/styleguide. See the code of conduct readme for more information.
+If you wish to contribute, please follow the Starsim style guide at: https://github.com/starsimhub/styleguide. See the code of conduct readme for more information.
 
 
 Disclaimer

{hpvsim-2.2.1 → hpvsim-2.2.6}/README.rst

@@ -1,6 +1,9 @@
 Human papillomavirus simulator (HPVsim)
 =======================================
 
+.. image:: https://badgen.net/pypi/v/hpvsim/?color=blue
+ :target: https://pypi.org/project/hpvsim
+
 .. image:: https://github.com/institutefordiseasemodeling/hpvsim/actions/workflows/tests.yaml/badge.svg
     :target: https://github.com/institutefordiseasemodeling/hpvsim/actions/workflows/tests.yaml
     :alt: pipeline status
@@ -32,7 +35,7 @@ HPVsim has been used for analyses in several countries. Academic papers that hav
 Installation
 ------------
 
-The easiest way to install is simply via pip: ``pip install hpvsim``. Alternatively, you can clone this repository, then run ``pip install -e .`` (don't forget the dot!) in this folder to install ``hpvsim`` and its dependencies. This will make ``hpvsim`` available on the Python path. The first time HPVsim is imported, it will automatically download the required data files (~30 MB).
+The easiest way to install is simply via pip: ``pip install hpvsim``. Alternatively, you can clone this repository, then run ``pip install -e .`` (don't forget the dot!) in this folder to install ``hpvsim`` and its dependencies. This will make ``hpvsim`` available on the Python path. The first time HPVsim is imported, it will automatically download the required data files (~30 MB). You can also download the data manually by running ``hpvsim-download-data`` from the terminal.
 
 
 Usage and documentation
@@ -44,7 +47,7 @@ Documentation is available at https://docs.hpvsim.org. Additional usage examples
 Contributing
 ------------
 
-If you wish to contribute, please follow the Starsim style guide at: https://github.com/amath-idm/styleguide. See the code of conduct readme for more information.
+If you wish to contribute, please follow the Starsim style guide at: https://github.com/starsimhub/styleguide. See the code of conduct readme for more information.
 
 
 Disclaimer

{hpvsim-2.2.1 → hpvsim-2.2.6}/docs/_templates/page.html

@@ -2,15 +2,6 @@
 
 {% set css_files = css_files + ["_static/theme_overrides.css"] %}
 
-{% block htmltitle %}
-{{ super() }}
-
-{% if not READTHEDOCS %}
-<meta name="robots" content="none">
-{% endif %}
-
-{% endblock %}
-
 {% block extrahead %}
 
 <script>(function(w,d,s,l,i){w[l]=w[l]||[];w[l].push({'gtm.start':

{hpvsim-2.2.1 → hpvsim-2.2.6}/docs/conf.py

@@ -101,9 +101,6 @@ html_context = {
     },
     "default_mode": "light",
 }
-# Add any extra paths that contain custom files
-if not on_rtd:
-    html_extra_path = ['robots.txt']
 
 
 # If true, "Created using Sphinx" is shown in the HTML footer. Default is True.

{hpvsim-2.2.1 → hpvsim-2.2.6}/docs/requirements.txt

@@ -6,7 +6,7 @@ pydata-sphinx-theme
 sphinx-design
 readthedocs-sphinx-search
 ipykernel # For tutorials
-nbconvert==7.13.0 # For tutorials; >=7.14 does not work
+nbconvert==7.17.0 # For tutorials; >=7.14 does not work
 nbsphinx # For tutorials
 plantweb
 ipykernel

