Local Estimates of the Covid 19 Reproduction Number (R) for the United Kingdom Based on Admissions (doi:10.7910/DVN/0NYGXE)

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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
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Document Description
Citation
Title:	Local Estimates of the Covid 19 Reproduction Number (R) for the United Kingdom Based on Admissions
Identification Number:	doi:10.7910/DVN/0NYGXE
Distributor:	Harvard Dataverse
Date of Distribution:	2021-01-19
Version:	382
Bibliographic Citation:	Abbott, Sam; Bennett, Christopher; Hickson, Joe; Allen, Jamie; Sherratt, Katharine; Funk, Sebastian, 2021, "Local Estimates of the Covid 19 Reproduction Number (R) for the United Kingdom Based on Admissions", https://doi.org/10.7910/DVN/0NYGXE, Harvard Dataverse, V382
Study Description
Citation
Title:	Local Estimates of the Covid 19 Reproduction Number (R) for the United Kingdom Based on Admissions
Identification Number:	doi:10.7910/DVN/0NYGXE
Authoring Entity:	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)
Date of Production:	2022-03-24
Software used in Production:	covidrtestimates
Software used in Production:	EpiNow2
Distributor:	Harvard Dataverse
Access Authority:	Abbott, Sam
Holdings Information:	https://doi.org/10.7910/DVN/0NYGXE
Study Scope
Keywords:	Medicine, Health and Life Sciences, Medicine, Health and Life Sciences, COVID-19, Coronavirus, Pandemic, Reproduction Number, united-kingdom-local-admissions
Abstract:	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 at the local authority level in the United Kingdom.
Country:	United Kingdom
Geographic Unit(s):	authority
Methodology and Processing
Sources Statement
Data Access
Notes:	CC0 Waiver
Other Study Description Materials
File Description--f6103819
File: cases_by_infection.tab
	Number of cases: 18787 No. of variables per record: 13 Type of File: text/tab-separated-values
Notes:	UNF:6:XJtesXQaD0fvhCB+RjDz+w==
File Description--f6103821
File: cases_by_report.tab
	Number of cases: 18787 No. of variables per record: 13 Type of File: text/tab-separated-values
Notes:	UNF:6:91fl5iLxBKmv00P3SNA26w==
File Description--f6103822
File: growth_rate.tab
	Number of cases: 18787 No. of variables per record: 13 Type of File: text/tab-separated-values
Notes:	UNF:6:avsqF4VJILJVS1f4AIG0Vg==
File Description--f6103839
File: reported_cases.tab
	Number of cases: 16837 No. of variables per record: 3 Type of File: text/tab-separated-values
Notes:	UNF:6:8/bYePp3JjCZNEYOAJfmfQ==
File Description--f6103843
File: rt.tab
	Number of cases: 18787 No. of variables per record: 13 Type of File: text/tab-separated-values
Notes:	UNF:6:rcwEzqAGTfgmGSUEWQuHQg==
File Description--f6103846
File: summary_data.tab
	Number of cases: 296 No. of variables per record: 14 Type of File: text/tab-separated-values
Notes:	UNF:6:1/i9Pyyl9McmV/PW1dNGaQ==
File Description--f6103849
File: summary_table.tab
	Number of cases: 148 No. of variables per record: 6 Type of File: text/tab-separated-values
Notes:	UNF:6:TW5xVAactaU13/IDI8Yt6g==
Variable Description
List of Variables:	region - region 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 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 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 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 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 Region - Region New confirmed cases by infection date - New confirmed cases by infection date Expected change in daily cases - Expected change in daily cases Effective reproduction no. - Effective reproduction no. Rate of growth - Rate of growth Doubling/halving time (days) - Doubling/halving time (days)
