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New Rt notebook model using MCMC #537

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Jul 7, 2020
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New Rt notebook model using MCMC #537

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New Rt notebook model using MCMC
Jul 7, 2020
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RT action run
Jul 7, 2020
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525 changes: 270 additions & 255 deletions data/calc/calculated_rt_gp_district_cumulative.csv
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132 changes: 132 additions & 0 deletions data/calc/calculated_rt_sa_mcmc.csv
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date,Median,High_80,Low_80
2020-02-26,1.894,2.184,1.567
2020-02-27,1.896,2.169,1.582
2020-02-28,1.884,2.148,1.573
2020-02-29,1.879,2.093,1.551
2020-03-01,1.865,2.113,1.611
2020-03-02,1.851,2.099,1.603
2020-03-03,1.830,2.041,1.585
2020-03-04,1.811,2.050,1.609
2020-03-05,1.780,1.959,1.551
2020-03-06,1.744,1.931,1.551
2020-03-07,1.701,1.900,1.543
2020-03-08,1.660,1.808,1.478
2020-03-09,1.613,1.766,1.461
2020-03-10,1.559,1.700,1.422
2020-03-11,1.503,1.632,1.376
2020-03-12,1.443,1.566,1.322
2020-03-13,1.390,1.504,1.285
2020-03-14,1.338,1.436,1.226
2020-03-15,1.290,1.385,1.186
2020-03-16,1.247,1.330,1.144
2020-03-17,1.207,1.290,1.105
2020-03-18,1.178,1.269,1.093
2020-03-19,1.148,1.233,1.067
2020-03-20,1.130,1.213,1.054
2020-03-21,1.115,1.190,1.036
2020-03-22,1.103,1.179,1.028
2020-03-23,1.095,1.167,1.010
2020-03-24,1.090,1.169,1.011
2020-03-25,1.084,1.157,1.006
2020-03-26,1.079,1.153,1.004
2020-03-27,1.075,1.155,1.004
2020-03-28,1.074,1.152,0.994
2020-03-29,1.077,1.156,0.995
2020-03-30,1.078,1.158,0.995
2020-03-31,1.078,1.166,0.997
2020-04-01,1.081,1.152,0.985
2020-04-02,1.082,1.168,1.000
2020-04-03,1.081,1.162,1.000
2020-04-04,1.086,1.159,0.999
2020-04-05,1.087,1.155,0.991
2020-04-06,1.088,1.172,1.009
2020-04-07,1.088,1.174,1.008
2020-04-08,1.087,1.168,1.007
2020-04-09,1.088,1.161,0.998
2020-04-10,1.088,1.162,0.999
2020-04-11,1.091,1.171,1.009
2020-04-12,1.096,1.178,1.020
2020-04-13,1.099,1.171,1.013
2020-04-14,1.102,1.183,1.024
2020-04-15,1.109,1.186,1.028
2020-04-16,1.114,1.196,1.039
2020-04-17,1.117,1.195,1.035
2020-04-18,1.125,1.199,1.037
2020-04-19,1.131,1.207,1.042
2020-04-20,1.137,1.215,1.053
2020-04-21,1.140,1.221,1.059
2020-04-22,1.146,1.225,1.062
2020-04-23,1.156,1.231,1.075
2020-04-24,1.160,1.242,1.075
2020-04-25,1.166,1.249,1.082
