benmaier / tacoma Goto Github PK

Temporal networks in Python. Provides fast tools to analyze temporal contact networks and simulate dynamic processes on them using Gillespie's SSA.

Home Page: http://tacoma.benmaier.org

License: Other

Makefile 0.03% C++ 61.27% Python 31.93% Shell 0.01% CSS 0.15% JavaScript 6.45% HTML 0.16%

networks network-visualization epidemics temporal-networks face2face face-to-face contact-networks

tacoma's Introduction

TemporAl COntact Modeling and Analysis. Provides fast tools to analyze temporal contact networks, produce surrogate networks using qualitative models and simulate Gillespie processes on them. Currently only working on OSX and Linux distributions. No Windows support yet!

Quick example

In order to download the SocioPatterns 'Hypertext 2009'-dataset and visualize it interactively, do the following.

>>> import tacoma as tc
>>> from tacoma.interactive import visualize
>>> temporal_network = tc.download_and_convert_sociopatterns_hypertext_2009()
100% [..............................................................................] 67463 / 67463
>>> visualize(temporal_network, frame_dt = 20)

What is tacoma?

tacoma is a joint C++/Python-package for the modeling and analysis of undirected and unweighted temporal networks, with a focus on (but not limited to) human face-to-face contact networks.

Pros of using tacoma

networks are natively described in continuous time (which includes descriptions in discrete time
two main native formats to describe temporal networks (tc.edge_lists and tc.edge_changes), a third way, a sorted list of on-intervals for each edge called tc.edge_trajectories is available, but algorithms work on the two native formats only
the simple portable file-format .taco as a standardized way to share temporal network data (which is just the data dumped to a .json-file, a simple file format readable from a variety of languages)
easy functions to produce surrogate temporal networks from four different models
easy way to simulate Gillespie (here, epidemic spreading) processes on temporal networks with an implementation of Vestergaard's and Génois's adapted algortihm
easy framework to develop new Gillespie-simulations algorithms on temporal networks
multiple and simple ways to interactively visualize temporal networks
simple functions to manipulate temporal networks (slice, concatenate, rescale time, sample, bin, convert)
simple functions to analyze structural and statistical properties of temporal networks (mean degree, degree distribution, group size distribution, group life time distributions, etc.)
fast algorithms due to C++-core (fast as in faster than pure Python)
relatively fast and easy to compile since it only depends on the C++11-stdlib and pybind11 without the large overhead of Boost

Cons of using tacoma

no support for directed temporal networks yet
no support for weighted temporal networks yet

Install

If you get compiling errors, make sure that pybind11 is installed.

$ git clone https://github.com/benmaier/tacoma
$ pip install ./tacoma

Note that a C++11-compiler has to be installed on the system before installing tacoma. On OS X it might happen that even though pip installed pybind11 it's not available during installation. If that happens please open a detailed issue here. You might want to try

$ brew install pybind11

as a work-around.

Packages not automatically installed during installation

The following packages are not installed during installation with pip since they're only required for drawing and drawing is not essential. If you want to use tacoma.drawing, please install

matplotlib
networkx
python-louvain (community)

Documentation

The documentation is currently available at http://tacoma.benmaier.org . It is full of typos and non-exhaustive but I think the important points are in there.

Examples

Check out the sandbox directory.

Here is an example for the temporal network format tc.edge_changes.

import tacoma as tc
from tacoma.interactive import visualize

# define temporal network as a list of edge changes
temporal_network = tc.edge_changes()
temporal_network.N = 10
temporal_network.edges_initial = [ (0,1), (2,3), (1,7), (3,5), (1,9), (7,2) ]
temporal_network.t0 = 0.0
temporal_network.t = [ 0.8, 2.4 ]
temporal_network.tmax = 3.1
temporal_network.edges_in = [ 
                              [ (0, 5), (3, 6) ], 
                              [ (3, 7), (4, 9), (7, 8) ],
                            ]
temporal_network.edges_out = [ 
                                [ (0, 1) ],
                                [ (2, 3), (3, 6) ],
                             ]

visualize(temporal_network, frame_dt = 0.05)

License

The whole software is published under the MIT software license. The documentation and all figures are copyrighted by Benjamin F. Maier. Ask for permission if you want to distribute parts.

tacoma's People

Contributors

Stargazers

Watchers

Forkers

franksh sjoerdapp lolipa diarm001 rmhilman subarna578 nadia-el

tacoma's Issues

convert edge_changes <-> edge_lists

Visualization only working once per session

Whenever a second visualization is started, temporary files are not created correctly and thus won't be found

changing directory to /Users/bfmaier/.tacoma/web
starting server here ... /Users/bfmaier/.tacoma/web
preparing network
127.0.0.1 - - [16/Oct/2018 10:25:13] "GET /?data=tmp_1667bfa9bea HTTP/1.1" 200 -
127.0.0.1 - - [16/Oct/2018 10:25:14] "GET /tmp_1667bfa9bea_config.json HTTP/1.1" 200 -
127.0.0.1 - - [16/Oct/2018 10:25:14] code 404, message File not found
127.0.0.1 - - [16/Oct/2018 10:25:14] "GET /tmp_1667bfa84c5/tmp_1667bfa84c5_0.taco HTTP/1.1" 404 -
127.0.0.1 - - [16/Oct/2018 10:25:14] code 404, message File not found
127.0.0.1 - - [16/Oct/2018 10:25:14] "GET /tmp_1667bfa84c5/tmp_1667bfa84c5_0.json HTTP/1.1" 404 -
127.0.0.1 - - [16/Oct/2018 10:25:14] "GET /tmp_1667bfa9bea/tmp_1667bfa9bea_0.taco HTTP/1.1" 200 -
127.0.0.1 - - [16/Oct/2018 10:25:14] "GET /tmp_1667bfa9bea/tmp_1667bfa9bea_0.json HTTP/1.1" 200 -

from javascript console

Failed to load resource: the server responded with a status of 404 (File not found)
temporalNetworkFigure.js:132 Uncaught TypeError: Cannot read property 't' of undefined
    at temporalNetworkFigure.js:132
    at Zo._call (d3.v4.min.js:2)
    at Jo (d3.v4.min.js:2)
    at Qo (d3.v4.min.js:2)
    at Object.<anonymous> (d3.v4.min.js:2)
    at k.call (d3.v4.min.js:2)
    at XMLHttpRequest.e (d3.v4.min.js:2)
:8226/tmp_1667bfa84c5/tmp_1667bfa84c5_0.json:1 Failed to load resource: the server responded with a status of 404 (File not found)

visualization not working

Hi, I don't replicate the visualization example. I attach a screenshot of the error message. I work on a Mac (High Sierra), python3.7

best

concatenate edge_lists, edge_changes

in the concatenation procedure, actively use the `int_to_node` map to create useful lists

When concatenating, it might happen that each network has an own set of nodes but those sets might overlap and might have been remapped to different integers. When concatenating those networks, it's necessary to find a common node set and remap the integers in all single temporal networks accordingly.

Setup fails when installing pybind11 with pip

The setup script failed on my Mac when I used

pip install pybind11

It worked after installing pybind11 via homebrew

brew install pybind11

Maybe update the install instructions

Add a `slice` function

It would work like giving a temporal network and a time interval [t0, t1] and the function returns a temporal network of the same type but only the stuff happening between [t0, t1]

Visualization of groups

Hi,
for the interactive visualization, it would be great to be able to see different groups in different colors, to see rightaway if the links join different groups or are rather within groups.

