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Merged
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Jul 13, 2022
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counterfactual excess covid deaths notebook #391

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7a8b65f
add excess deaths files
Jul 4, 2022
30afd04
add myst file
Jul 4, 2022
65b6f7b
add tags
Jul 6, 2022
a11a2ca
fix typo
Jul 6, 2022
418232c
edit text about temperature and deaths
Jul 6, 2022
f4945f8
Covid-19 -> COVID-19. And grammatical fix
Jul 6, 2022
a18967f
grammatical fix
Jul 6, 2022
5e684b5
simpler data import + ZeroSumNormal + update figure title + remove sa…
Jul 9, 2022
8029c1b
bring in retrodiction as a more specific description of what we are d…
Jul 12, 2022
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1,445 changes: 1,445 additions & 0 deletions examples/case_studies/excess_deaths.ipynb
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198 changes: 198 additions & 0 deletions examples/data/deaths_and_temps_england_wales.csv
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Original file line number Diff line number Diff line change
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date,temp,deaths,year,month,t,pre
2006-01-01,3.8,49124,2006,1,0,True
2006-02-01,3.4,42664,2006,2,1,True
2006-03-01,3.9,49207,2006,3,2,True
2006-04-01,7.4,40645,2006,4,3,True
2006-05-01,10.7,42425,2006,5,4,True
2006-06-01,14.5,40797,2006,6,5,True
2006-07-01,17.8,38870,2006,7,6,True
2006-08-01,14.9,39140,2006,8,7,True
2006-09-01,15.2,36594,2006,9,8,True
2006-10-01,11.6,40390,2006,10,9,True
2006-11-01,7.2,42326,2006,11,10,True
2006-12-01,5.5,40417,2006,12,11,True
2007-01-01,5.9,50305,2007,1,12,True
2007-02-01,5.1,44669,2007,2,13,True
2007-03-01,6.3,44358,2007,3,14,True
2007-04-01,10.2,41416,2007,4,15,True
2007-05-01,10.6,41579,2007,5,16,True
2007-06-01,13.7,38028,2007,6,17,True
2007-07-01,14.2,39729,2007,7,18,True
2007-08-01,14.3,39048,2007,8,19,True
2007-09-01,12.6,35215,2007,9,20,True
2007-10-01,10.2,42935,2007,10,21,True
2007-11-01,6.8,42832,2007,11,22,True
2007-12-01,4.4,43938,2007,12,23,True
2008-01-01,5.3,52057,2008,1,24,True
2008-02-01,4.9,42338,2008,2,25,True
2008-03-01,5.1,41999,2008,3,26,True
2008-04-01,7.0,46016,2008,4,27,True
2008-05-01,12.1,39240,2008,5,28,True
2008-06-01,12.9,37845,2008,6,29,True
2008-07-01,15.3,40084,2008,7,30,True
2008-08-01,15.1,34980,2008,8,31,True
2008-09-01,12.5,39238,2008,9,32,True
2008-10-01,8.7,42195,2008,10,33,True
2008-11-01,6.1,39504,2008,11,34,True
2008-12-01,3.1,53594,2008,12,35,True
2009-01-01,2.8,55045,2009,1,36,True
2009-02-01,3.7,41433,2009,2,37,True
2009-03-01,6.1,42395,2009,3,38,True
2009-04-01,8.9,40270,2009,4,39,True
2009-05-01,10.8,36568,2009,5,40,True
2009-06-01,13.7,38851,2009,6,41,True
2009-07-01,15.1,37975,2009,7,42,True
2009-08-01,15.3,33606,2009,8,43,True
2009-09-01,13.2,39127,2009,9,44,True
2009-10-01,10.4,40187,2009,10,45,True
2009-11-01,7.3,40122,2009,11,46,True
2009-12-01,2.1,45769,2009,12,47,True
2010-01-01,0.9,48363,2010,1,48,True
2010-02-01,1.8,41048,2010,2,49,True
2010-03-01,5.1,45138,2010,3,50,True
2010-04-01,7.9,40584,2010,4,51,True