{hpvsim-2.2.1 → hpvsim-2.2.6}/hpvsim/analysis.py

@@ -785,9 +785,9 @@ class age_results(Analyzer):
                 if rdict.result_type == 'flow':
                     if not rdict.by_genotype:  # Results across all genotypes
                         if rdict.by_hiv:
-                            if rdict.hiv_attr:
+                            if rdict.hiv_attr == 'with':
                                 inds = ((ppl[rdict.date_attr] == sim.t) * (ppl[rdict.attr]) * (ppl['hiv'])).nonzero()[-1]
-                            else:
+                            elif rdict.hiv_attr == 'no':
                                 inds = ((ppl[rdict.date_attr] == sim.t) * (ppl[rdict.attr]) * (~ppl['hiv'])).nonzero()[-1]
                         else:
                             inds = ((ppl[rdict.date_attr] == sim.t) * (ppl[rdict.attr])).nonzero()[-1]
@@ -1111,6 +1111,7 @@ class age_causal_infection(Analyzer):
         if self.start_year is None:
             self.start_year = sim['start']
         self.age_causal = []
+        self.age_cin = []
         self.age_cancer = []
         self.dwelltime = dict()
         for state in ['precin', 'cin', 'total']:
@@ -1127,6 +1128,7 @@ class age_causal_infection(Analyzer):
                 cin_time = (sim.t - date_cin) * sim['dt']
                 total_time = (sim.t - date_exposed) * sim['dt']
                 self.age_causal += (current_age - total_time).tolist()
+                self.age_cin += (current_age - cin_time).tolist()
                 self.age_cancer += current_age.tolist()
                 self.dwelltime['precin'] += hpv_time.tolist()
                 self.dwelltime['cin'] += cin_time.tolist()

{hpvsim-2.2.1 → hpvsim-2.2.6}/hpvsim/calibration.py

@@ -715,6 +715,7 @@ class Calibration(sc.prettyobj):
                     # Set title and labels
                     ax.set_xlabel('Age group')
                     ax.set_title(f'{self.result_args[resname].name}, {date}')
+                    sc.setylim(data=[ydata, modeldf['values']], ax=ax)
                     ax.legend()
                     ax.set_xticks(x, age_labels[resname], rotation=45)
                     plot_count += 1

{hpvsim-2.2.1 → hpvsim-2.2.6}/hpvsim/data/loaders.py

@@ -314,6 +314,8 @@ def get_birth_rates(location=None):
         raise ValueError(errormsg) from E
 
     raw_df = map_entries(birth_rate_data, location)
+    raw_df = raw_df.dropna()
     df = sc.dataframe(raw_df).reset_index().rename(columns={'Time':'year', 'CBR':'cbr'})
+
     return df
 