Thanks!

invent/implement edge similarity algorithm to efficiently draw edge visualizations

command 'C:\\Program Files (x86)\\Microsoft Visual Studio 14.0\\VC\\BIN\\x86_amd64\\cl.exe' failed with exit status 2

I get this error when installing tacoma with python setup.py install

_tacoma/Utilities.cpp(49): warning C4244: '=': conversion from 'double' to 'std::size_t', possible loss of data
_tacoma/Utilities.cpp(50): warning C4244: '=': conversion from 'double' to 'std::size_t', possible loss of data
_tacoma/Utilities.cpp(110): warning C4267: 'initializing': conversion from 'size_t' to 'int', possible loss of data
_tacoma/Utilities.cpp(137): warning C4267: 'initializing': conversion from 'size_t' to 'int', possible loss of data
_tacoma/Utilities.cpp(603): error C2065: 'ssize_t': undeclared identifier
_tacoma/Utilities.cpp(603): error C2146: syntax error: missing ';' before identifier 'w'
_tacoma/Utilities.cpp(603): error C2065: 'w': undeclared identifier
_tacoma/Utilities.cpp(607): error C2065: 'w': undeclared identifier
_tacoma/Utilities.cpp(608): error C2065: 'w': undeclared identifier
_tacoma/Utilities.cpp(610): error C2065: 'w': undeclared identifier
_tacoma/Utilities.cpp(615): error C2065: 'w': undeclared identifier
_tacoma/Utilities.cpp(615): error C2228: left of '.insert' must have class/struct/union
_tacoma/Utilities.cpp(616): error C2065: 'w': undeclared identifier
error: command 'C:\\Program Files (x86)\\Microsoft Visual Studio 14.0\\VC\\BIN\\x86_amd64\\cl.exe' failed with exit status 2

I installed Visual Studio 14.0 earlier then here's this problem. Any clues how to solve this?

(WIndows 10
Python 3.6.2)

Add options for directed and weighted temporal networks

Windows support

Get access to a Windows computer and test compilation and visualization
fix the usage of "/" as the directory operator and use os.path.join() instead

in the verification process, make sure that no edges are duplicates

in properties edges_initial, edges, edges_in and edges_out

write extensive documentation

M_PI undefined

@benmaier Thank you for the package. I have the following error when installing. Any idea what could be causing the issue?