2010-05-01,9.7,36517,2010,5,52,True
2010-06-01,14.1,40168,2010,6,53,True
2010-07-01,15.6,36888,2010,7,54,True
2010-08-01,14.2,36083,2010,8,55,True
2010-09-01,12.8,39423,2010,9,56,True
2010-10-01,9.4,38613,2010,10,57,True
2010-11-01,4.3,42123,2010,11,58,True
2010-12-01,-0.9,48294,2010,12,59,True
2011-01-01,3.1,49992,2011,1,60,True
2011-02-01,5.3,39350,2011,2,61,True
2011-03-01,5.8,44209,2011,3,62,True
2011-04-01,10.7,36943,2011,4,63,True
2011-05-01,11.0,40100,2011,5,64,True
2011-06-01,12.6,40000,2011,6,65,True
2011-07-01,14.2,35646,2011,7,66,True
2011-08-01,14.1,38383,2011,8,67,True
2011-09-01,13.8,38358,2011,9,68,True
2011-10-01,11.2,37200,2011,10,69,True
2011-11-01,8.7,40624,2011,11,70,True
2011-12-01,4.8,43562,2011,12,71,True
2012-01-01,4.6,46897,2012,1,72,True
2012-02-01,4.2,44537,2012,2,73,True
2012-03-01,7.7,44142,2012,3,74,True
2012-04-01,6.3,41685,2012,4,75,True
2012-05-01,10.5,44008,2012,5,76,True
2012-06-01,12.3,36680,2012,6,77,True
2012-07-01,14.1,39293,2012,7,78,True
2012-08-01,15.3,39035,2012,8,79,True
2012-09-01,11.9,35216,2012,9,80,True
2012-10-01,8.2,43169,2012,10,81,True
2012-11-01,5.7,42124,2012,11,82,True
2012-12-01,3.8,42545,2012,12,83,True
2013-01-01,3.3,52898,2013,1,84,True
2013-02-01,2.7,43778,2013,2,85,True
2013-03-01,2.2,44915,2013,3,86,True
2013-04-01,6.3,49735,2013,4,87,True
2013-05-01,9.5,42273,2013,5,88,True
2013-06-01,12.8,35866,2013,6,89,True
2013-07-01,17.0,39806,2013,7,90,True
2013-08-01,15.6,35691,2013,8,91,True
2013-09-01,12.7,36775,2013,9,92,True
2013-10-01,11.2,42322,2013,10,93,True
2013-11-01,5.5,39941,2013,11,94,True
2013-12-01,5.7,42790,2013,12,95,True
2014-01-01,4.7,49026,2014,1,96,True
2014-02-01,5.2,41199,2014,2,97,True
2014-03-01,6.7,41217,2014,3,98,True
2014-04-01,9.2,41487,2014,4,99,True
2014-05-01,11.2,39422,2014,5,100,True
2014-06-01,14.2,38505,2014,6,101,True
2014-07-01,16.3,41244,2014,7,102,True
2014-08-01,13.9,35959,2014,8,103,True
2014-09-01,13.9,40979,2014,9,104,True
2014-10-01,11.0,43159,2014,10,105,True
2014-11-01,7.6,39457,2014,11,106,True
2014-12-01,4.4,49770,2014,12,107,True
2015-01-01,3.7,60891,2015,1,108,True
2015-02-01,3.5,46721,2015,2,109,True
2015-03-01,5.5,47895,2015,3,110,True
2015-04-01,7.9,45178,2015,4,111,True
2015-05-01,9.5,39343,2015,5,112,True
2015-06-01,12.7,42082,2015,6,113,True
2015-07-01,14.4,40512,2015,7,114,True
2015-08-01,14.7,36199,2015,8,115,True
2015-09-01,11.9,41573,2015,9,116,True
2015-10-01,10.0,42232,2015,10,117,True
2015-11-01,8.1,41520,2015,11,118,True
2015-12-01,7.9,45509,2015,12,119,True
2016-01-01,4.5,47457,2016,1,120,True
2016-02-01,3.8,46021,2016,2,121,True
2016-03-01,5.3,48665,2016,3,122,True
2016-04-01,6.5,46856,2016,4,123,True
2016-05-01,11.3,41384,2016,5,124,True
2016-06-01,13.9,42012,2016,6,125,True
2016-07-01,15.3,38983,2016,7,126,True
2016-08-01,15.5,40786,2016,8,127,True
2016-09-01,14.6,40367,2016,9,128,True
2016-10-01,9.8,40448,2016,10,129,True
2016-11-01,4.9,46514,2016,11,130,True
2016-12-01,5.9,45555,2016,12,131,True
2017-01-01,3.8,57368,2017,1,132,True
2017-02-01,5.2,47766,2017,2,133,True
2017-03-01,7.3,48664,2017,3,134,True
2017-04-01,8.0,39101,2017,4,135,True