2020-04-26,1.171,1.251,1.085
2020-04-27,1.172,1.262,1.087
2020-04-28,1.176,1.249,1.070
2020-04-29,1.179,1.263,1.081
2020-04-30,1.182,1.263,1.089
2020-05-01,1.183,1.280,1.097
2020-05-02,1.183,1.279,1.107
2020-05-03,1.184,1.261,1.096
2020-05-04,1.182,1.267,1.091
2020-05-05,1.182,1.270,1.095
2020-05-06,1.182,1.264,1.095
2020-05-07,1.177,1.255,1.088
2020-05-08,1.177,1.263,1.092
2020-05-09,1.173,1.251,1.081
2020-05-10,1.170,1.263,1.094
2020-05-11,1.166,1.269,1.096
2020-05-12,1.167,1.249,1.078
2020-05-13,1.168,1.242,1.079
2020-05-14,1.165,1.252,1.086
2020-05-15,1.161,1.254,1.082
2020-05-16,1.160,1.237,1.069
2020-05-17,1.158,1.241,1.076
2020-05-18,1.159,1.238,1.065
2020-05-19,1.157,1.235,1.067
2020-05-20,1.156,1.236,1.066
2020-05-21,1.154,1.250,1.075
2020-05-22,1.154,1.238,1.061
2020-05-23,1.152,1.241,1.064
2020-05-24,1.160,1.243,1.067
2020-05-25,1.163,1.264,1.088
2020-05-26,1.164,1.260,1.082
2020-05-27,1.171,1.263,1.088
2020-05-28,1.177,1.253,1.084
2020-05-29,1.177,1.253,1.085
2020-05-30,1.176,1.263,1.098
2020-05-31,1.183,1.264,1.100
2020-06-01,1.184,1.266,1.102
2020-06-02,1.184,1.272,1.102
2020-06-03,1.187,1.268,1.104
2020-06-04,1.188,1.268,1.096
2020-06-05,1.188,1.279,1.114
2020-06-06,1.194,1.266,1.100
2020-06-07,1.192,1.279,1.104
2020-06-08,1.194,1.285,1.112
2020-06-09,1.193,1.291,1.109
2020-06-10,1.193,1.298,1.110
2020-06-11,1.195,1.283,1.093
2020-06-12,1.193,1.289,1.087
2020-06-13,1.196,1.294,1.088
2020-06-14,1.202,1.304,1.085
2020-06-15,1.199,1.323,1.100
2020-06-16,1.195,1.316,1.083
2020-06-17,1.191,1.330,1.092
2020-06-18,1.189,1.304,1.063
2020-06-19,1.191,1.300,1.030
2020-06-20,1.188,1.325,1.046
2020-06-21,1.186,1.332,1.037
2020-06-22,1.191,1.344,1.030
2020-06-23,1.185,1.353,1.023
2020-06-24,1.185,1.373,1.027
2020-06-25,1.190,1.348,0.984
2020-06-26,1.185,1.351,0.973
2020-06-27,1.187,1.379,0.984
2020-06-28,1.184,1.386,0.977
2020-06-29,1.188,1.388,0.957
2020-06-30,1.184,1.393,0.959
2020-07-01,1.176,1.406,0.965
2020-07-02,1.182,1.394,0.943
2020-07-03,1.190,1.430,0.960
2020-07-04,1.190,1.440,0.949
2020-07-05,1.195,1.447,0.943
70 changes: 40 additions & 30 deletions data/calc/calculated_rt_sa_provincial_cumulative.csv
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Original file line number Diff line number Diff line change
Expand Up @@ -82,9 +82,10 @@ EC,2020-06-29,1.05,1.26,0.81
EC,2020-06-30,1.03,1.24,0.79
EC,2020-07-01,1.12,1.33,0.88
EC,2020-07-02,1.19,1.39,0.94
EC,2020-07-03,1.24,1.44,1.00
EC,2020-07-04,1.19,1.38,0.94
EC,2020-07-05,1.12,1.33,0.90