    ERROR: Command errored out with exit status 1:
     command: 'C:\Users\Etienne Gagnon\Anaconda3\envs\china_network\python.exe' -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'C:\\Users\\ETIENN~1\\AppData\\Local\\Temp\\pip-req-build-h12oc1_2\\setup.py'"'"'; __file__='"'"'C:\\Users\\ETIENN~1\\AppData\\
Local\\Temp\\pip-req-build-h12oc1_2\\setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record 'C:\Users\ETIENN~1\AppData\Local\Temp
\pip-record-qn45nd_8\install-record.txt' --single-version-externally-managed --compile --install-headers 'C:\Users\Etienne Gagnon\Anaconda3\envs\china_network\Include\tacoma'
         cwd: C:\Users\ETIENN~1\AppData\Local\Temp\pip-req-build-h12oc1_2\
    Complete output (226 lines):
    running install
    running build
    running build_py
    creating build
    creating build\lib.win-amd64-3.7
    creating build\lib.win-amd64-3.7\tacoma
    copying tacoma\analysis.py -> build\lib.win-amd64-3.7\tacoma
    copying tacoma\api.py -> build\lib.win-amd64-3.7\tacoma
    copying tacoma\ccdf.py -> build\lib.win-amd64-3.7\tacoma
    copying tacoma\data_io.py -> build\lib.win-amd64-3.7\tacoma
    copying tacoma\drawing.py -> build\lib.win-amd64-3.7\tacoma
    copying tacoma\edgeactivity.py -> build\lib.win-amd64-3.7\tacoma
    copying tacoma\epidemics.py -> build\lib.win-amd64-3.7\tacoma
    copying tacoma\flockwork.py -> build\lib.win-amd64-3.7\tacoma
    copying tacoma\interactive.py -> build\lib.win-amd64-3.7\tacoma
    copying tacoma\load_model_parameters.py -> build\lib.win-amd64-3.7\tacoma
    copying tacoma\metadata.py -> build\lib.win-amd64-3.7\tacoma
    copying tacoma\model_conversions.py -> build\lib.win-amd64-3.7\tacoma
    copying tacoma\network_formats.py -> build\lib.win-amd64-3.7\tacoma
    copying tacoma\power_law_fitting.py -> build\lib.win-amd64-3.7\tacoma
    copying tacoma\tools.py -> build\lib.win-amd64-3.7\tacoma
    copying tacoma\__init__.py -> build\lib.win-amd64-3.7\tacoma
    running egg_info
    writing tacoma.egg-info\PKG-INFO
    writing dependency_links to tacoma.egg-info\dependency_links.txt
    writing requirements to tacoma.egg-info\requires.txt
    writing top-level names to tacoma.egg-info\top_level.txt
    reading manifest file 'tacoma.egg-info\SOURCES.txt'
    reading manifest template 'MANIFEST.in'
    writing manifest file 'tacoma.egg-info\SOURCES.txt'
    creating build\lib.win-amd64-3.7\tacoma\interactive
    copying tacoma\interactive\index.html -> build\lib.win-amd64-3.7\tacoma\interactive
    creating build\lib.win-amd64-3.7\tacoma\interactive\css
    copying tacoma\interactive\css\main.css -> build\lib.win-amd64-3.7\tacoma\interactive\css
    creating build\lib.win-amd64-3.7\tacoma\interactive\custom_js
    copying tacoma\interactive\custom_js\fisheye.js -> build\lib.win-amd64-3.7\tacoma\interactive\custom_js
    copying tacoma\interactive\custom_js\temporalEdgesView.js -> build\lib.win-amd64-3.7\tacoma\interactive\custom_js
    copying tacoma\interactive\custom_js\temporalNetworkControlWidget.js -> build\lib.win-amd64-3.7\tacoma\interactive\custom_js
    copying tacoma\interactive\custom_js\temporalNetworkFigure.js -> build\lib.win-amd64-3.7\tacoma\interactive\custom_js
    copying tacoma\interactive\custom_js\temporalNetworkView.js -> build\lib.win-amd64-3.7\tacoma\interactive\custom_js
    creating build\lib.win-amd64-3.7\tacoma\interactive\img
    copying tacoma\interactive\img\new_logo_small_grey.png -> build\lib.win-amd64-3.7\tacoma\interactive\img
    copying tacoma\interactive\img\new_logo_small_grey_rotated.png -> build\lib.win-amd64-3.7\tacoma\interactive\img
    creating build\lib.win-amd64-3.7\tacoma\interactive\widgets_js
    copying tacoma\interactive\widgets_js\widget.v3.4.js -> build\lib.win-amd64-3.7\tacoma\interactive\widgets_js
    copying tacoma\interactive\widgets_js\widgets_white_bg.css -> build\lib.win-amd64-3.7\tacoma\interactive\widgets_js
    creating build\lib.win-amd64-3.7\tacoma\resources
    copying tacoma\resources\dtu_dyn_RGG_params.json -> build\lib.win-amd64-3.7\tacoma\resources
    copying tacoma\resources\dtu_fwP_params_scaled.json -> build\lib.win-amd64-3.7\tacoma\resources
    copying tacoma\resources\dtu_fwP_params_unscaled.json -> build\lib.win-amd64-3.7\tacoma\resources
    copying tacoma\resources\dtu_zsbb_params.json -> build\lib.win-amd64-3.7\tacoma\resources
    copying tacoma\resources\hs13_dyn_RGG_params.json -> build\lib.win-amd64-3.7\tacoma\resources
    copying tacoma\resources\hs13_fwP_params_scaled.json -> build\lib.win-amd64-3.7\tacoma\resources
    copying tacoma\resources\hs13_fwP_params_unscaled.json -> build\lib.win-amd64-3.7\tacoma\resources
    copying tacoma\resources\hs13_zsbb_params.json -> build\lib.win-amd64-3.7\tacoma\resources
    copying tacoma\resources\ht09_dyn_RGG_params.json -> build\lib.win-amd64-3.7\tacoma\resources
    copying tacoma\resources\ht09_fwP_params_scaled.json -> build\lib.win-amd64-3.7\tacoma\resources
    copying tacoma\resources\ht09_fwP_params_unscaled.json -> build\lib.win-amd64-3.7\tacoma\resources
    copying tacoma\resources\ht09_zsbb_params.json -> build\lib.win-amd64-3.7\tacoma\resources
    running build_ext
    building '_tacoma' extension
    creating build\temp.win-amd64-3.7
    creating build\temp.win-amd64-3.7\Release
    creating build\temp.win-amd64-3.7\Release\_tacoma
    C:\Program Files (x86)\Microsoft Visual Studio\2019\Community\VC\Tools\MSVC\14.24.28314\bin\HostX86\x64\cl.exe /c /nologo /Ox /W3 /GL /DNDEBUG /MD "-IC:\Users\Etienne Gagnon\Anaconda3\envs\china_network\Library\include" "-IC:\Users\Etienne Gagnon\Anaconda3\envs\
china_network\Library\include" -I./_tacoma/ "-IC:\Users\Etienne Gagnon\Anaconda3\envs\china_network\include" "-IC:\Users\Etienne Gagnon\Anaconda3\envs\china_network\include" "-IC:\Program Files (x86)\Microsoft Visual Studio\2019\Community\VC\Tools\MSVC\14.24.28314\A
TLMFC\include" "-IC:\Program Files (x86)\Microsoft Visual Studio\2019\Community\VC\Tools\MSVC\14.24.28314\include" "-IC:\Program Files (x86)\Windows Kits\NETFXSDK\4.8\include\um" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.18362.0\ucrt" "-IC:\Program File
s (x86)\Windows Kits\10\include\10.0.18362.0\shared" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.18362.0\um" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.18362.0\winrt" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.18362.0\cppwinrt" /EH
sc /Tp_tacoma/Utilities.cpp /Fobuild\temp.win-amd64-3.7\Release\_tacoma/Utilities.obj /EHsc
    Utilities.cpp
    _tacoma/Utilities.cpp(49): warning C4244: '=': conversion from 'double' to 'size_t', possible loss of data
    _tacoma/Utilities.cpp(50): warning C4244: '=': conversion from 'double' to 'size_t', possible loss of data
    _tacoma/Utilities.cpp(110): warning C4267: 'initializing': conversion from 'size_t' to 'int', possible loss of data
    _tacoma/Utilities.cpp(137): warning C4267: 'initializing': conversion from 'size_t' to 'int', possible loss of data
    _tacoma/Utilities.cpp(607): warning C4244: '=': conversion from 'double' to 'long', possible loss of data
    _tacoma/Utilities.cpp(610): warning C4267: '=': conversion from 'size_t' to 'long', possible loss of data
    C:\Program Files (x86)\Microsoft Visual Studio\2019\Community\VC\Tools\MSVC\14.24.28314\include\xutility(1586): warning C4244: 'argument': conversion from '_Diff' to 'const __int64', possible loss of data
            with
            [
                _Diff=double
            ]
    _tacoma/Utilities.cpp(92): note: see reference to function template instantiation 'void std::advance<std::_Vector_iterator<std::_Vector_val<std::_Simple_types<_Ty>>>,double>(_InIt &,_Diff)' being compiled
            with
            [
                _Ty=size_t,
                _InIt=std::_Vector_iterator<std::_Vector_val<std::_Simple_types<size_t>>>,
                _Diff=double
            ]
    C:\Program Files (x86)\Microsoft Visual Studio\2019\Community\VC\Tools\MSVC\14.24.28314\include\numeric(35): warning C4267: '=': conversion from 'size_t' to '_Ty', possible loss of data
            with
            [
                _Ty=int
            ]
    C:\Program Files (x86)\Microsoft Visual Studio\2019\Community\VC\Tools\MSVC\14.24.28314\include\numeric(44): note: see reference to function template instantiation '_Ty std::accumulate<_InIt,_Ty,std::plus<void>>(const _InIt,const _InIt,_Ty,_Fn)' being compiled
            with
            [
                _Ty=int,
                _InIt=std::_Vector_const_iterator<std::_Vector_val<std::_Simple_types<size_t>>>,
                _Fn=std::plus<void>
            ]
    _tacoma/Utilities.cpp(133): note: see reference to function template instantiation '_Ty std::accumulate<std::_Vector_const_iterator<std::_Vector_val<std::_Simple_types<unsigned __int64>>>,int>(const _InIt,const _InIt,_Ty)' being compiled
            with
            [
                _Ty=int,
                _InIt=std::_Vector_const_iterator<std::_Vector_val<std::_Simple_types<size_t>>>
            ]
    C:\Program Files (x86)\Microsoft Visual Studio\2019\Community\VC\Tools\MSVC\14.24.28314\bin\HostX86\x64\cl.exe /c /nologo /Ox /W3 /GL /DNDEBUG /MD "-IC:\Users\Etienne Gagnon\Anaconda3\envs\china_network\Library\include" "-IC:\Users\Etienne Gagnon\Anaconda3\envs\
