National Reproduction Number (R) Based on Reported Cases (doi:10.7910/DVN/TTLQRN)

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Part 1: Document Description
Part 2: Study Description
Part 3: Data Files Description
Part 4: Variable Description
Part 5: Other Study-Related Materials
Entire Codebook

National Reproduction Number (R) Based on Reported Cases

doi:10.7910/DVN/TTLQRN

Harvard Dataverse

2020-10-23

280

Abbott, Sam; Bennett, Christopher; Hickson, Joe; Allen, Jamie; Sherratt, Katharine; Funk, Sebastian, 2020, "National Reproduction Number (R) Based on Reported Cases", https://doi.org/10.7910/DVN/TTLQRN, Harvard Dataverse, V280, UNF:6:ZCentiztRe+smcx5jdTKQA== [fileUNF]

National Reproduction Number (R) Based on Reported Cases

doi:10.7910/DVN/TTLQRN

Abbott, Sam (Centre for the Mathematical Modelling of Infectious Diseases, Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, UK)

Bennett, Christopher (Met Office, Exeter, UK)

Hickson, Joe (Met Office, Exeter, UK)

Allen, Jamie (Met Office, Exeter, UK)

Sherratt, Katharine (Centre for the Mathematical Modelling of Infectious Diseases, Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, UK)

Funk, Sebastian (Centre for the Mathematical Modelling of Infectious Diseases, Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, UK)

2022-03-24

covidrtestimates

EpiNow2

Harvard Dataverse

Abbott, Sam

https://doi.org/10.7910/DVN/TTLQRN

Medicine, Health and Life Sciences, COVID-19, Coronavirus, Pandemic, Reproduction Number, cases

Identifying changes in the reproduction number, rate of spread, and doubling time during the course of the COVID-19 outbreak whilst accounting for potential biases due to delays in case reporting both nationally and subnationally. These results are impacted by changes in testing effort, increases and decreases in testing effort will increase and decrease reproduction number estimates respectively.

Afghanistan, Albania, Algeria, American Samoa, Andorra, Angola, Anguilla, Argentina, Armenia, Aruba, Australia, Austria, Azerbaijan, Bahamas, Bahrain, Bangladesh, Barbados, Belarus, Belgium, Belize, Bermuda, Bhutan, Botswana, Brazil, Bulgaria, Burkina Faso, Burundi, Cambodia, Cameroon, Canada, Cape Verde, Cayman Islands, Central African Republic, Chile, China, Colombia, Comoros, Cook Islands, Costa Rica, Croatia, Cuba, Curaçao, Cyprus, Denmark, Djibouti, Dominica, Dominican Republic, Ecuador, Egypt, El Salvador, Equatorial Guinea, Eritrea, Estonia, Ethiopia, Faroe Islands, Fiji, Finland, France, French Guiana, French Polynesia, Gabon, Gambia, Georgia, Germany, Ghana, Gibraltar, Greece, Greenland, Grenada, Guadeloupe, Guam, Guatemala, Guernsey, Guinea, Guinea-Bissau, Guyana, Haiti, Honduras, Hungary, Iceland, Indonesia, Iraq, Ireland, Isle of Man, Israel, Italy, Jamaica, Japan, Jersey, Jordan, Kazakhstan, Kenya, Kiribati, Kuwait, Kyrgyzstan, Latvia, Lebanon, Lesotho, Liberia, Libya, Liechtenstein, Lithuania, Luxembourg, Madagascar, Malawi, Malaysia, Maldives, Mali, Malta, Martinique, Mauritania, Mauritius, Mayotte, Mexico, Monaco, Mongolia, Montenegro, Montserrat, Morocco, Mozambique, Nepal, Netherlands, New Caledonia, New Zealand, Nicaragua, Niger, Nigeria, Northern Mariana Islands, Norway, Oman, Pakistan, Palau, Panama, Papua New Guinea, Paraguay, Peru, Philippines, Poland, Portugal, Puerto Rico, Qatar, Romania, Rwanda, Réunion, Saint Martin (French part), Samoa, San Marino, Saudi Arabia, Senegal, Serbia, Seychelles, Sierra Leone, Singapore, Slovakia, Slovenia, Solomon Islands, Somalia, South Africa, South Sudan, Spain, Sri Lanka, Sudan, Suriname, Sweden, Switzerland, Tajikistan, Thailand, Timor-Leste, Togo, Tonga, Tunisia, Turkey, Uganda, Ukraine, United Arab Emirates, United Kingdom, United States, Uruguay, Uzbekistan, Vanuatu, Yemen, Zambia, Zimbabwe