{hpvsim-2.2.1 → hpvsim-2.2.6}/hpvsim/data/products_dx.csv

@@ -93,6 +93,12 @@ hpv,susceptible,hpv18,inadequate,0
 hpv,susceptible,hi5,positive,0
 hpv,susceptible,hi5,negative,1
 hpv,susceptible,hi5,inadequate,0
+hpv,susceptible,hpv45,positive,0
+hpv,susceptible,hpv45,negative,1
+hpv,susceptible,hpv45,inadequate,0
+hpv,susceptible,hi4,positive,0
+hpv,susceptible,hi4,negative,1
+hpv,susceptible,hi4,inadequate,0
 hpv,susceptible,ohr,positive,0
 hpv,susceptible,ohr,negative,1
 hpv,susceptible,ohr,inadequate,0
@@ -111,6 +117,12 @@ hpv,latent,hpv18,inadequate,0
 hpv,latent,hi5,positive,0
 hpv,latent,hi5,negative,1
 hpv,latent,hi5,inadequate,0
+hpv,latent,hpv45,positive,0
+hpv,latent,hpv45,negative,1
+hpv,latent,hpv45,inadequate,0
+hpv,latent,hi4,positive,0
+hpv,latent,hi4,negative,1
+hpv,latent,hi4,inadequate,0
 hpv,latent,ohr,positive,0
 hpv,latent,ohr,negative,1
 hpv,latent,ohr,inadequate,0
@@ -129,6 +141,12 @@ hpv,precin,hpv18,inadequate,0
 hpv,precin,hi5,positive,0.9
 hpv,precin,hi5,negative,0.1
 hpv,precin,hi5,inadequate,0
+hpv,precin,hpv45,positive,0.9
+hpv,precin,hpv45,negative,0.1
+hpv,precin,hpv45,inadequate,0
+hpv,precin,hi4,positive,0.9
+hpv,precin,hi4,negative,0.1
+hpv,precin,hi4,inadequate,0
 hpv,precin,ohr,positive,0.9
 hpv,precin,ohr,negative,0.1
 hpv,precin,ohr,inadequate,0
@@ -147,6 +165,12 @@ hpv,cin,hpv18,inadequate,0
 hpv,cin,hi5,positive,0.9
 hpv,cin,hi5,negative,0.1
 hpv,cin,hi5,inadequate,0
+hpv,cin,hpv45,positive,0.9
+hpv,cin,hpv45,negative,0.1
+hpv,cin,hpv45,inadequate,0
+hpv,cin,hi4,positive,0.9
+hpv,cin,hi4,negative,0.1
+hpv,cin,hi4,inadequate,0
 hpv,cin,ohr,positive,0.9
 hpv,cin,ohr,negative,0.1
 hpv,cin,ohr,inadequate,0
@@ -165,6 +189,12 @@ hpv,cancerous,hpv18,inadequate,0
 hpv,cancerous,hi5,positive,0.9
 hpv,cancerous,hi5,negative,0.1
 hpv,cancerous,hi5,inadequate,0
+hpv,cancerous,hpv45,positive,0.9
+hpv,cancerous,hpv45,negative,0.1
+hpv,cancerous,hpv45,inadequate,0
+hpv,cancerous,hi4,positive,0.9
+hpv,cancerous,hi4,negative,0.1
+hpv,cancerous,hi4,inadequate,0
 hpv,cancerous,ohr,positive,0.9
 hpv,cancerous,ohr,negative,0.1
 hpv,cancerous,ohr,inadequate,0
@@ -183,6 +213,12 @@ hpv1618,susceptible,hpv18,inadequate,0
 hpv1618,susceptible,hi5,positive,0
 hpv1618,susceptible,hi5,negative,1
 hpv1618,susceptible,hi5,inadequate,0
+hpv1618,susceptible,hpv45,positive,0
+hpv1618,susceptible,hpv45,negative,1
+hpv1618,susceptible,hpv45,inadequate,0
+hpv1618,susceptible,hi4,positive,0
+hpv1618,susceptible,hi4,negative,1
+hpv1618,susceptible,hi4,inadequate,0
 hpv1618,susceptible,ohr,positive,0
 hpv1618,susceptible,ohr,negative,1
 hpv1618,susceptible,ohr,inadequate,0
@@ -201,6 +237,12 @@ hpv1618,latent,hpv18,inadequate,0
 hpv1618,latent,hi5,positive,0
 hpv1618,latent,hi5,negative,1
 hpv1618,latent,hi5,inadequate,0
+hpv1618,latent,hpv45,positive,0
+hpv1618,latent,hpv45,negative,1
+hpv1618,latent,hpv45,inadequate,0
+hpv1618,latent,hi4,positive,0
+hpv1618,latent,hi4,negative,1
+hpv1618,latent,hi4,inadequate,0
 hpv1618,latent,ohr,positive,0
 hpv1618,latent,ohr,negative,1
 hpv1618,latent,ohr,inadequate,0
@@ -219,6 +261,12 @@ hpv1618,precin,hpv18,inadequate,0
 hpv1618,precin,hi5,positive,0
 hpv1618,precin,hi5,negative,1
 hpv1618,precin,hi5,inadequate,0
+hpv1618,precin,hpv45,positive,0
+hpv1618,precin,hpv45,negative,1
+hpv1618,precin,hpv45,inadequate,0
+hpv1618,precin,hi4,positive,0
+hpv1618,precin,hi4,negative,1
+hpv1618,precin,hi4,inadequate,0
 hpv1618,precin,ohr,positive,0
 hpv1618,precin,ohr,negative,1
 hpv1618,precin,ohr,inadequate,0
@@ -237,6 +285,12 @@ hpv1618,cin,hpv18,inadequate,0
 hpv1618,cin,hi5,positive,0
 hpv1618,cin,hi5,negative,1
 hpv1618,cin,hi5,inadequate,0
+hpv1618,cin,hpv45,positive,0
+hpv1618,cin,hpv45,negative,1
+hpv1618,cin,hpv45,inadequate,0
+hpv1618,cin,hi4,positive,0
+hpv1618,cin,hi4,negative,1
+hpv1618,cin,hi4,inadequate,0
 hpv1618,cin,ohr,positive,0