china_network\Library\include" -I./_tacoma/ "-IC:\Users\Etienne Gagnon\Anaconda3\envs\china_network\include" "-IC:\Users\Etienne Gagnon\Anaconda3\envs\china_network\include" "-IC:\Program Files (x86)\Microsoft Visual Studio\2019\Community\VC\Tools\MSVC\14.24.28314\A
TLMFC\include" "-IC:\Program Files (x86)\Microsoft Visual Studio\2019\Community\VC\Tools\MSVC\14.24.28314\include" "-IC:\Program Files (x86)\Windows Kits\NETFXSDK\4.8\include\um" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.18362.0\ucrt" "-IC:\Program File
s (x86)\Windows Kits\10\include\10.0.18362.0\shared" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.18362.0\um" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.18362.0\winrt" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.18362.0\cppwinrt" /EH
sc /Tp_tacoma/Events.cpp /Fobuild\temp.win-amd64-3.7\Release\_tacoma/Events.obj /EHsc
    Events.cpp
    _tacoma/Events.cpp(554): warning C4244: '=': conversion from 'double' to 'size_t', possible loss of data
    _tacoma/Events.cpp(703): warning C4244: '=': conversion from 'double' to 'size_t', possible loss of data
    _tacoma/Events.cpp(797): warning C4244: 'initializing': conversion from 'double' to 'size_t', possible loss of data
    _tacoma/Events.cpp(866): warning C4244: 'initializing': conversion from 'double' to 'size_t', possible loss of data
    C:\Program Files (x86)\Microsoft Visual Studio\2019\Community\VC\Tools\MSVC\14.24.28314\bin\HostX86\x64\cl.exe /c /nologo /Ox /W3 /GL /DNDEBUG /MD "-IC:\Users\Etienne Gagnon\Anaconda3\envs\china_network\Library\include" "-IC:\Users\Etienne Gagnon\Anaconda3\envs\
china_network\Library\include" -I./_tacoma/ "-IC:\Users\Etienne Gagnon\Anaconda3\envs\china_network\include" "-IC:\Users\Etienne Gagnon\Anaconda3\envs\china_network\include" "-IC:\Program Files (x86)\Microsoft Visual Studio\2019\Community\VC\Tools\MSVC\14.24.28314\A
TLMFC\include" "-IC:\Program Files (x86)\Microsoft Visual Studio\2019\Community\VC\Tools\MSVC\14.24.28314\include" "-IC:\Program Files (x86)\Windows Kits\NETFXSDK\4.8\include\um" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.18362.0\ucrt" "-IC:\Program File
s (x86)\Windows Kits\10\include\10.0.18362.0\shared" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.18362.0\um" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.18362.0\winrt" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.18362.0\cppwinrt" /EH
sc /Tp_tacoma/FlockworkPModel.cpp /Fobuild\temp.win-amd64-3.7\Release\_tacoma/FlockworkPModel.obj /EHsc
    FlockworkPModel.cpp
    C:\Program Files (x86)\Microsoft Visual Studio\2019\Community\VC\Tools\MSVC\14.24.28314\bin\HostX86\x64\cl.exe /c /nologo /Ox /W3 /GL /DNDEBUG /MD "-IC:\Users\Etienne Gagnon\Anaconda3\envs\china_network\Library\include" "-IC:\Users\Etienne Gagnon\Anaconda3\envs\
china_network\Library\include" -I./_tacoma/ "-IC:\Users\Etienne Gagnon\Anaconda3\envs\china_network\include" "-IC:\Users\Etienne Gagnon\Anaconda3\envs\china_network\include" "-IC:\Program Files (x86)\Microsoft Visual Studio\2019\Community\VC\Tools\MSVC\14.24.28314\A
TLMFC\include" "-IC:\Program Files (x86)\Microsoft Visual Studio\2019\Community\VC\Tools\MSVC\14.24.28314\include" "-IC:\Program Files (x86)\Windows Kits\NETFXSDK\4.8\include\um" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.18362.0\ucrt" "-IC:\Program File
s (x86)\Windows Kits\10\include\10.0.18362.0\shared" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.18362.0\um" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.18362.0\winrt" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.18362.0\cppwinrt" /EH
sc /Tp_tacoma/slice.cpp /Fobuild\temp.win-amd64-3.7\Release\_tacoma/slice.obj /EHsc
    slice.cpp
    C:\Program Files (x86)\Microsoft Visual Studio\2019\Community\VC\Tools\MSVC\14.24.28314\bin\HostX86\x64\cl.exe /c /nologo /Ox /W3 /GL /DNDEBUG /MD "-IC:\Users\Etienne Gagnon\Anaconda3\envs\china_network\Library\include" "-IC:\Users\Etienne Gagnon\Anaconda3\envs\
china_network\Library\include" -I./_tacoma/ "-IC:\Users\Etienne Gagnon\Anaconda3\envs\china_network\include" "-IC:\Users\Etienne Gagnon\Anaconda3\envs\china_network\include" "-IC:\Program Files (x86)\Microsoft Visual Studio\2019\Community\VC\Tools\MSVC\14.24.28314\A
TLMFC\include" "-IC:\Program Files (x86)\Microsoft Visual Studio\2019\Community\VC\Tools\MSVC\14.24.28314\include" "-IC:\Program Files (x86)\Windows Kits\NETFXSDK\4.8\include\um" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.18362.0\ucrt" "-IC:\Program File
s (x86)\Windows Kits\10\include\10.0.18362.0\shared" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.18362.0\um" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.18362.0\winrt" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.18362.0\cppwinrt" /EH
sc /Tp_tacoma/coverage_SIS.cpp /Fobuild\temp.win-amd64-3.7\Release\_tacoma/coverage_SIS.obj /EHsc
    coverage_SIS.cpp
    C:\Program Files (x86)\Microsoft Visual Studio\2019\Community\VC\Tools\MSVC\14.24.28314\bin\HostX86\x64\cl.exe /c /nologo /Ox /W3 /GL /DNDEBUG /MD "-IC:\Users\Etienne Gagnon\Anaconda3\envs\china_network\Library\include" "-IC:\Users\Etienne Gagnon\Anaconda3\envs\
china_network\Library\include" -I./_tacoma/ "-IC:\Users\Etienne Gagnon\Anaconda3\envs\china_network\include" "-IC:\Users\Etienne Gagnon\Anaconda3\envs\china_network\include" "-IC:\Program Files (x86)\Microsoft Visual Studio\2019\Community\VC\Tools\MSVC\14.24.28314\A
TLMFC\include" "-IC:\Program Files (x86)\Microsoft Visual Studio\2019\Community\VC\Tools\MSVC\14.24.28314\include" "-IC:\Program Files (x86)\Windows Kits\NETFXSDK\4.8\include\um" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.18362.0\ucrt" "-IC:\Program File
s (x86)\Windows Kits\10\include\10.0.18362.0\shared" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.18362.0\um" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.18362.0\winrt" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.18362.0\cppwinrt" /EH
sc /Tp_tacoma/cluster_size_SIS.cpp /Fobuild\temp.win-amd64-3.7\Release\_tacoma/cluster_size_SIS.obj /EHsc
    cluster_size_SIS.cpp
    C:\Program Files (x86)\Microsoft Visual Studio\2019\Community\VC\Tools\MSVC\14.24.28314\bin\HostX86\x64\cl.exe /c /nologo /Ox /W3 /GL /DNDEBUG /MD "-IC:\Users\Etienne Gagnon\Anaconda3\envs\china_network\Library\include" "-IC:\Users\Etienne Gagnon\Anaconda3\envs\
china_network\Library\include" -I./_tacoma/ "-IC:\Users\Etienne Gagnon\Anaconda3\envs\china_network\include" "-IC:\Users\Etienne Gagnon\Anaconda3\envs\china_network\include" "-IC:\Program Files (x86)\Microsoft Visual Studio\2019\Community\VC\Tools\MSVC\14.24.28314\A
TLMFC\include" "-IC:\Program Files (x86)\Microsoft Visual Studio\2019\Community\VC\Tools\MSVC\14.24.28314\include" "-IC:\Program Files (x86)\Windows Kits\NETFXSDK\4.8\include\um" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.18362.0\ucrt" "-IC:\Program File
s (x86)\Windows Kits\10\include\10.0.18362.0\shared" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.18362.0\um" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.18362.0\winrt" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.18362.0\cppwinrt" /EH
sc /Tp_tacoma/eSIS.cpp /Fobuild\temp.win-amd64-3.7\Release\_tacoma/eSIS.obj /EHsc
    eSIS.cpp
    C:\Program Files (x86)\Microsoft Visual Studio\2019\Community\VC\Tools\MSVC\14.24.28314\bin\HostX86\x64\cl.exe /c /nologo /Ox /W3 /GL /DNDEBUG /MD "-IC:\Users\Etienne Gagnon\Anaconda3\envs\china_network\Library\include" "-IC:\Users\Etienne Gagnon\Anaconda3\envs\
china_network\Library\include" -I./_tacoma/ "-IC:\Users\Etienne Gagnon\Anaconda3\envs\china_network\include" "-IC:\Users\Etienne Gagnon\Anaconda3\envs\china_network\include" "-IC:\Program Files (x86)\Microsoft Visual Studio\2019\Community\VC\Tools\MSVC\14.24.28314\A
TLMFC\include" "-IC:\Program Files (x86)\Microsoft Visual Studio\2019\Community\VC\Tools\MSVC\14.24.28314\include" "-IC:\Program Files (x86)\Windows Kits\NETFXSDK\4.8\include\um" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.18362.0\ucrt" "-IC:\Program File
s (x86)\Windows Kits\10\include\10.0.18362.0\shared" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.18362.0\um" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.18362.0\winrt" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.18362.0\cppwinrt" /EH
sc /Tp_tacoma/QS_SIS.cpp /Fobuild\temp.win-amd64-3.7\Release\_tacoma/QS_SIS.obj /EHsc
    QS_SIS.cpp
    C:\Program Files (x86)\Microsoft Visual Studio\2019\Community\VC\Tools\MSVC\14.24.28314\bin\HostX86\x64\cl.exe /c /nologo /Ox /W3 /GL /DNDEBUG /MD "-IC:\Users\Etienne Gagnon\Anaconda3\envs\china_network\Library\include" "-IC:\Users\Etienne Gagnon\Anaconda3\envs\
china_network\Library\include" -I./_tacoma/ "-IC:\Users\Etienne Gagnon\Anaconda3\envs\china_network\include" "-IC:\Users\Etienne Gagnon\Anaconda3\envs\china_network\include" "-IC:\Program Files (x86)\Microsoft Visual Studio\2019\Community\VC\Tools\MSVC\14.24.28314\A
TLMFC\include" "-IC:\Program Files (x86)\Microsoft Visual Studio\2019\Community\VC\Tools\MSVC\14.24.28314\include" "-IC:\Program Files (x86)\Windows Kits\NETFXSDK\4.8\include\um" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.18362.0\ucrt" "-IC:\Program File