Variables
region
f6103819 Location:	Variable Format: character Notes: UNF:6:xL4UK0sM9yIsLkL62QEE0w==
date
f6103819 Location:	Variable Format: character Notes: UNF:6:ZUxJ0K2kO5ZBMfH4tpe9xg==
strat
f6103819 Location:	Summary Statistics: Mean NaN; Max. NaN; Min. NaN; Valid 0.0; StDev NaN Variable Format: numeric Notes: UNF:6:kqb2QN3jx0/icjVnnsljig==
type
f6103819 Location:	Variable Format: character Notes: UNF:6:MU0uZWm4LMn1RxiTMB4KFQ==
median
f6103819 Location:	Summary Statistics: Mean 9.665401607494513; Max. 444.0; StDev 13.084575165557032; Valid 18787.0; Min. 0.5 Variable Format: numeric Notes: UNF:6:DtEnUtC3iY1N6VjfOD6fAA==
mean
f6103819 Location:	Summary Statistics: Mean 78.79280885718839; Max. 654209.3; StDev 5213.891898514932; Min. 0.6; Valid 18787.0; Variable Format: numeric Notes: UNF:6:Lo0Mnwtt/+pWNnVwuhdTmA==
sd
f6103819 Location:	Summary Statistics: Valid 18787.0; Max. 1.38761768E7; Min. 0.2; StDev 110059.2408515489; Mean 1501.6336775430016 Variable Format: numeric Notes: UNF:6:HExgZW87RAP/f2doRNH4DQ==
lower_90
f6103819 Location:	Summary Statistics: StDev 6.457946820451735; Valid 18787.0; Max. 64.1; Min. 0.0; Mean 6.485010911800683; Variable Format: numeric Notes: UNF:6:OCS2JhWX6kTbZZ8DCSRRVw==
lower_50
f6103819 Location:	Summary Statistics: Mean 7.975137062862621; Max. 129.7; StDev 8.341823365532846; Valid 18787.0; Min. 0.3 Variable Format: numeric Notes: UNF:6:iDzhSBzXyPXtrp6BhZd5aA==
lower_20
f6103819 Location:	Summary Statistics: Max. 276.3; Valid 18787.0; StDev 10.584030146928894; Min. 0.5; Mean 8.92299462394207 Variable Format: numeric Notes: UNF:6:8TS2e1x9lP+src9OV7Ya8w==
upper_20
f6103819 Location:	Summary Statistics: Mean 10.619683823920768; StDev 17.384978729077538; Valid 18787.0; Max. 734.7; Min. 0.6; Variable Format: numeric Notes: UNF:6:HtoObRiW+erU/sGMOoZlUQ==
upper_50
f6103819 Location:	Summary Statistics: StDev 34.05924843280252; Max. 1774.2; Min. 0.7; Mean 13.014132112631032; Valid 18787.0 Variable Format: numeric Notes: UNF:6:umbnKzZ4lmL86kbMEp84GQ==
upper_90
f6103819 Location:	Summary Statistics: Min. 0.9; Valid 18787.0; Mean 40.987874594135114; StDev 878.5788628219246; Max. 93412.2 Variable Format: numeric Notes: UNF:6:4ua/pVGvcAVjQVFJsYCF4w==
region
f6103821 Location:	Variable Format: character Notes: UNF:6:xL4UK0sM9yIsLkL62QEE0w==
date
f6103821 Location:	Variable Format: character Notes: UNF:6:ZUxJ0K2kO5ZBMfH4tpe9xg==
strat
f6103821 Location:	Summary Statistics: Valid 0.0; Max. NaN; Mean NaN; Min. NaN; StDev NaN; Variable Format: numeric Notes: UNF:6:kqb2QN3jx0/icjVnnsljig==
type
f6103821 Location:	Variable Format: character Notes: UNF:6:MU0uZWm4LMn1RxiTMB4KFQ==
median
f6103821 Location:	Summary Statistics: Mean 8.010139990418846; StDev 8.17567617694582; Min. 0.0; Max. 149.0; Valid 18787.0; Variable Format: numeric Notes: UNF:6:ZARMAGiNMvR4VRrwtHiNEA==
mean
f6103821 Location:	Summary Statistics: Max. 9701.3; Valid 18787.0; Mean 9.962479374035167; Min. 0.4; StDev 79.67350998560806 Variable Format: numeric Notes: UNF:6:cEd7ekUrzsj4RKn0dRBf1g==
sd