 hpv1618,cin,ohr,negative,1
 hpv1618,cin,ohr,inadequate,0
@@ -255,6 +309,24 @@ hpv1618,cancerous,hpv18,inadequate,0
 hpv1618,cancerous,hrhpv,positive,0
 hpv1618,cancerous,hrhpv,negative,1
 hpv1618,cancerous,hrhpv,inadequate,0
+hpv1618,cancerous,hi5,positive,0
+hpv1618,cancerous,hi5,negative,1
+hpv1618,cancerous,hi5,inadequate,0
+hpv1618,cancerous,hpv45,positive,0
+hpv1618,cancerous,hpv45,negative,1
+hpv1618,cancerous,hpv45,inadequate,0
+hpv1618,cancerous,hi4,positive,0
+hpv1618,cancerous,hi4,negative,1
+hpv1618,cancerous,hi4,inadequate,0
+hpv1618,cancerous,ohr,positive,0
+hpv1618,cancerous,ohr,negative,1
+hpv1618,cancerous,ohr,inadequate,0
+hpv1618,cancerous,hr,positive,0
+hpv1618,cancerous,hr,negative,1
+hpv1618,cancerous,hr,inadequate,0
+hpv1618,cancerous,lr,positive,0
+hpv1618,cancerous,lr,negative,1
+hpv1618,cancerous,lr,inadequate,0
 hpv_type,susceptible,hpv16,positive_1618,0
 hpv_type,susceptible,hpv16,positive_ohr,0
 hpv_type,susceptible,hpv16,negative,1
@@ -267,6 +339,14 @@ hpv_type,susceptible,hi5,positive_1618,0
 hpv_type,susceptible,hi5,positive_ohr,0
 hpv_type,susceptible,hi5,negative,1
 hpv_type,susceptible,hi5,inadequate,0
+hpv_type,susceptible,hpv45,positive_1618,0
+hpv_type,susceptible,hpv45,positive_ohr,0
+hpv_type,susceptible,hpv45,negative,1
+hpv_type,susceptible,hpv45,inadequate,0
+hpv_type,susceptible,hi4,positive_1618,0
+hpv_type,susceptible,hi4,positive_ohr,0
+hpv_type,susceptible,hi4,negative,1
+hpv_type,susceptible,hi4,inadequate,0
 hpv_type,susceptible,ohr,positive_1618,0
 hpv_type,susceptible,ohr,positive_ohr,0
 hpv_type,susceptible,ohr,negative,1
@@ -291,6 +371,14 @@ hpv_type,latent,hi5,positive_1618,0
 hpv_type,latent,hi5,positive_ohr,0
 hpv_type,latent,hi5,negative,1
 hpv_type,latent,hi5,inadequate,0
+hpv_type,latent,hpv45,positive_1618,0
+hpv_type,latent,hpv45,positive_ohr,0
+hpv_type,latent,hpv45,negative,1
+hpv_type,latent,hpv45,inadequate,0
+hpv_type,latent,hi4,positive_1618,0
+hpv_type,latent,hi4,positive_ohr,0
+hpv_type,latent,hi4,negative,1
+hpv_type,latent,hi4,inadequate,0
 hpv_type,latent,ohr,positive_1618,0
 hpv_type,latent,ohr,positive_ohr,0
 hpv_type,latent,ohr,negative,1
@@ -315,6 +403,14 @@ hpv_type,precin,hi5,positive_1618,0
 hpv_type,precin,hi5,positive_ohr,0.9
 hpv_type,precin,hi5,negative,0.1
 hpv_type,precin,hi5,inadequate,0
+hpv_type,precin,hpv45,positive_1618,0
+hpv_type,precin,hpv45,positive_ohr,0.9
+hpv_type,precin,hpv45,negative,0.1
+hpv_type,precin,hpv45,inadequate,0
+hpv_type,precin,hi4,positive_1618,0
+hpv_type,precin,hi4,positive_ohr,0.9
+hpv_type,precin,hi4,negative,0.1
+hpv_type,precin,hi4,inadequate,0
 hpv_type,precin,ohr,positive_1618,0
 hpv_type,precin,ohr,positive_ohr,0.9
 hpv_type,precin,ohr,negative,0.1
@@ -339,6 +435,14 @@ hpv_type,cin,hi5,positive_1618,0
 hpv_type,cin,hi5,positive_ohr,0.9
 hpv_type,cin,hi5,negative,0.1
 hpv_type,cin,hi5,inadequate,0
+hpv_type,cin,hpv45,positive_1618,0
+hpv_type,cin,hpv45,positive_ohr,0.9
+hpv_type,cin,hpv45,negative,0.1
+hpv_type,cin,hpv45,inadequate,0
+hpv_type,cin,hi4,positive_1618,0
+hpv_type,cin,hi4,positive_ohr,0.9
+hpv_type,cin,hi4,negative,0.1
+hpv_type,cin,hi4,inadequate,0
 hpv_type,cin,ohr,positive_1618,0
 hpv_type,cin,ohr,positive_ohr,0.9
 hpv_type,cin,ohr,negative,0.1
@@ -363,6 +467,14 @@ hpv_type,cancerous,hi5,positive_1618,0
 hpv_type,cancerous,hi5,positive_ohr,0.9
 hpv_type,cancerous,hi5,negative,0.1
 hpv_type,cancerous,hi5,inadequate,0
+hpv_type,cancerous,hpv45,positive_1618,0
+hpv_type,cancerous,hpv45,positive_ohr,0.9
+hpv_type,cancerous,hpv45,negative,0.1
+hpv_type,cancerous,hpv45,inadequate,0
+hpv_type,cancerous,hi4,positive_1618,0
+hpv_type,cancerous,hi4,positive_ohr,0.9
+hpv_type,cancerous,hi4,negative,0.1
+hpv_type,cancerous,hi4,inadequate,0
 hpv_type,cancerous,ohr,positive_1618,0
 hpv_type,cancerous,ohr,positive_ohr,0.9
 hpv_type,cancerous,ohr,negative,0.1