s (x86)\Windows Kits\10\include\10.0.18362.0\shared" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.18362.0\um" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.18362.0\winrt" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.18362.0\cppwinrt" /EH
sc /Tp_tacoma/Markov_SIS.cpp /Fobuild\temp.win-amd64-3.7\Release\_tacoma/Markov_SIS.obj /EHsc
    Markov_SIS.cpp
    C:\Program Files (x86)\Microsoft Visual Studio\2019\Community\VC\Tools\MSVC\14.24.28314\bin\HostX86\x64\cl.exe /c /nologo /Ox /W3 /GL /DNDEBUG /MD "-IC:\Users\Etienne Gagnon\Anaconda3\envs\china_network\Library\include" "-IC:\Users\Etienne Gagnon\Anaconda3\envs\
china_network\Library\include" -I./_tacoma/ "-IC:\Users\Etienne Gagnon\Anaconda3\envs\china_network\include" "-IC:\Users\Etienne Gagnon\Anaconda3\envs\china_network\include" "-IC:\Program Files (x86)\Microsoft Visual Studio\2019\Community\VC\Tools\MSVC\14.24.28314\A
TLMFC\include" "-IC:\Program Files (x86)\Microsoft Visual Studio\2019\Community\VC\Tools\MSVC\14.24.28314\include" "-IC:\Program Files (x86)\Windows Kits\NETFXSDK\4.8\include\um" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.18362.0\ucrt" "-IC:\Program File
s (x86)\Windows Kits\10\include\10.0.18362.0\shared" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.18362.0\um" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.18362.0\winrt" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.18362.0\cppwinrt" /EH
sc /Tp_tacoma/EdgeActivityModel.cpp /Fobuild\temp.win-amd64-3.7\Release\_tacoma/EdgeActivityModel.obj /EHsc
    EdgeActivityModel.cpp
    C:\Program Files (x86)\Microsoft Visual Studio\2019\Community\VC\Tools\MSVC\14.24.28314\bin\HostX86\x64\cl.exe /c /nologo /Ox /W3 /GL /DNDEBUG /MD "-IC:\Users\Etienne Gagnon\Anaconda3\envs\china_network\Library\include" "-IC:\Users\Etienne Gagnon\Anaconda3\envs\
china_network\Library\include" -I./_tacoma/ "-IC:\Users\Etienne Gagnon\Anaconda3\envs\china_network\include" "-IC:\Users\Etienne Gagnon\Anaconda3\envs\china_network\include" "-IC:\Program Files (x86)\Microsoft Visual Studio\2019\Community\VC\Tools\MSVC\14.24.28314\A
TLMFC\include" "-IC:\Program Files (x86)\Microsoft Visual Studio\2019\Community\VC\Tools\MSVC\14.24.28314\include" "-IC:\Program Files (x86)\Windows Kits\NETFXSDK\4.8\include\um" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.18362.0\ucrt" "-IC:\Program File
s (x86)\Windows Kits\10\include\10.0.18362.0\shared" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.18362.0\um" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.18362.0\winrt" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.18362.0\cppwinrt" /EH
sc /Tp_tacoma/activity_model.cpp /Fobuild\temp.win-amd64-3.7\Release\_tacoma/activity_model.obj /EHsc
    activity_model.cpp
    C:\Program Files (x86)\Microsoft Visual Studio\2019\Community\VC\Tools\MSVC\14.24.28314\bin\HostX86\x64\cl.exe /c /nologo /Ox /W3 /GL /DNDEBUG /MD "-IC:\Users\Etienne Gagnon\Anaconda3\envs\china_network\Library\include" "-IC:\Users\Etienne Gagnon\Anaconda3\envs\
china_network\Library\include" -I./_tacoma/ "-IC:\Users\Etienne Gagnon\Anaconda3\envs\china_network\include" "-IC:\Users\Etienne Gagnon\Anaconda3\envs\china_network\include" "-IC:\Program Files (x86)\Microsoft Visual Studio\2019\Community\VC\Tools\MSVC\14.24.28314\A
TLMFC\include" "-IC:\Program Files (x86)\Microsoft Visual Studio\2019\Community\VC\Tools\MSVC\14.24.28314\include" "-IC:\Program Files (x86)\Windows Kits\NETFXSDK\4.8\include\um" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.18362.0\ucrt" "-IC:\Program File
s (x86)\Windows Kits\10\include\10.0.18362.0\shared" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.18362.0\um" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.18362.0\winrt" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.18362.0\cppwinrt" /EH
sc /Tp_tacoma/verify_formats.cpp /Fobuild\temp.win-amd64-3.7\Release\_tacoma/verify_formats.obj /EHsc
    verify_formats.cpp
    C:\Program Files (x86)\Microsoft Visual Studio\2019\Community\VC\Tools\MSVC\14.24.28314\bin\HostX86\x64\cl.exe /c /nologo /Ox /W3 /GL /DNDEBUG /MD "-IC:\Users\Etienne Gagnon\Anaconda3\envs\china_network\Library\include" "-IC:\Users\Etienne Gagnon\Anaconda3\envs\
china_network\Library\include" -I./_tacoma/ "-IC:\Users\Etienne Gagnon\Anaconda3\envs\china_network\include" "-IC:\Users\Etienne Gagnon\Anaconda3\envs\china_network\include" "-IC:\Program Files (x86)\Microsoft Visual Studio\2019\Community\VC\Tools\MSVC\14.24.28314\A
TLMFC\include" "-IC:\Program Files (x86)\Microsoft Visual Studio\2019\Community\VC\Tools\MSVC\14.24.28314\include" "-IC:\Program Files (x86)\Windows Kits\NETFXSDK\4.8\include\um" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.18362.0\ucrt" "-IC:\Program File
s (x86)\Windows Kits\10\include\10.0.18362.0\shared" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.18362.0\um" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.18362.0\winrt" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.18362.0\cppwinrt" /EH
sc /Tp_tacoma/measurements.cpp /Fobuild\temp.win-amd64-3.7\Release\_tacoma/measurements.obj /EHsc
    measurements.cpp
    _tacoma/measurements.cpp(228): warning C4244: 'initializing': conversion from 'double' to 'size_t', possible loss of data
    _tacoma/measurements.cpp(229): warning C4244: 'argument': conversion from 'size_t' to 'const _Ty', possible loss of data
            with
            [
                _Ty=double
            ]
    _tacoma/measurements.cpp(448): warning C4267: '-=': conversion from 'size_t' to 'long', possible loss of data
    _tacoma/measurements.cpp(657): warning C4267: '+=': conversion from 'size_t' to 'long', possible loss of data
    _tacoma/measurements.cpp(658): warning C4267: '-=': conversion from 'size_t' to 'long', possible loss of data
    C:\Program Files (x86)\Microsoft Visual Studio\2019\Community\VC\Tools\MSVC\14.24.28314\bin\HostX86\x64\cl.exe /c /nologo /Ox /W3 /GL /DNDEBUG /MD "-IC:\Users\Etienne Gagnon\Anaconda3\envs\china_network\Library\include" "-IC:\Users\Etienne Gagnon\Anaconda3\envs\
china_network\Library\include" -I./_tacoma/ "-IC:\Users\Etienne Gagnon\Anaconda3\envs\china_network\include" "-IC:\Users\Etienne Gagnon\Anaconda3\envs\china_network\include" "-IC:\Program Files (x86)\Microsoft Visual Studio\2019\Community\VC\Tools\MSVC\14.24.28314\A
TLMFC\include" "-IC:\Program Files (x86)\Microsoft Visual Studio\2019\Community\VC\Tools\MSVC\14.24.28314\include" "-IC:\Program Files (x86)\Windows Kits\NETFXSDK\4.8\include\um" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.18362.0\ucrt" "-IC:\Program File
s (x86)\Windows Kits\10\include\10.0.18362.0\shared" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.18362.0\um" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.18362.0\winrt" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.18362.0\cppwinrt" /EH
sc /Tp_tacoma/social_trajectories.cpp /Fobuild\temp.win-amd64-3.7\Release\_tacoma/social_trajectories.obj /EHsc
    social_trajectories.cpp
    _tacoma/social_trajectories.cpp(150): warning C4244: 'initializing': conversion from 'double' to 'size_t', possible loss of data
    _tacoma/social_trajectories.cpp(295): warning C4244: 'initializing': conversion from 'double' to 'size_t', possible loss of data
    C:\Program Files (x86)\Microsoft Visual Studio\2019\Community\VC\Tools\MSVC\14.24.28314\bin\HostX86\x64\cl.exe /c /nologo /Ox /W3 /GL /DNDEBUG /MD "-IC:\Users\Etienne Gagnon\Anaconda3\envs\china_network\Library\include" "-IC:\Users\Etienne Gagnon\Anaconda3\envs\
china_network\Library\include" -I./_tacoma/ "-IC:\Users\Etienne Gagnon\Anaconda3\envs\china_network\include" "-IC:\Users\Etienne Gagnon\Anaconda3\envs\china_network\include" "-IC:\Program Files (x86)\Microsoft Visual Studio\2019\Community\VC\Tools\MSVC\14.24.28314\A
TLMFC\include" "-IC:\Program Files (x86)\Microsoft Visual Studio\2019\Community\VC\Tools\MSVC\14.24.28314\include" "-IC:\Program Files (x86)\Windows Kits\NETFXSDK\4.8\include\um" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.18362.0\ucrt" "-IC:\Program File
s (x86)\Windows Kits\10\include\10.0.18362.0\shared" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.18362.0\um" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.18362.0\winrt" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.18362.0\cppwinrt" /EH
sc /Tp_tacoma/edge_trajectories.cpp /Fobuild\temp.win-amd64-3.7\Release\_tacoma/edge_trajectories.obj /EHsc
    edge_trajectories.cpp
    C:\Program Files (x86)\Microsoft Visual Studio\2019\Community\VC\Tools\MSVC\14.24.28314\bin\HostX86\x64\cl.exe /c /nologo /Ox /W3 /GL /DNDEBUG /MD "-IC:\Users\Etienne Gagnon\Anaconda3\envs\china_network\Library\include" "-IC:\Users\Etienne Gagnon\Anaconda3\envs\
china_network\Library\include" -I./_tacoma/ "-IC:\Users\Etienne Gagnon\Anaconda3\envs\china_network\include" "-IC:\Users\Etienne Gagnon\Anaconda3\envs\china_network\include" "-IC:\Program Files (x86)\Microsoft Visual Studio\2019\Community\VC\Tools\MSVC\14.24.28314\A