f6103821 Location:	Summary Statistics: Min. 0.6; Mean 26.620764358331673; Valid 18787.0; StDev 1360.2073815876365; Max. 166789.8 Variable Format: numeric Notes: UNF:6:DZR9QLxiy+T8iuOrKAwxqA==
lower_90
f6103821 Location:	Summary Statistics: Max. 52.0; Mean 3.328934901793754; Min. 0.0; Valid 18787.0; StDev 4.815140732301405; Variable Format: numeric Notes: UNF:6:9JQF9q2ciwf33/11PsxQSQ==
lower_50
f6103821 Location:	Summary Statistics: Min. 0.0; Valid 18787.0; Mean 5.808452653430613; Max. 72.0; StDev 6.460659917426974 Variable Format: numeric Notes: UNF:6:WR1u7eHxWkNLw587sliLWg==
lower_20
f6103821 Location:	Summary Statistics: Mean 7.123287379571104; Max. 104.0; Min. 0.0; StDev 7.426983591210704; Valid 18787.0 Variable Format: numeric Notes: UNF:6:SodJw3nb39y8UH7zYJZRwA==
upper_20
f6103821 Location:	Summary Statistics: Max. 218.0; Valid 18787.0; StDev 9.133433416323154; Min. 0.0; Mean 8.97170383776006 Variable Format: numeric Notes: UNF:6:oq2oqU92vMY4NzmyJv5Ppg==
upper_50
f6103821 Location:	Summary Statistics: StDev 11.680940697638196; Valid 18787.0; Mean 10.805461223186219; Min. 1.0; Max. 421.0 Variable Format: numeric Notes: UNF:6:5KjUmMwFEc+7przST5EkUg==
upper_90
f6103821 Location:	Summary Statistics: Valid 18787.0; Max. 5345.2; StDev 57.43549882417513; Mean 17.58222174908148; Min. 2.0 Variable Format: numeric Notes: UNF:6:Byjzp0q2WW6VnW+wPWuxxw==
region
f6103822 Location:	Variable Format: character Notes: UNF:6:xL4UK0sM9yIsLkL62QEE0w==
date
f6103822 Location:	Variable Format: character Notes: UNF:6:ZUxJ0K2kO5ZBMfH4tpe9xg==
strat
f6103822 Location:	Summary Statistics: Min. NaN; StDev NaN; Valid 0.0; Max. NaN; Mean NaN; Variable Format: numeric Notes: UNF:6:kqb2QN3jx0/icjVnnsljig==
type
f6103822 Location:	Variable Format: character Notes: UNF:6:MU0uZWm4LMn1RxiTMB4KFQ==
median
f6103822 Location:	Summary Statistics: Mean 0.012253389351764865; Valid 18787.0; Min. -0.0858813049462853; Max. 0.199257158637862; StDev 0.0359491270099344; Variable Format: numeric Notes: UNF:6:WBLGlPxKF7fvTZotBA7y1w==
mean
f6103822 Location:	Summary Statistics: Min. -0.0861010327871725; Max. 0.238993825210351; StDev 0.0374006317121855; Valid 18787.0; Mean 0.013169242740350225 Variable Format: numeric Notes: UNF:6:FjKOh9t/O7fNpGn4PG26EQ==
sd
f6103822 Location:	Summary Statistics: Max. 0.192675547200295; Valid 18787.0; Mean 0.02251962958275617; Min. 0.003633553842218; StDev 0.018747400724141477 Variable Format: numeric Notes: UNF:6:8s835zjVMPyMTr40aCaqaA==
lower_90
f6103822 Location:	Summary Statistics: Mean -0.021634809688814982; Valid 18787.0; Max. 0.0911790698025376; Min. -0.199974630294043; StDev 0.03430355978777803; Variable Format: numeric Notes: UNF:6:A6CVp7+yoVzW2RIq+HdLvg==
lower_50
f6103822 Location:	Summary Statistics: Max. 0.125674843895328; Valid 18787.0; Min. -0.128188533541998; StDev 0.03261133849703813; Mean -0.0013371224991638826 Variable Format: numeric Notes: UNF:6:+tzZdv22FoE5kChspXhj3Q==
lower_20
f6103822 Location:	Summary Statistics: Mean 0.007098375023759967; Max. 0.163093205171695; Min. -0.0965207256937452; StDev 0.034245951517347516; Valid 18787.0; Variable Format: numeric Notes: UNF:6:zgfr499G5m+OXko0BUV6rA==
upper_20
f6103822 Location:	Summary Statistics: Mean 0.017531095719993426; Max. 0.244004283708353; Min. -0.0797086338147046; StDev 0.0382137558783135; Valid 18787.0; Variable Format: numeric Notes: UNF:6:slOFnAHWjdkjJKIdVNjtCQ==
upper_50