{hpvsim-2.2.1 → hpvsim-2.2.6}/hpvsim/data/products_tx.csv

@@ -8,48 +8,64 @@ excision,cancerous,all,0
 txvx1,latent,hpv16,0.01
 txvx1,latent,hpv18,0.01
 txvx1,latent,hi5,0.01
+txvx1,latent,hpv45,0.01
+txvx1,latent,hi4,0.01
 txvx1,latent,ohr,0.01
 txvx1,latent,hr,0.01
 txvx1,latent,lr,0.01
 txvx1,precin,hpv16,0.01
 txvx1,precin,hpv18,0.01
 txvx1,precin,hi5,0.01
+txvx1,precin,hpv45,0.01
+txvx1,precin,hi4,0.01
 txvx1,precin,ohr,0.01
 txvx1,precin,hr,0.01
 txvx1,precin,lr,0.01
 txvx1,cin,hpv16,0.01
 txvx1,cin,hpv18,0.01
 txvx1,cin,hi5,0.01
+txvx1,cin,hpv45,0.01
+txvx1,cin,hi4,0.01
 txvx1,cin,ohr,0.01
 txvx1,cin,hr,0.01
 txvx1,cin,lr,0.01
 txvx1,cancerous,hpv16,0
 txvx1,cancerous,hpv18,0
 txvx1,cancerous,hi5,0
+txvx1,cancerous,hpv45,0
+txvx1,cancerous,hi4,0
 txvx1,cancerous,ohr,0
 txvx1,cancerous,hr,0
 txvx1,cancerous,lr,0
 txvx2,latent,hpv16,0.9
 txvx2,latent,hpv18,0.9
 txvx2,latent,hi5,0.01
+txvx2,latent,hpv45,0.01
+txvx2,latent,hi4,0.01
 txvx2,latent,ohr,0.01
 txvx2,latent,hr,0.01
 txvx2,latent,lr,0.01
 txvx2,precin,hpv16,0.9
 txvx2,precin,hpv18,0.9
 txvx2,precin,hi5,0.01
+txvx2,precin,hpv45,0.01
+txvx2,precin,hi4,0.01
 txvx2,precin,ohr,0.01
 txvx2,precin,hr,0.01
 txvx2,precin,lr,0.01
 txvx2,cin,hpv16,0.5
 txvx2,cin,hpv18,0.5
 txvx2,cin,hi5,0.01
+txvx2,cin,hpv45,0.01
+txvx2,cin,hi4,0.01
 txvx2,cin,ohr,0.01
 txvx2,cin,hr,0.01
 txvx2,cin,lr,0.01
 txvx2,cancerous,hpv16,0
 txvx2,cancerous,hpv18,0
 txvx2,cancerous,hi5,0
+txvx2,cancerous,hpv45,0
+txvx2,cancerous,hi4,0
 txvx2,cancerous,ohr,0
 txvx2,cancerous,hr,0
 txvx2,cancerous,lr,0