TLMFC\include" "-IC:\Program Files (x86)\Microsoft Visual Studio\2019\Community\VC\Tools\MSVC\14.24.28314\include" "-IC:\Program Files (x86)\Windows Kits\NETFXSDK\4.8\include\um" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.18362.0\ucrt" "-IC:\Program File
s (x86)\Windows Kits\10\include\10.0.18362.0\shared" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.18362.0\um" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.18362.0\winrt" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.18362.0\cppwinrt" /EH
sc /Tp_tacoma/concatenation.cpp /Fobuild\temp.win-amd64-3.7\Release\_tacoma/concatenation.obj /EHsc
    concatenation.cpp
    C:\Program Files (x86)\Microsoft Visual Studio\2019\Community\VC\Tools\MSVC\14.24.28314\bin\HostX86\x64\cl.exe /c /nologo /Ox /W3 /GL /DNDEBUG /MD "-IC:\Users\Etienne Gagnon\Anaconda3\envs\china_network\Library\include" "-IC:\Users\Etienne Gagnon\Anaconda3\envs\
china_network\Library\include" -I./_tacoma/ "-IC:\Users\Etienne Gagnon\Anaconda3\envs\china_network\include" "-IC:\Users\Etienne Gagnon\Anaconda3\envs\china_network\include" "-IC:\Program Files (x86)\Microsoft Visual Studio\2019\Community\VC\Tools\MSVC\14.24.28314\A
TLMFC\include" "-IC:\Program Files (x86)\Microsoft Visual Studio\2019\Community\VC\Tools\MSVC\14.24.28314\include" "-IC:\Program Files (x86)\Windows Kits\NETFXSDK\4.8\include\um" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.18362.0\ucrt" "-IC:\Program File
s (x86)\Windows Kits\10\include\10.0.18362.0\shared" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.18362.0\um" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.18362.0\winrt" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.18362.0\cppwinrt" /EH
sc /Tp_tacoma/FW_P_varying.cpp /Fobuild\temp.win-amd64-3.7\Release\_tacoma/FW_P_varying.obj /EHsc
    FW_P_varying.cpp
    _tacoma/FW_P_varying.cpp(311): warning C4244: '=': conversion from 'unsigned __int64' to 'double', possible loss of data
    C:\Program Files (x86)\Microsoft Visual Studio\2019\Community\VC\Tools\MSVC\14.24.28314\bin\HostX86\x64\cl.exe /c /nologo /Ox /W3 /GL /DNDEBUG /MD "-IC:\Users\Etienne Gagnon\Anaconda3\envs\china_network\Library\include" "-IC:\Users\Etienne Gagnon\Anaconda3\envs\
china_network\Library\include" -I./_tacoma/ "-IC:\Users\Etienne Gagnon\Anaconda3\envs\china_network\include" "-IC:\Users\Etienne Gagnon\Anaconda3\envs\china_network\include" "-IC:\Program Files (x86)\Microsoft Visual Studio\2019\Community\VC\Tools\MSVC\14.24.28314\A
TLMFC\include" "-IC:\Program Files (x86)\Microsoft Visual Studio\2019\Community\VC\Tools\MSVC\14.24.28314\include" "-IC:\Program Files (x86)\Windows Kits\NETFXSDK\4.8\include\um" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.18362.0\ucrt" "-IC:\Program File
s (x86)\Windows Kits\10\include\10.0.18362.0\shared" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.18362.0\um" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.18362.0\winrt" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.18362.0\cppwinrt" /EH
sc /Tp_tacoma/FW_P_varying_alpha_beta.cpp /Fobuild\temp.win-amd64-3.7\Release\_tacoma/FW_P_varying_alpha_beta.obj /EHsc
    FW_P_varying_alpha_beta.cpp
    C:\Program Files (x86)\Microsoft Visual Studio\2019\Community\VC\Tools\MSVC\14.24.28314\bin\HostX86\x64\cl.exe /c /nologo /Ox /W3 /GL /DNDEBUG /MD "-IC:\Users\Etienne Gagnon\Anaconda3\envs\china_network\Library\include" "-IC:\Users\Etienne Gagnon\Anaconda3\envs\
china_network\Library\include" -I./_tacoma/ "-IC:\Users\Etienne Gagnon\Anaconda3\envs\china_network\include" "-IC:\Users\Etienne Gagnon\Anaconda3\envs\china_network\include" "-IC:\Program Files (x86)\Microsoft Visual Studio\2019\Community\VC\Tools\MSVC\14.24.28314\A
TLMFC\include" "-IC:\Program Files (x86)\Microsoft Visual Studio\2019\Community\VC\Tools\MSVC\14.24.28314\include" "-IC:\Program Files (x86)\Windows Kits\NETFXSDK\4.8\include\um" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.18362.0\ucrt" "-IC:\Program File
s (x86)\Windows Kits\10\include\10.0.18362.0\shared" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.18362.0\um" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.18362.0\winrt" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.18362.0\cppwinrt" /EH
sc /Tp_tacoma/resampling.cpp /Fobuild\temp.win-amd64-3.7\Release\_tacoma/resampling.obj /EHsc
    resampling.cpp
    C:\Program Files (x86)\Microsoft Visual Studio\2019\Community\VC\Tools\MSVC\14.24.28314\bin\HostX86\x64\cl.exe /c /nologo /Ox /W3 /GL /DNDEBUG /MD "-IC:\Users\Etienne Gagnon\Anaconda3\envs\china_network\Library\include" "-IC:\Users\Etienne Gagnon\Anaconda3\envs\
china_network\Library\include" -I./_tacoma/ "-IC:\Users\Etienne Gagnon\Anaconda3\envs\china_network\include" "-IC:\Users\Etienne Gagnon\Anaconda3\envs\china_network\include" "-IC:\Program Files (x86)\Microsoft Visual Studio\2019\Community\VC\Tools\MSVC\14.24.28314\A
TLMFC\include" "-IC:\Program Files (x86)\Microsoft Visual Studio\2019\Community\VC\Tools\MSVC\14.24.28314\include" "-IC:\Program Files (x86)\Windows Kits\NETFXSDK\4.8\include\um" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.18362.0\ucrt" "-IC:\Program File
s (x86)\Windows Kits\10\include\10.0.18362.0\shared" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.18362.0\um" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.18362.0\winrt" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.18362.0\cppwinrt" /EH
sc /Tp_tacoma/flockwork_parameter_estimation.cpp /Fobuild\temp.win-amd64-3.7\Release\_tacoma/flockwork_parameter_estimation.obj /EHsc
    flockwork_parameter_estimation.cpp
    _tacoma/flockwork_parameter_estimation.cpp(681): warning C4244: 'initializing': conversion from 'size_t' to 'double', possible loss of data
    _tacoma/flockwork_parameter_estimation.cpp(1252): warning C4244: 'initializing': conversion from 'size_t' to 'double', possible loss of data
    _tacoma/flockwork_parameter_estimation.cpp(1536): warning C4244: 'initializing': conversion from 'size_t' to 'double', possible loss of data
    _tacoma/flockwork_parameter_estimation.cpp(1755): warning C4244: '=': conversion from 'double' to '_Ty', possible loss of data
            with
            [
                _Ty=size_t
            ]
    _tacoma/flockwork_parameter_estimation.cpp(1756): warning C4244: '=': conversion from 'double' to '_Ty', possible loss of data
            with
            [
                _Ty=size_t
            ]
    C:\Program Files (x86)\Microsoft Visual Studio\2019\Community\VC\Tools\MSVC\14.24.28314\bin\HostX86\x64\cl.exe /c /nologo /Ox /W3 /GL /DNDEBUG /MD "-IC:\Users\Etienne Gagnon\Anaconda3\envs\china_network\Library\include" "-IC:\Users\Etienne Gagnon\Anaconda3\envs\
china_network\Library\include" -I./_tacoma/ "-IC:\Users\Etienne Gagnon\Anaconda3\envs\china_network\include" "-IC:\Users\Etienne Gagnon\Anaconda3\envs\china_network\include" "-IC:\Program Files (x86)\Microsoft Visual Studio\2019\Community\VC\Tools\MSVC\14.24.28314\A
TLMFC\include" "-IC:\Program Files (x86)\Microsoft Visual Studio\2019\Community\VC\Tools\MSVC\14.24.28314\include" "-IC:\Program Files (x86)\Windows Kits\NETFXSDK\4.8\include\um" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.18362.0\ucrt" "-IC:\Program File
s (x86)\Windows Kits\10\include\10.0.18362.0\shared" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.18362.0\um" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.18362.0\winrt" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.18362.0\cppwinrt" /EH
sc /Tp_tacoma/conversion.cpp /Fobuild\temp.win-amd64-3.7\Release\_tacoma/conversion.obj /EHsc
    conversion.cpp
    C:\Program Files (x86)\Microsoft Visual Studio\2019\Community\VC\Tools\MSVC\14.24.28314\bin\HostX86\x64\cl.exe /c /nologo /Ox /W3 /GL /DNDEBUG /MD "-IC:\Users\Etienne Gagnon\Anaconda3\envs\china_network\Library\include" "-IC:\Users\Etienne Gagnon\Anaconda3\envs\
china_network\Library\include" -I./_tacoma/ "-IC:\Users\Etienne Gagnon\Anaconda3\envs\china_network\include" "-IC:\Users\Etienne Gagnon\Anaconda3\envs\china_network\include" "-IC:\Program Files (x86)\Microsoft Visual Studio\2019\Community\VC\Tools\MSVC\14.24.28314\A
TLMFC\include" "-IC:\Program Files (x86)\Microsoft Visual Studio\2019\Community\VC\Tools\MSVC\14.24.28314\include" "-IC:\Program Files (x86)\Windows Kits\NETFXSDK\4.8\include\um" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.18362.0\ucrt" "-IC:\Program File
s (x86)\Windows Kits\10\include\10.0.18362.0\shared" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.18362.0\um" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.18362.0\winrt" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.18362.0\cppwinrt" /EH
sc /Tp_tacoma/SIS.cpp /Fobuild\temp.win-amd64-3.7\Release\_tacoma/SIS.obj /EHsc
    SIS.cpp
    C:\Program Files (x86)\Microsoft Visual Studio\2019\Community\VC\Tools\MSVC\14.24.28314\bin\HostX86\x64\cl.exe /c /nologo /Ox /W3 /GL /DNDEBUG /MD "-IC:\Users\Etienne Gagnon\Anaconda3\envs\china_network\Library\include" "-IC:\Users\Etienne Gagnon\Anaconda3\envs\
china_network\Library\include" -I./_tacoma/ "-IC:\Users\Etienne Gagnon\Anaconda3\envs\china_network\include" "-IC:\Users\Etienne Gagnon\Anaconda3\envs\china_network\include" "-IC:\Program Files (x86)\Microsoft Visual Studio\2019\Community\VC\Tools\MSVC\14.24.28314\A