2017-05-01,12.1,44279,2017,5,136,True
2017-06-01,14.4,42175,2017,6,137,True
2017-07-01,15.1,38425,2017,7,138,True
2017-08-01,14.5,41074,2017,8,139,True
2017-09-01,12.5,40095,2017,9,140,True
2017-10-01,11.2,43597,2017,10,141,True
2017-11-01,5.7,45580,2017,11,142,True
2017-12-01,4.1,45129,2017,12,143,True
2018-01-01,4.0,64154,2018,1,144,True
2018-02-01,2.3,49177,2018,2,145,True
2018-03-01,3.8,51229,2018,3,146,True
2018-04-01,8.4,46469,2018,4,147,True
2018-05-01,12.0,42784,2018,5,148,True
2018-06-01,14.8,39767,2018,6,149,True
2018-07-01,17.2,40723,2018,7,150,True
2018-08-01,15.2,40192,2018,8,151,True
2018-09-01,12.4,37137,2018,9,152,True
2018-10-01,9.5,44440,2018,10,153,True
2018-11-01,7.3,43978,2018,11,154,True
2018-12-01,5.8,41539,2018,12,155,True
2019-01-01,3.4,53910,2019,1,156,True
2019-02-01,6.0,45795,2019,2,157,True
2019-03-01,6.8,43944,2019,3,158,True
2019-04-01,8.4,44121,2019,4,159,True
2019-05-01,10.0,44389,2019,5,160,True
2019-06-01,13.2,38603,2019,6,161,True
2019-07-01,16.4,42308,2019,7,162,True
2019-08-01,15.8,38843,2019,8,163,True
2019-09-01,13.1,40011,2019,9,164,True
2019-10-01,8.9,46238,2019,10,165,True
2019-11-01,5.3,45219,2019,11,166,True
2019-12-01,5.1,47460,2019,12,167,True
2020-01-01,5.6,56704,2020,1,168,False
2020-02-01,5.1,43650,2020,2,169,False
2020-03-01,5.6,49723,2020,3,170,False
2020-04-01,9.1,88141,2020,4,171,False
2020-05-01,11.3,52363,2020,5,172,False
2020-06-01,14.0,42614,2020,6,173,False
2020-07-01,14.3,40778,2020,7,174,False
2020-08-01,15.9,37184,2020,8,175,False
2020-09-01,12.8,42494,2020,9,176,False
2020-10-01,9.4,46282,2020,10,177,False
2020-11-01,7.7,51317,2020,11,178,False
2020-12-01,4.3,56672,2020,12,179,False
2021-01-01,2.2,73315,2021,1,180,False
2021-02-01,4.1,58767,2021,2,181,False
2021-03-01,6.4,48624,2021,3,182,False
2021-04-01,5.7,41513,2021,4,183,False
2021-05-01,9.1,37864,2021,5,184,False
2021-06-01,14.2,41223,2021,6,185,False
2021-07-01,16.6,43264,2021,7,186,False
2021-08-01,15.0,43151,2021,8,187,False
2021-09-01,14.7,47520,2021,9,188,False
2021-10-01,10.9,46511,2021,10,189,False
2021-11-01,7.0,51602,2021,11,190,False
2021-12-01,5.3,52859,2021,12,191,False
2022-01-01,4.7,53158,2022,1,192,False
2022-02-01,5.6,45869,2022,2,193,False
2022-03-01,6.7,49489,2022,3,194,False
2022-04-01,8.1,45919,2022,4,195,False
2022-05-01,11.8,48611,2022,5,196,False
8 changes: 8 additions & 0 deletions examples/references.bib
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Expand Up @@ -131,6 +131,14 @@ @article{goodman1999
title = {Toward Evidence-Based Medical Statistics. 1: The P Value Fallacy},
journal = {Annals of Internal Medicine}
}
@article{google_causal_impact2015,
title = {Inferring causal impact using Bayesian structural time-series models},
author = {Kay H. Brodersen and Fabian Gallusser and Jim Koehler and Nicolas Remy and Steven L. Scott},
year = {2015},
journal = {Annals of Applied Statistics},
pages = {247--274},
volume = {9}
}
@misc{harper2015movielens,
title = {The MovieLens Datasets: History and Context},
author = {Harper, F. Maxwell and Konstan, Joseph A.},
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