f6103822 Location:	Summary Statistics: Max. 0.331280779143704; Mean 0.026660046468746486; StDev 0.04321396300232165; Min. -0.07013710380746; Valid 18787.0 Variable Format: numeric Notes: UNF:6:f32SdzFUILDBlUvtEQGUfg==
upper_90
f6103822 Location:	Summary Statistics: StDev 0.06200592627680932; Min. -0.0546133092598619; Max. 0.610890538044394; Mean 0.0510208517001381; Valid 18787.0 Variable Format: numeric Notes: UNF:6:Qou3Cqq7RRMG7/McwfiAlQ==
region
f6103839 Location:	Variable Format: character Notes: UNF:6:ZJsIumT4k65hqotUmolRRw==
date
f6103839 Location:	Variable Format: character Notes: UNF:6:5KvC/g7FpH1U18OajJbd7A==
confirm
f6103839 Location:	Summary Statistics: Mean 7.5302607352852355; StDev 7.288483416032663; Valid 16837.0; Min. 0.0; Max. 77.0; Variable Format: numeric Notes: UNF:6:vybb2GQbrnQD8ZZGyzpRDw==
region
f6103843 Location:	Variable Format: character Notes: UNF:6:xL4UK0sM9yIsLkL62QEE0w==
date
f6103843 Location:	Variable Format: character Notes: UNF:6:ZUxJ0K2kO5ZBMfH4tpe9xg==
strat
f6103843 Location:	Summary Statistics: Max. NaN; StDev NaN; Min. NaN; Valid 0.0; Mean NaN Variable Format: numeric Notes: UNF:6:kqb2QN3jx0/icjVnnsljig==
type
f6103843 Location:	Variable Format: character Notes: UNF:6:MU0uZWm4LMn1RxiTMB4KFQ==
median
f6103843 Location:	Summary Statistics: Max. 1.7913847373606; Min. 0.702269515271146; StDev 0.13376305678652445; Mean 1.047177413478681; Valid 18787.0; Variable Format: numeric Notes: UNF:6:F7vmoOqYXT1JzHpZvV/zAA==
mean
f6103843 Location:	Summary Statistics: Valid 18787.0; Max. 2.01195658827052; Min. 0.702684862089325; StDev 0.1410410905931847; Mean 1.0521994673048691 Variable Format: numeric Notes: UNF:6:xXTHAsz8VXZfIbJyYuUPsA==
sd
f6103843 Location:	Summary Statistics: StDev 0.07612898779980917; Valid 18787.0; Mean 0.084776003024245; Min. 0.0132649891565854; Max. 0.903375356246955 Variable Format: numeric Notes: UNF:6:EWtIDLkHdkZqexljmLBA6w==
lower_90
f6103843 Location:	Summary Statistics: Max. 1.34662249904281; Min. 0.358270236136744; Mean 0.9245126480241938; StDev 0.12175041855449129; Valid 18787.0; Variable Format: numeric Notes: UNF:6:8qzWLIh9lWsnE/zEX4L31Q==
lower_50
f6103843 Location:	Summary Statistics: Max. 1.48579314548148; Valid 18787.0; Mean 0.9971288322402043; StDev 0.11901001998125613; Min. 0.566940654084809 Variable Format: numeric Notes: UNF:6:c24PcSKBXHg0fzWo3/EWNQ==
lower_20
f6103843 Location:	Summary Statistics: Mean 1.028055945588661; StDev 0.1264188582749406; Max. 1.63872684008914; Min. 0.667872947759488; Valid 18787.0 Variable Format: numeric Notes: UNF:6:bpPQmpWu3weXgD831CtNPg==
upper_20
f6103843 Location:	Summary Statistics: Mean 1.0669356927111453; Max. 1.98769273048214; Min. 0.722479224112534; StDev 0.1434278452215586; Valid 18787.0 Variable Format: numeric Notes: UNF:6:QBjw0UQoJvyO8riuLSqtDw==
upper_50
f6103843 Location:	Summary Statistics: Min. 0.754180711660811; Valid 18787.0; Max. 2.3736363154617; Mean 1.101521474525572; StDev 0.16485515210546156; Variable Format: numeric Notes: UNF:6:P6eCazSOmDgCpFBIGmpdgA==
upper_90
f6103843 Location:	Summary Statistics: Valid 18787.0; Max. 3.76733002190656; Min. 0.807207486299775; StDev 0.2484588672041571; Mean 1.1965100786620102 Variable Format: numeric Notes: UNF:6:PhSLEQfN+o9gRYOz8nJdcw==
region
f6103846 Location:	Variable Format: character Notes: UNF:6:7IT5C4lDnlvAh7h1RcqFqg==
estimate
f6103846 Location:	Variable Format: character Notes: UNF:6:LDi1HscVWrnJKykUPl+4iw==
median