TLMFC\include" "-IC:\Program Files (x86)\Microsoft Visual Studio\2019\Community\VC\Tools\MSVC\14.24.28314\include" "-IC:\Program Files (x86)\Windows Kits\NETFXSDK\4.8\include\um" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.18362.0\ucrt" "-IC:\Program File
s (x86)\Windows Kits\10\include\10.0.18362.0\shared" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.18362.0\um" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.18362.0\winrt" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.18362.0\cppwinrt" /EH
sc /Tp_tacoma/SIS_node_based.cpp /Fobuild\temp.win-amd64-3.7\Release\_tacoma/SIS_node_based.obj /EHsc
    SIS_node_based.cpp
    C:\Program Files (x86)\Microsoft Visual Studio\2019\Community\VC\Tools\MSVC\14.24.28314\bin\HostX86\x64\cl.exe /c /nologo /Ox /W3 /GL /DNDEBUG /MD "-IC:\Users\Etienne Gagnon\Anaconda3\envs\china_network\Library\include" "-IC:\Users\Etienne Gagnon\Anaconda3\envs\
china_network\Library\include" -I./_tacoma/ "-IC:\Users\Etienne Gagnon\Anaconda3\envs\china_network\include" "-IC:\Users\Etienne Gagnon\Anaconda3\envs\china_network\include" "-IC:\Program Files (x86)\Microsoft Visual Studio\2019\Community\VC\Tools\MSVC\14.24.28314\A
TLMFC\include" "-IC:\Program Files (x86)\Microsoft Visual Studio\2019\Community\VC\Tools\MSVC\14.24.28314\include" "-IC:\Program Files (x86)\Windows Kits\NETFXSDK\4.8\include\um" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.18362.0\ucrt" "-IC:\Program File
s (x86)\Windows Kits\10\include\10.0.18362.0\shared" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.18362.0\um" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.18362.0\winrt" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.18362.0\cppwinrt" /EH
sc /Tp_tacoma/SIR.cpp /Fobuild\temp.win-amd64-3.7\Release\_tacoma/SIR.obj /EHsc
    SIR.cpp
    C:\Program Files (x86)\Microsoft Visual Studio\2019\Community\VC\Tools\MSVC\14.24.28314\bin\HostX86\x64\cl.exe /c /nologo /Ox /W3 /GL /DNDEBUG /MD "-IC:\Users\Etienne Gagnon\Anaconda3\envs\china_network\Library\include" "-IC:\Users\Etienne Gagnon\Anaconda3\envs\
china_network\Library\include" -I./_tacoma/ "-IC:\Users\Etienne Gagnon\Anaconda3\envs\china_network\include" "-IC:\Users\Etienne Gagnon\Anaconda3\envs\china_network\include" "-IC:\Program Files (x86)\Microsoft Visual Studio\2019\Community\VC\Tools\MSVC\14.24.28314\A
TLMFC\include" "-IC:\Program Files (x86)\Microsoft Visual Studio\2019\Community\VC\Tools\MSVC\14.24.28314\include" "-IC:\Program Files (x86)\Windows Kits\NETFXSDK\4.8\include\um" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.18362.0\ucrt" "-IC:\Program File
s (x86)\Windows Kits\10\include\10.0.18362.0\shared" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.18362.0\um" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.18362.0\winrt" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.18362.0\cppwinrt" /EH
sc /Tp_tacoma/SIRS.cpp /Fobuild\temp.win-amd64-3.7\Release\_tacoma/SIRS.obj /EHsc
    SIRS.cpp
    C:\Program Files (x86)\Microsoft Visual Studio\2019\Community\VC\Tools\MSVC\14.24.28314\bin\HostX86\x64\cl.exe /c /nologo /Ox /W3 /GL /DNDEBUG /MD "-IC:\Users\Etienne Gagnon\Anaconda3\envs\china_network\Library\include" "-IC:\Users\Etienne Gagnon\Anaconda3\envs\
china_network\Library\include" -I./_tacoma/ "-IC:\Users\Etienne Gagnon\Anaconda3\envs\china_network\include" "-IC:\Users\Etienne Gagnon\Anaconda3\envs\china_network\include" "-IC:\Program Files (x86)\Microsoft Visual Studio\2019\Community\VC\Tools\MSVC\14.24.28314\A
TLMFC\include" "-IC:\Program Files (x86)\Microsoft Visual Studio\2019\Community\VC\Tools\MSVC\14.24.28314\include" "-IC:\Program Files (x86)\Windows Kits\NETFXSDK\4.8\include\um" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.18362.0\ucrt" "-IC:\Program File
s (x86)\Windows Kits\10\include\10.0.18362.0\shared" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.18362.0\um" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.18362.0\winrt" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.18362.0\cppwinrt" /EH
sc /Tp_tacoma/SI.cpp /Fobuild\temp.win-amd64-3.7\Release\_tacoma/SI.obj /EHsc
    SI.cpp
    C:\Program Files (x86)\Microsoft Visual Studio\2019\Community\VC\Tools\MSVC\14.24.28314\bin\HostX86\x64\cl.exe /c /nologo /Ox /W3 /GL /DNDEBUG /MD "-IC:\Users\Etienne Gagnon\Anaconda3\envs\china_network\Library\include" "-IC:\Users\Etienne Gagnon\Anaconda3\envs\
china_network\Library\include" -I./_tacoma/ "-IC:\Users\Etienne Gagnon\Anaconda3\envs\china_network\include" "-IC:\Users\Etienne Gagnon\Anaconda3\envs\china_network\include" "-IC:\Program Files (x86)\Microsoft Visual Studio\2019\Community\VC\Tools\MSVC\14.24.28314\A
TLMFC\include" "-IC:\Program Files (x86)\Microsoft Visual Studio\2019\Community\VC\Tools\MSVC\14.24.28314\include" "-IC:\Program Files (x86)\Windows Kits\NETFXSDK\4.8\include\um" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.18362.0\ucrt" "-IC:\Program File
s (x86)\Windows Kits\10\include\10.0.18362.0\shared" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.18362.0\um" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.18362.0\winrt" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.18362.0\cppwinrt" /EH
sc /Tp_tacoma/ZSBB_model.cpp /Fobuild\temp.win-amd64-3.7\Release\_tacoma/ZSBB_model.obj /EHsc
    ZSBB_model.cpp
    _tacoma/ZSBB_model.cpp(195): warning C4244: 'initializing': conversion from 'size_t' to 'double', possible loss of data
    _tacoma/ZSBB_model.cpp(251): warning C4244: 'initializing': conversion from 'size_t' to 'double', possible loss of data
    _tacoma/ZSBB_model.cpp(320): warning C4244: 'argument': conversion from 'double' to 'const _Ty', possible loss of data
            with
            [
                _Ty=size_t
            ]
    _tacoma/ZSBB_model.cpp(321): warning C4244: 'argument': conversion from 'double' to 'const _Ty', possible loss of data
            with
            [
                _Ty=size_t
            ]
    _tacoma/ZSBB_model.cpp(340): warning C4244: 'argument': conversion from 'double' to 'const _Ty', possible loss of data
            with
            [
                _Ty=size_t
            ]
    _tacoma/ZSBB_model.cpp(380): warning C4244: 'argument': conversion from 'double' to 'const _Ty', possible loss of data
            with
            [
                _Ty=size_t
            ]
    _tacoma/ZSBB_model.cpp(393): warning C4244: 'argument': conversion from 'double' to 'const _Ty', possible loss of data
            with
            [
                _Ty=size_t
            ]
    _tacoma/ZSBB_model.cpp(407): warning C4244: 'argument': conversion from 'size_t' to 'const _Ty', possible loss of data
            with
            [
                _Ty=double
            ]
    _tacoma/ZSBB_model.cpp(467): warning C4244: '=': conversion from 'size_t' to 'double', possible loss of data
    C:\Program Files (x86)\Microsoft Visual Studio\2019\Community\VC\Tools\MSVC\14.24.28314\bin\HostX86\x64\cl.exe /c /nologo /Ox /W3 /GL /DNDEBUG /MD "-IC:\Users\Etienne Gagnon\Anaconda3\envs\china_network\Library\include" "-IC:\Users\Etienne Gagnon\Anaconda3\envs\
china_network\Library\include" -I./_tacoma/ "-IC:\Users\Etienne Gagnon\Anaconda3\envs\china_network\include" "-IC:\Users\Etienne Gagnon\Anaconda3\envs\china_network\include" "-IC:\Program Files (x86)\Microsoft Visual Studio\2019\Community\VC\Tools\MSVC\14.24.28314\A
TLMFC\include" "-IC:\Program Files (x86)\Microsoft Visual Studio\2019\Community\VC\Tools\MSVC\14.24.28314\include" "-IC:\Program Files (x86)\Windows Kits\NETFXSDK\4.8\include\um" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.18362.0\ucrt" "-IC:\Program File
s (x86)\Windows Kits\10\include\10.0.18362.0\shared" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.18362.0\um" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.18362.0\winrt" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.18362.0\cppwinrt" /EH
sc /Tp_tacoma/dyn_RGG.cpp /Fobuild\temp.win-amd64-3.7\Release\_tacoma/dyn_RGG.obj /EHsc
    dyn_RGG.cpp
    _tacoma/dyn_RGG.cpp(53): error C2065: 'M_PI': undeclared identifier
    _tacoma/dyn_RGG.cpp(259): warning C4244: 'argument': conversion from 'size_t' to 'const _Ty', possible loss of data
            with
            [
                _Ty=double
            ]
    _tacoma/dyn_RGG.cpp(266): warning C4244: '=': conversion from 'const size_t' to 'double', possible loss of data
    error: command 'C:\\Program Files (x86)\\Microsoft Visual Studio\\2019\\Community\\VC\\Tools\\MSVC\\14.24.28314\\bin\\HostX86\\x64\\cl.exe' failed with exit status 2
    ----------------------------------------
ERROR: Command errored out with exit status 1: 'C:\Users\Etienne Gagnon\Anaconda3\envs\china_network\python.exe' -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'C:\\Users\\ETIENN~1\\AppData\\Local\\Temp\\pip-req-build-h12oc1_2\\setup.py'"'"'; __file__='"
'"'C:\\Users\\ETIENN~1\\AppData\\Local\\Temp\\pip-req-build-h12oc1_2\\setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record 'C:\
Users\ETIENN~1\AppData\Local\Temp\pip-record-qn45nd_8\install-record.txt' --single-version-externally-managed --compile --install-headers 'C:\Users\Etienne Gagnon\Anaconda3\envs\china_network\Include\tacoma' Check the logs for full command output.