country

<a href="http://creativecommons.org/publicdomain/zero/1.0">CC0 1.0</a>

• Number of cases: 27082

• No. of variables per record: 13

• Type of File: text/tab-separated-values

UNF:6:dFPBm3jt4bFReZkH4XPXWQ==

• Number of cases: 27082

• No. of variables per record: 13

• Type of File: text/tab-separated-values

UNF:6:YY479A3U6TntiZqCOPNRDQ==

• Number of cases: 26781

• No. of variables per record: 3

• Type of File: text/tab-separated-values

UNF:6:F5GkvxxcxqrkvslQYSqc6g==

• Number of cases: 434

• No. of variables per record: 14

• Type of File: text/tab-separated-values

UNF:6:yHS0xKkr+3zRUHsQn8GjwQ==

• country - country
• date - date
• strat - strat
• type - type
• median - median
• mean - mean
• sd - sd
• lower_90 - lower_90
• lower_50 - lower_50
• lower_20 - lower_20
• upper_20 - upper_20
• upper_50 - upper_50
• upper_90 - upper_90
• country - country
• date - date
• strat - strat
• type - type
• median - median
• mean - mean
• sd - sd
• lower_90 - lower_90
• lower_50 - lower_50
• lower_20 - lower_20
• upper_20 - upper_20
• upper_50 - upper_50
• upper_90 - upper_90
• region - region
• date - date
• confirm - confirm
• region - region
• estimate - estimate
• median - median
• mean - mean
• sd - sd
• lower_90 - lower_90
• lower_50 - lower_50
• lower_20 - lower_20
• upper_20 - upper_20
• upper_50 - upper_50
• upper_90 - upper_90
• metric - metric
• Expected change in daily cases - Expected change in daily cases
• prob_control - prob_control

f6153018 Location:

Variable Format: character

Notes: UNF:6:jfbbcNCM91E/fs5Pz4ABBg==

f6153018 Location:

Variable Format: character

Notes: UNF:6:3bSlcImXAsCoYc3sDdXAfw==

f6153018 Location:

Summary Statistics: Valid 0.0; StDev NaN; Max. NaN; Mean NaN; Min. NaN;

Variable Format: numeric

Notes: UNF:6:Tn/OCO6fOrexp6UHJgdRGw==

f6153018 Location:

Variable Format: character

Notes: UNF:6:5Pt2ohewBHoGm6DzQOlcZQ==

f6153018 Location:

Summary Statistics: Mean 11554.987308913811; Valid 27082.0; Max. 3.76955049E7; Min. 0.0; StDev 268828.06187799486;

Variable Format: numeric

Notes: UNF:6:jVLQb2XdvyEhLDGf9AGBrg==

f6153018 Location:

Summary Statistics: Max. 1.7216795067E10; Min. 0.0; Mean 1659065.9376486072; Valid 27082.0; StDev 1.2178632867183538E8

Variable Format: numeric

Notes: UNF:6:jIN55xV36sghABtSzO5+qQ==

f6153018 Location:

Summary Statistics: Min. 0.0; Valid 27082.0; Mean 2.4077501000606157E7; StDev 1.4788635108366816E9; Max. 1.809666211592E11

Variable Format: numeric

Notes: UNF:6:DtRXzs2ZEowhbU+uNLetoA==

f6153018 Location:

Summary Statistics: Mean 7105.197843586259; Valid 27082.0; Min. 0.0; Max. 811414.0; StDev 32789.571924681215;

Variable Format: numeric

Notes: UNF:6:PQlMHjvzu43wxbUexLF76g==

f6153018 Location:

Summary Statistics: Mean 8004.45813824675; Max. 856449.8; StDev 36098.73290069623; Valid 27082.0; Min. 0.0

Variable Format: numeric

Notes: UNF:6:2DXd4By/9fLoo/VyALi0Tg==

f6153018 Location:

Summary Statistics: Valid 27082.0; StDev 75578.08485139045; Mean 9135.43977180412; Min. 0.0; Max. 8951828.0

Variable Format: numeric

Notes: UNF:6:kcTR2us4Pzsc/YmNKEg7uA==

f6153018 Location:

Summary Statistics: Min. 0.0; Mean 21438.023321763103; StDev 1212819.5181431186; Max. 1.758521587E8; Valid 27082.0

Variable Format: numeric

Notes: UNF:6:pGmngd64cKMjd6YkcyDSZg==

f6153018 Location:

Summary Statistics: Valid 27082.0; Max. 2.21817936E9; StDev 1.478332382966461E7; Min. 0.0; Mean 148984.4720367803;

Variable Format: numeric

Notes: UNF:6:LP0yzt2JIXpJL0zO+ZNyIg==

f6153018 Location:

Summary Statistics: StDev 4.241499339737105E8; Max. 6.54559066587E10; Valid 27082.0; Min. 0.0; Mean 3747937.327959282

Variable Format: numeric

Notes: UNF:6:u3/h88SFy3ovFARSqXpwCg==

f6153021 Location:

Variable Format: character

Notes: UNF:6:jfbbcNCM91E/fs5Pz4ABBg==

f6153021 Location:

Variable Format: character

Notes: UNF:6:3bSlcImXAsCoYc3sDdXAfw==

f6153021 Location:

Summary Statistics: Min. NaN; Max. NaN; StDev NaN; Valid 0.0; Mean NaN;

Variable Format: numeric

Notes: UNF:6:Tn/OCO6fOrexp6UHJgdRGw==

f6153021 Location:

Variable Format: character

Notes: UNF:6:5Pt2ohewBHoGm6DzQOlcZQ==

f6153021 Location:

Summary Statistics: Min. -0.372727781865932; StDev 0.09574543201418638; Max. 0.803106267017853; Valid 27082.0; Mean -0.0068566834093243415;

Variable Format: numeric

Notes: UNF:6:bbDOOUPVTpa21y6ECygZbQ==

f6153021 Location:

Summary Statistics: Mean -0.004595993463265817; Max. 0.829747521279091; Valid 27082.0; StDev 0.09689418175519543; Min. -0.371728137055308;

Variable Format: numeric

Notes: UNF:6:GqiDOo1WO4IvG4f5gvmDMA==

f6153021 Location:

Summary Statistics: Valid 27082.0; Mean 0.03631605294518189; StDev 0.03749963724448111; Max. 0.398167278362116; Min. 0.00313718545092347

Variable Format: numeric

Notes: UNF:6:27aUDQyqFv4/6rZy9M1LIQ==

f6153021 Location:

Summary Statistics: Max. 0.402090785771673; Mean -0.05917112736363204; StDev 0.10031677251590437; Valid 27082.0; Min. -0.408715945268588

Variable Format: numeric

Notes: UNF:6:5pfBclXfEJoa8dhnZJsjgw==

f6153021 Location:

Summary Statistics: StDev 0.09508217652632459; Mean -0.028613551826359086; Valid 27082.0; Min. -0.387545573699932; Max. 0.522886355114975

Variable Format: numeric

Notes: UNF:6:oUjb/dLwDha/DBJx4bIoIg==

f6153021 Location:

Summary Statistics: Mean -0.015152607930292866; Min. -0.378438475501288; Valid 27082.0; Max. 0.693331506444413; StDev 0.09492118595596843;

Variable Format: numeric

Notes: UNF:6:seRcnC1URtyUXnv3HIhd4w==

f6153021 Location:

Summary Statistics: Max. 0.924393982630659; Valid 27082.0; Min. -0.367659581083015; StDev 0.09749972381002062; Mean 0.0016974830679903792;

Variable Format: numeric

Notes: UNF:6:yMpTLSsFrW626LOwIPGIqQ==

f6153021 Location:

Summary Statistics: Max. 1.13376988487345; Min. -0.35828720259251; Mean 0.016700047006532576; StDev 0.10276142333982038; Valid 27082.0

Variable Format: numeric

Notes: UNF:6:yZdZ2ivQRjwzsYJwqjuCJQ==

f6153021 Location:

Summary Statistics: StDev 0.12975017448536558; Mean 0.05751544717429629; Valid 27082.0; Min. -0.337420124178685; Max. 1.48586128916982

Variable Format: numeric

Notes: UNF:6:k63pLT/XcZD4qfpRosqQgg==

f6153028 Location:

Variable Format: character

Notes: UNF:6:oVWRgkn65zI6rZnJNf3WMQ==

f6153028 Location:

Variable Format: character

Notes: UNF:6:WN+2P3+k2ntUO1nTKCVrkA==

f6153028 Location:

Summary Statistics: Valid 26781.0; Max. 1294889.0; Mean 7863.978865614042; StDev 36900.18449410009; Min. 0.0;

Variable Format: numeric

Notes: UNF:6:AD5lm0MQGYp7JgLQ/qrmrg==

f6153029 Location:

Variable Format: character

Notes: UNF:6:etSSo4/dQoSAkAkhWjN1tQ==

f6153029 Location:

Variable Format: character

Notes: UNF:6:DagvSILnpuUsgLVoJ1CUyQ==

f6153029 Location:

Summary Statistics: StDev 23838.017442793036; Valid 434.0; Max. 323650.0; Min. 0.0; Mean 3503.826509446995;

Variable Format: numeric

Notes: UNF:6:49j9WsPFNcp8r/ZWf0KcRw==

f6153029 Location:

Summary Statistics: Mean 3830.8476635944876; Max. 330295.0; Min. 0.0; Valid 434.0; StDev 24945.81250645258;

Variable Format: numeric

Notes: UNF:6:wkPZ0uoj0rPzZaEnjM3VDg==

f6153029 Location:

Summary Statistics: Max. 104598.0; Valid 434.0; StDev 9310.199640494113; Mean 1946.0162142857062; Min. 0.0;

Variable Format: numeric

Notes: UNF:6:ODKwKxhp8RqmxPhQok6c6Q==

f6153029 Location:

Summary Statistics: Valid 434.0; Max. 212621.0; Mean 1918.966501198165; StDev 14407.570485884857; Min. 0.0;

Variable Format: numeric

Notes: UNF:6:n17T3Vvj5c/4KeFXsg3eYg==

f6153029 Location:

Summary Statistics: Max. 274758.0; StDev 19468.93554040878; Valid 434.0; Mean 2740.7899039170657; Min. 0.0

Variable Format: numeric

Notes: UNF:6:2JrQ6Kjeg53ubhtKR+RglQ==

f6153029 Location:

Summary Statistics: StDev 22114.57261088039; Min. 0.0; Mean 3196.0634082949337; Valid 434.0; Max. 304655.0;

Variable Format: numeric

Notes: UNF:6:pvn/ysIDq46SQPSU9tabtg==

f6153029 Location:

Summary Statistics: Max. 341683.0; StDev 25640.03729049465; Min. 0.0; Valid 434.0; Mean 3838.5655428571326

Variable Format: numeric

Notes: UNF:6:OcVMqmAJ/qhPJRtm9XWRIw==

f6153029 Location:

Summary Statistics: Min. 0.0; Valid 434.0; Mean 4497.627587557631; StDev 29134.226048285585; Max. 376046.0

Variable Format: numeric

Notes: UNF:6:amjvoVlwKeyrR1u6j7X4jw==

f6153029 Location:

Summary Statistics: Min. 0.0; StDev 40009.11276111796; Mean 6715.928488479219; Valid 434.0; Max. 475850.0

Variable Format: numeric

Notes: UNF:6:4a7lTR7xWaLGmdDYrue1ww==

f6153029 Location:

Variable Format: character

Notes: UNF:6:MKKGGDopjteAgkWi0/K7LQ==

f6153029 Location:

Variable Format: character

Notes: UNF:6:XyhymFD6CT9apAxo1beJRQ==

f6153029 Location:

Summary Statistics: Mean 0.6375191244239631; StDev 0.2807834960502433; Max. 1.0; Valid 434.0; Min. 2.5E-4

Variable Format: numeric

Notes: UNF:6:noogL+qsHo2BA691DACOgg==

Label:

high_reported_cases_plot.png

Text:

image/png

Label:

high_rt_plot.png

Text:

image/png

Label:

latest_date.rds

Text:

application/gzip