EC,2020-07-03,1.39,1.59,1.15
EC,2020-07-04,1.38,1.57,1.14
EC,2020-07-05,1.37,1.56,1.14
EC,2020-07-06,1.40,1.59,1.18
FS,2020-05-29,2.28,4.74,0.00
FS,2020-05-30,2.17,3.90,0.10
FS,2020-05-31,1.91,3.38,0.20
Expand Down Expand Up @@ -120,9 +121,10 @@ FS,2020-06-29,1.82,2.30,1.28
FS,2020-06-30,1.90,2.36,1.38
FS,2020-07-01,1.97,2.43,1.50
FS,2020-07-02,1.91,2.33,1.44
FS,2020-07-03,1.82,2.21,1.35
FS,2020-07-04,1.65,2.05,1.22
FS,2020-07-05,1.47,1.86,1.04
FS,2020-07-03,1.85,2.24,1.38
FS,2020-07-04,1.68,2.07,1.24
FS,2020-07-05,1.52,1.89,1.07
FS,2020-07-06,1.38,1.75,0.94
GP,2020-03-17,2.84,5.17,0.05
GP,2020-03-18,2.62,4.47,0.50
GP,2020-03-19,2.30,3.83,0.59
Expand Down Expand Up @@ -231,9 +233,10 @@ GP,2020-06-29,1.34,1.50,1.15
GP,2020-06-30,1.45,1.61,1.27
GP,2020-07-01,1.60,1.75,1.42
GP,2020-07-02,1.63,1.77,1.45
GP,2020-07-03,1.52,1.66,1.35
GP,2020-07-04,1.38,1.52,1.22
GP,2020-07-05,1.24,1.38,1.08
GP,2020-07-03,1.46,1.60,1.29
GP,2020-07-04,1.28,1.41,1.10
GP,2020-07-05,1.09,1.23,0.92
GP,2020-07-06,0.90,1.04,0.73
KZN,2020-03-23,3.62,6.09,0.75
KZN,2020-03-24,3.01,4.74,0.96
KZN,2020-03-25,2.58,3.97,0.97
Expand Down Expand Up @@ -336,9 +339,10 @@ KZN,2020-06-29,1.65,1.92,1.34
KZN,2020-06-30,1.70,1.97,1.41
KZN,2020-07-01,1.76,2.02,1.48
KZN,2020-07-02,1.77,2.01,1.49
KZN,2020-07-03,1.66,1.89,1.38
KZN,2020-07-04,1.52,1.75,1.26
KZN,2020-07-05,1.34,1.56,1.07
KZN,2020-07-03,1.57,1.80,1.29
KZN,2020-07-04,1.36,1.59,1.09
KZN,2020-07-05,1.11,1.34,0.84
KZN,2020-07-06,0.91,1.14,0.63
LP,2020-06-10,2.28,4.74,0.00
LP,2020-06-11,1.89,3.64,0.03
LP,2020-06-12,2.11,3.62,0.31
Expand All @@ -362,9 +366,10 @@ LP,2020-06-29,1.65,2.19,1.04
LP,2020-06-30,1.62,2.14,1.02
LP,2020-07-01,1.64,2.14,1.05
LP,2020-07-02,1.68,2.16,1.10
LP,2020-07-03,1.68,2.17,1.15
LP,2020-07-04,1.64,2.12,1.13
LP,2020-07-05,1.64,2.08,1.11
LP,2020-07-03,1.64,2.11,1.08
LP,2020-07-04,1.56,2.03,1.03
LP,2020-07-05,1.48,1.94,0.96
LP,2020-07-06,1.34,1.79,0.82
MP,2020-06-11,2.88,5.02,0.20
MP,2020-06-12,2.65,4.31,0.69
MP,2020-06-13,2.25,3.62,0.71
Expand All @@ -387,9 +392,10 @@ MP,2020-06-29,1.67,2.20,1.10
MP,2020-06-30,1.73,2.22,1.15
MP,2020-07-01,1.81,2.28,1.25
MP,2020-07-02,1.82,2.29,1.31
MP,2020-07-03,1.75,2.19,1.24
MP,2020-07-04,1.65,2.08,1.16
MP,2020-07-05,1.54,1.96,1.06
MP,2020-07-03,1.80,2.23,1.28
MP,2020-07-04,1.71,2.15,1.24
MP,2020-07-05,1.61,2.02,1.13
MP,2020-07-06,1.49,1.91,1.04
NC,2020-06-14,2.00,4.23,0.00
NC,2020-06-15,1.48,3.10,0.00
NC,2020-06-16,0.99,2.40,0.00
Expand All @@ -409,9 +415,10 @@ NC,2020-06-29,1.67,2.46,0.80