Originally posted by @EtienneGagnon1 in #21 (comment)

Dragging the time bar should update the visualization at own pace

Add option to save internal variables during SI-simulation

Currently only some variables of the SI-simulation are saved and accessible via the Python-API: The time (SI.time), number of infected (SI.I) and a list of susceptible-infected contacts (SI.SI).

It would be nice to have to option to save more detailed internal variables, such as a list of infection events, such that for instance information on transmission chains is extractable. These variables are currently computed during the simulation but not kept for memory efficiency.

The option could be added to the tc.SI() interface as a flag save_internal_variables=True/False

Adding labels to the sliders in the visualization

add epidemic classes with `exposed` component

SEIR
SEIS
SEIRS

`tn.edges` does not support `.append` method

Commonly I will have some code like the following:

# Setup
tn = tc.edge_lists()
tn = num_nodes
tn = list(range(num_timesteps))
tn = num_timesteps

# Add edges conditional on criterion
for t in range(0, num_timesteps):
    edges_t = []
    for i in range(num_nodes):
        for j in range(i+1, num_nodes):
            if some_criterion(i, j):
                edges_t.append((i, j))
    tn.edges.append(edges_t)  # <-- `edges_t` DOESN'T ACTUALLY APPEND TO `tn.edges`

As indicated by the last comment, appending to tn.edges like this does nothing so after the loop has run tn.edges == []. Also no error is raised. Instead, when trying to do edge_activity_plot(tn) I received ValueError: min() arg is an empty sequence

Easy to reproduce just set tn.edges = [] and call edge_activity_plot(tn). I recommend either raising an error when appending to tn.edges, or enabling appending to tn.edges somehow.

fit (1-(1-p)^t) to the edge illustration of a temporal network

verify edge_lists

go through edge list format and check whether or not everything is in the right place.

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