{hpvsim-2.2.1 → hpvsim-2.2.6}/hpvsim/data/products_txvx.csv

@@ -2,12 +2,16 @@ name,genotype,rel_imm
 txvx1,hpv16,1
 txvx1,hpv18,1
 txvx1,hi5,0.5
+txvx1,hpv45,0.5
+txvx1,hi4,0.5
 txvx1,ohr,0.5
 txvx1,hr,0.5
 txvx1,lr,0.3
 txvx2,hpv16,1
 txvx2,hpv18,1
 txvx2,hi5,0.5
+txvx2,hpv45,0.5
+txvx2,hi4,0.5
 txvx2,ohr,0.5
 txvx2,hr,0.5
 txvx2,lr,0.3

{hpvsim-2.2.1 → hpvsim-2.2.6}/hpvsim/data/products_vx.csv

@@ -2,18 +2,24 @@ name,genotype,rel_imm
 bivalent,hpv16,1
 bivalent,hpv18,1
 bivalent,hi5,0.5
+bivalent,hpv45,0.5
+bivalent,hi4,0.5
 bivalent,ohr,0.1
 bivalent,hr,0.3
 bivalent,lr,0.3
 quadrivalent,hpv16,1
 quadrivalent,hpv18,1
 quadrivalent,hi5,0.5
+quadrivalent,hpv45,0.5
+quadrivalent,hi4,0.5
 quadrivalent,ohr,0.1
 quadrivalent,hr,0.3
 quadrivalent,lr,1
 nonavalent,hpv16,1
 nonavalent,hpv18,1
 nonavalent,hi5,1
+nonavalent,hpv45,1
+nonavalent,hi4,1
 nonavalent,ohr,0.1
 nonavalent,hr,0.5
 nonavalent,lr,1