NC,2020-06-30,1.82,2.57,1.01
NC,2020-07-01,1.87,2.56,1.09
NC,2020-07-02,1.80,2.46,1.07
NC,2020-07-03,1.72,2.35,1.02
NC,2020-07-04,1.59,2.22,0.94
NC,2020-07-05,1.49,2.09,0.84
NC,2020-07-03,1.77,2.39,1.06
NC,2020-07-04,1.67,2.26,0.98
NC,2020-07-05,1.61,2.18,0.94
NC,2020-07-06,1.54,2.09,0.88
NW,2020-05-27,0.26,3.96,0.00
NW,2020-05-28,1.34,3.32,0.00
NW,2020-05-29,1.22,2.83,0.00
Expand Down Expand Up @@ -449,9 +456,10 @@ NW,2020-06-29,1.20,1.59,0.81
NW,2020-06-30,1.30,1.65,0.87
NW,2020-07-01,1.47,1.83,1.07
NW,2020-07-02,1.60,1.94,1.20
NW,2020-07-03,1.61,1.93,1.21
NW,2020-07-04,1.57,1.88,1.18
NW,2020-07-05,1.51,1.82,1.14
NW,2020-07-03,1.59,1.92,1.20
NW,2020-07-04,1.53,1.85,1.15
NW,2020-07-05,1.41,1.74,1.06
NW,2020-07-06,1.23,1.54,0.86
WC,2020-03-20,2.17,4.55,0.00
WC,2020-03-21,1.82,3.51,0.03
WC,2020-03-22,2.18,3.69,0.44
Expand Down Expand Up @@ -557,9 +565,10 @@ WC,2020-06-29,0.95,1.17,0.69
WC,2020-06-30,1.13,1.34,0.86
WC,2020-07-01,1.22,1.42,0.95
WC,2020-07-02,1.16,1.37,0.91
WC,2020-07-03,1.06,1.27,0.81
WC,2020-07-04,0.95,1.16,0.70
WC,2020-07-05,0.79,1.00,0.53
WC,2020-07-03,1.07,1.28,0.82
WC,2020-07-04,0.97,1.18,0.72
WC,2020-07-05,0.87,1.07,0.60
WC,2020-07-06,0.93,1.14,0.67
Total RSA,2020-03-19,2.11,3.70,0.22
Total RSA,2020-03-20,2.50,3.73,1.09
Total RSA,2020-03-21,2.75,3.71,1.67
Expand Down Expand Up @@ -666,6 +675,7 @@ Total RSA,2020-06-29,1.25,1.36,1.09
Total RSA,2020-06-30,1.40,1.52,1.26
Total RSA,2020-07-01,1.54,1.66,1.41
Total RSA,2020-07-02,1.51,1.63,1.39
Total RSA,2020-07-03,1.40,1.50,1.26
Total RSA,2020-07-04,1.25,1.36,1.13
Total RSA,2020-07-05,1.12,1.22,0.99
Total RSA,2020-07-03,1.39,1.50,1.26
Total RSA,2020-07-04,1.22,1.31,1.07
Total RSA,2020-07-05,1.07,1.17,0.94
Total RSA,2020-07-06,0.98,1.09,0.86
13 changes: 13 additions & 0 deletions notebooks/covid-model/LICENSE
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Copyright 2020 Kevin Systrom, rt.live

Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
You may obtain a copy of the License at

http://www.apache.org/licenses/LICENSE-2.0

Unless required by applicable law or agreed to in writing, software
distributed under the License is distributed on an "AS IS" BASIS,
WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
See the License for the specific language governing permissions and
limitations under the License.
1 change: 1 addition & 0 deletions notebooks/covid-model/covid/__init__.py
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__version__ = "0.1.0"
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