f6103846 Location:	Summary Statistics: Valid 296.0; Mean 7.187635135135108; Max. 66.0; StDev 10.840614427610516; Min. 0.73; Variable Format: numeric Notes: UNF:6:sN2VIpNrcV4Mi18lJIMVVw==
mean
f6103846 Location:	Summary Statistics: Max. 70.0; Valid 296.0; StDev 12.211752191995927; Mean 8.241621621621631; Min. 0.76 Variable Format: numeric Notes: UNF:6:1X4hqCz8W/9txn2HsqipBw==
sd
f6103846 Location:	Summary Statistics: Min. 0.041; Valid 296.0; StDev 6.87724362056026; Max. 46.0; Mean 4.502479729729722; Variable Format: numeric Notes: UNF:6:5ZRgkw3rORKq5MIt7pbFCg==
lower_90
f6103846 Location:	Summary Statistics: Max. 37.0; StDev 5.572089617972702; Min. 0.0; Mean 3.4100337837837893; Valid 296.0 Variable Format: numeric Notes: UNF:6:px04Afc/DCPhd1mobQJTxg==
lower_50
f6103846 Location:	Summary Statistics: StDev 8.222743029098263; Mean 5.308783783783805; Valid 296.0; Max. 52.0; Min. 0.57 Variable Format: numeric Notes: UNF:6:c5HQJ0+vztpFi1AsjtX2jg==
lower_20
f6103846 Location:	Summary Statistics: Valid 296.0; Max. 60.0; Min. 0.67; Mean 6.398716216216193; StDev 9.758280188876377; Variable Format: numeric Notes: UNF:6:yHC4Y34aMriAp7weIC++0w==
upper_20
f6103846 Location:	Summary Statistics: StDev 12.161281318062983; Valid 296.0; Mean 8.092804054054023; Min. 0.79; Max. 72.0 Variable Format: numeric Notes: UNF:6:jpjnGAQYYSsbRyDXCl0QLA==
upper_50
f6103846 Location:	Summary Statistics: Max. 84.0; Mean 9.930777027027021; StDev 14.678780917524819; Valid 296.0; Min. 0.91 Variable Format: numeric Notes: UNF:6:p5VJPt4RTJSO0+JJNNPrUQ==
upper_90
f6103846 Location:	Summary Statistics: Valid 296.0; Mean 16.605743243243293; Min. 1.1; StDev 24.124546907942378; Max. 146.0; Variable Format: numeric Notes: UNF:6:x+gobqjm1VHWHAozipyqzw==
metric
f6103846 Location:	Variable Format: character Notes: UNF:6:9544UcAtaLHK0akOz6sHHQ==
Expected change in daily cases
f6103846 Location:	Variable Format: character Notes: UNF:6:W7SoObEK1R5FRH0Ih44ojA==
prob_control
f6103846 Location:	Summary Statistics: Mean 0.23127702702702702; Valid 296.0; Max. 0.83; StDev 0.1553795493358424; Min. 0.004 Variable Format: numeric Notes: UNF:6:Ig0UCY0r7SUw7LEswCR7EA==
Region
f6103849 Location:	Variable Format: character Notes: UNF:6:x0JPZhxCqVw8wKHzMnG8PA==
New confirmed cases by infection date
f6103849 Location:	Variable Format: character Notes: UNF:6:0GId9WGy7bqZlmtbCpd4fQ==
Expected change in daily cases
f6103849 Location:	Variable Format: character Notes: UNF:6:BU+6wIbz9HbU6gwPqhqtDw==
Effective reproduction no.
f6103849 Location:	Variable Format: character Notes: UNF:6:1PRSVTPixjagKGuhY5C91g==
Rate of growth
f6103849 Location:	Variable Format: character Notes: UNF:6:h4EcvIFrq8SjGzDaSgo1Cw==
Doubling/halving time (days)
f6103849 Location:	Variable Format: character Notes: UNF:6:3yGs5ht2CENBFNXP1Hmxrw==
Other Study-Related Materials
Label:	high_infections_plot.png
Text:
Notes:	image/png
Other Study-Related Materials
Label:	high_reported_cases_plot.png
Text:
Notes:	image/png
Other Study-Related Materials
Label:	high_rt_plot.png
Text:
Notes:	image/png
Other Study-Related Materials
Label:	infections_plot.png
Text:
Notes:	image/png
Other Study-Related Materials
Label:	latest_date.rds
Text:
Notes:	application/gzip
Other Study-Related Materials
Label:	reported_cases_plot.png
Text:
Notes:	image/png
Other Study-Related Materials
Label:	rt_plot.png
Text:
Notes:	image/png
Other Study-Related Materials
Label:	summary_plot.png
Text:
Notes:	image/png