{hpvsim-2.2.1 → hpvsim-2.2.6}/hpvsim/hiv.py

@@ -45,15 +45,11 @@ class HIVsim(hpb.ParsObj):
             "rel_reactivation_prob": 3,  # Unused for now
             "model_hiv_death": True,  # whether or not to model HIV mortality. Typically only set to False for testing purposes
             "time_to_hiv_death_shape": 2,  # shape parameter for weibull distribution, based on https://royalsocietypublishing.org/action/downloadSupplement?doi=10.1098%2Frsif.2013.0613&file=rsif20130613supp1.pdf
-            "time_to_hiv_death_scale": lambda a: 21.182
-            - 0.2717
-            * a,  # scale parameter for weibull distribution, based on https://royalsocietypublishing.org/action/downloadSupplement?doi=10.1098%2Frsif.2013.0613&file=rsif20130613supp1.pdf
+            "time_to_hiv_death_scale_pars": dict(m=21.182, b=-0.2717),  # scale parameter for weibull distribution, based on https://royalsocietypublishing.org/action/downloadSupplement?doi=10.1098%2Frsif.2013.0613&file=rsif20130613supp1.pdf
             "hiv_death_adj": 1,
             "cd4_start": dict(dist="normal", par1=594, par2=20),
-            "cd4_trajectory": lambda f: (24.363 - 16.672 * f)
-            ** 2,  # based on https://docs.idmod.org/projects/emod-hiv/en/latest/hiv-model-healthcare-systems.html?highlight=art#art-s-impact-on-cd4-count
-            "cd4_reconstitution": lambda m: 15.584 * m
-            - 0.2113 * m**2,  # growth in CD4 count following ART initiation
+            "cd4_pars": dict(m=24.363, b=-16.672),  # based on https://docs.idmod.org/projects/emod-hiv/en/latest/hiv-model-healthcare-systems.html?highlight=art#art-s-impact-on-cd4-count
+            "cd4_reconstitution_pars": dict(b1=15.584, b2=-0.2113),  # growth in CD4 count following ART initiation
             "art_failure_prob": 0.0,  # Percentage of people on ART who will fail treatment
             "dt_art": 1.0,  # Timestep for art updates (in years)
         }
@@ -63,7 +59,9 @@ class HIVsim(hpb.ParsObj):
         self.init_results(sim)
 
         y = np.linspace(0, 1, 101)
-        cd4_decline = self["hiv_pars"]["cd4_trajectory"](y)
+        # Calculate the CD4 trajectory based on the parameters
+        m, b = self["hiv_pars"]["cd4_pars"]["m"], self["hiv_pars"]["cd4_pars"]["b"]
+        cd4_decline = m + b* y  # CD4 decline trajectory
         self.cd4_decline_diff = np.diff(cd4_decline)
         sim.pars["hiv_pars"]["mortality_rates"] = self.pars["mortality_rates"]
         return
@@ -235,7 +233,8 @@ class HIVsim(hpb.ParsObj):
         shape = self["hiv_pars"]["time_to_hiv_death_shape"]
         dt = people.pars["dt"]
         if self["hiv_pars"]["model_hiv_death"]:
-            scale = self["hiv_pars"]["time_to_hiv_death_scale"](people.age[inds])
+            m, b = self["hiv_pars"]["time_to_hiv_death_scale_pars"]["m"], self["hiv_pars"]["time_to_hiv_death_scale_pars"]["b"]
+            scale = m + b*people.age[inds]
             adjust = self["hiv_pars"]["hiv_death_adj"]
             scale = np.maximum(scale, 0)
             time_to_hiv_death = adjust * weibull_min.rvs(
@@ -300,7 +299,8 @@ class HIVsim(hpb.ParsObj):
             # Now take care of people successfully on ART (CD4 reconstitutes)
             mpy = 12
             months_on_ART = (people.t - people.date_art[art_success_inds]) * mpy
-            cd4_change = self["hiv_pars"]["cd4_reconstitution"](months_on_ART)
+            b1, b2 = self["hiv_pars"]["cd4_reconstitution_pars"]["b1"], self["hiv_pars"]["cd4_reconstitution_pars"]["b2"]
+            cd4_change = b1*months_on_ART + b2*months_on_ART**2
             cd4_change[cd4_change < 0] = 0
             people.cd4[art_success_inds] += cd4_change
 

{hpvsim-2.2.1 → hpvsim-2.2.6}/hpvsim/immunity.py

@@ -212,7 +212,7 @@ def check_immunity(people):
     Now suppose we have 3 people, whose immunity levels are
 
         people.nab_imm = np.array([[0.9, 0.0, 0.0],
-                               [0.0, 0.7, 0.0]])
+                                   [0.0, 0.7, 0.0]])
 
     This indicates that person 1 has a prior HPV16 infection, person 2 has a prior HPV18
     infection, and person 3 has no history of infection.