Replication Data for: Genomic surveillance reveals the spread patterns of SARS-CoV-2 in coastal Kenya during the first two waves (doi:10.7910/DVN/4ZZYIM)

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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:

Replication Data for: Genomic surveillance reveals the spread patterns of SARS-CoV-2 in coastal Kenya during the first two waves

Identification Number:

doi:10.7910/DVN/4ZZYIM

Distributor:

Harvard Dataverse

Date of Distribution:

2021-08-03

Version:

3

Bibliographic Citation:

Agoti, Charles N., 2021, "Replication Data for: Genomic surveillance reveals the spread patterns of SARS-CoV-2 in coastal Kenya during the first two waves", https://doi.org/10.7910/DVN/4ZZYIM, Harvard Dataverse, V3, UNF:6:RL6Vg7q0JyS7YoCkjhHe1A== [fileUNF]

Study Description

Citation

Title:

Replication Data for: Genomic surveillance reveals the spread patterns of SARS-CoV-2 in coastal Kenya during the first two waves

Identification Number:

doi:10.7910/DVN/4ZZYIM

Authoring Entity:

Agoti, Charles N. (KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya)

Distributor:

Harvard Dataverse

Access Authority:

Agoti, Charles N.

Access Authority:

The Data Governance Committee

Depositor:

Agoti, Charles N.

Date of Deposit:

2021-08-03

Holdings Information:

https://doi.org/10.7910/DVN/4ZZYIM

Study Scope

Keywords:

Medicine, Health and Life Sciences, COVID-19, SARS-CoV-2

Abstract:

This is a replication dataset for the manuscript titled: "<a href="https://doi.org/10.1101/2021.07.01.21259583">Genomic surveillance reveals the spread patterns of SARS-CoV-2 in coastal Kenya during the first two waves</a>."

Notes:

<p><strong>Data Access: </strong> Open</p> <p><a href="https://creativecommons.org/licenses/by/4.0/legalcode">Creative Commons Attribution 4.0 International</a> <a href="https://creativecommons.org/licenses/by/4.0/legalcode"><img src="https://i.creativecommons.org/l/by/3.0/88x31.png"> </a> </p> <p><strong> Genomic Data Availability:</strong> Coastal Kenya genomes have been deposited to both GISAID (Accession numbers: EPI_ISL_1039223-29; EPI_ISL1440075-109, IPI_ISL_457845-931; EPI_ISL_568695-872; EPI_ISL806548-717; EPI_ISL_855494-548; EPI_ISL_968807-9245).</p>

Methodology and Processing

Sources Statement

Data Access

Citation Requirement:

<p>Publications based on this data collection should acknowledge this source by means of bibliographic citation.</p>

Notes:

<p>This data is licensed under the <a href="https://creativecommons.org/licenses/by/4.0/legalcode">Creative Commons Attribution 4.0 International</a> <a href="https://creativecommons.org/licenses/by/4.0/legalcode"><img src="https://i.creativecommons.org/l/by/3.0/88x31.png"> </a> </p>

Other Study Description Materials

Related Publications

Citation

Title:

Genomic surveillance reveals the spread patterns of SARS-CoV-2 in coastal Kenya during the first two waves Charles N. Agoti, Lynette Isabella Ochola-Oyier, Khadija Said Mohammed, Arnold W. Lambisia, Zaydah R. de Laurent, John M. Morobe, Maureen W. Mburu, Donwilliams O. Omuoyo, Edidah M. Ongera, Leonard Ndwiga, Eric Maitha, Benson Kitole, Thani Suleiman, Mohamed Mwakinangu, John Nyambu, John Otieno, Barke Salim, Jennifer Musyoki, Nickson Murunga, Edward Otieno, John Kiiru, Kadondi Kasera, Patrick Amoth, Mercy Mwangangi, Rashid Aman, Samson Kinyanjui, George Warimwe, My Phan, Ambrose Agweyu, Matthew Cotten, Edwine Barasa, Benjamin Tsofa, D. James Nokes, Philip Bejon, George Githinji medRxiv 2021.07.01.21259583;

Identification Number:

10.1101/2021.07.01.21259583

Bibliographic Citation:

Genomic surveillance reveals the spread patterns of SARS-CoV-2 in coastal Kenya during the first two waves Charles N. Agoti, Lynette Isabella Ochola-Oyier, Khadija Said Mohammed, Arnold W. Lambisia, Zaydah R. de Laurent, John M. Morobe, Maureen W. Mburu, Donwilliams O. Omuoyo, Edidah M. Ongera, Leonard Ndwiga, Eric Maitha, Benson Kitole, Thani Suleiman, Mohamed Mwakinangu, John Nyambu, John Otieno, Barke Salim, Jennifer Musyoki, Nickson Murunga, Edward Otieno, John Kiiru, Kadondi Kasera, Patrick Amoth, Mercy Mwangangi, Rashid Aman, Samson Kinyanjui, George Warimwe, My Phan, Ambrose Agweyu, Matthew Cotten, Edwine Barasa, Benjamin Tsofa, D. James Nokes, Philip Bejon, George Githinji medRxiv 2021.07.01.21259583;

File Description--f5191731

File: All_Africa_lineage_report_11Aug2021.tab

  • Number of cases: 13372

  • No. of variables per record: 13

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

Notes:

UNF:6:kp4xiWLP5d3lfZSt+qA3ew==

File Description--f5191734

File: coastal_counties_smoothed.tab

  • Number of cases: 352

  • No. of variables per record: 8

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

Notes:

UNF:6:w/6knXKJjjJMoWoPHGuu1w==

File Description--f5191773

File: Coast_sequences_05Sep2021.insertions.tab

  • Number of cases: 748

  • No. of variables per record: 2

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

Notes:

UNF:6:ZESTYUCV3zYYYcH/aDuHWQ==

File Description--f5191733

File: coast_sequences_12Aug2021.tab

  • Number of cases: 752

  • No. of variables per record: 2

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

Notes:

UNF:6:b5q6NGD4B17nYQxz5ff+Cg==

File Description--f5191735

File: daily_summaries_26_Feb_2020.tab

  • Number of cases: 292

  • No. of variables per record: 52

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

Notes:

UNF:6:nmetVXRJAVQNe/RMx7xbxg==

File Description--f5191752

File: meta_globe+Ken_subsampleone_B.1.1_wave2.tab

  • Number of cases: 1661

  • No. of variables per record: 11

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

Notes:

UNF:6:5snawHrOgX5tkb0aRk2hZg==

File Description--f5191755

File: meta_globe+Ken_subsampleone_B.1.333_wave2.tab

  • Number of cases: 1043

  • No. of variables per record: 11

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

Notes:

UNF:6:KNT+4pBB8D0gjnsNhZILjw==

File Description--f5191757

File: meta_globe_Ken_subsampleone_B.1.530_wave2.tab

  • Number of cases: 57

  • No. of variables per record: 11

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

Notes:

UNF:6:XX5J3LzpBVZkjv7GwB3oAg==

File Description--f5191758

File: meta_globe_Ken_subsampleone_B.1.535_wave2.tab

  • Number of cases: 1964

  • No. of variables per record: 11

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

Notes:

UNF:6:33Isb2R6XtS3qc/KzwvXBQ==

File Description--f5191761

File: meta_globe_Ken_subsampleone_B.1.549_wave2.tab

  • Number of cases: 56

  • No. of variables per record: 11

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

Notes:

UNF:6:NfXZKiRW5CULqETUGxn/qg==

File Description--f5191763

File: meta_globe_Ken_subsampleone_B.1.596.1_wave2.tab

  • Number of cases: 51

  • No. of variables per record: 11

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

Notes:

UNF:6:NNQZIH8kHEYNNeh5nFsMyQ==

File Description--f5191750

File: meta_globe_Ken_subsampleone_B.1_wave2.tab

  • Number of cases: 2777

  • No. of variables per record: 14

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

Notes:

UNF:6:yuDb+lErNqD1ViYT5wgE6A==

File Description--f5191764

File: meta_globe_Ken_subsampleone_N.8_wave2.tab

  • Number of cases: 604

  • No. of variables per record: 11

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

Notes:

UNF:6:LTira8/k2i513w/xXApCFg==

File Description--f5191779

File: meta_globe_Ken_subsampleone_wave2.tab

  • Number of cases: 4748

  • No. of variables per record: 13

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

Notes:

UNF:6:F/9nE5VTOhe+kQIpN+ItiQ==

File Description--f5191732

File: monthly_sequencing_2.tab

  • Number of cases: 12

  • No. of variables per record: 7

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

Notes:

UNF:6:nh2xdDPIN02wFKaKQ0Yw5A==

File Description--f5191737

File: owid-covid-data.tab

  • Number of cases: 96225

  • No. of variables per record: 60

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

Notes:

UNF:6:blhFoQ/mKXJ9wT3WgNdnEQ==

File Description--f5191744

File: subsample_one_12Aug21.tab

  • Number of cases: 4000

  • No. of variables per record: 2

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

Notes:

UNF:6:8TGYVmKv1G2dLZ1UOn1CgA==

Variable Description

List of Variables:

Variables

taxon

f5191731 Location:

Variable Format: character

Notes: UNF:6:5xrNYIWrg/3xzHmsVe1dOg==

lineage

f5191731 Location:

Variable Format: character

Notes: UNF:6:NR1cYFwf6O2I9Sk6GXZB5w==

conflict

f5191731 Location:

Summary Statistics: StDev 0.0; Mean 0.0; Valid 6250.0; Max. 0.0; Min. 0.0

Variable Format: numeric

Notes: UNF:6:mxbzjtlq2kzn1p0SCoquTQ==

ambiguity_score

f5191731 Location:

Summary Statistics: Max. 1.0; Min. 0.504762972094587; Valid 6250.0; StDev 0.08522002173312301; Mean 0.9416055787154402;

Variable Format: numeric

Notes: UNF:6:z/wYTDqXOTwM6IQVYI7fkg==

scorpio_call

f5191731 Location:

Variable Format: character

Notes: UNF:6:SVB3tGaYbwviKH36My07EA==

scorpio_support

f5191731 Location:

Summary Statistics: Mean 0.8250777628935029; StDev 0.08973644610735598; Min. 0.4286; Valid 4479.0; Max. 1.0

Variable Format: numeric

Notes: UNF:6:einFwOeSUAxoHi/gcSKu4g==

scorpio_conflict

f5191731 Location:

Summary Statistics: Min. 0.0; StDev 0.049137998968447755; Valid 4479.0; Max. 0.25; Mean 0.02427334226389809

Variable Format: numeric

Notes: UNF:6:dlWwhOrRX9wt0HcsSI1zeQ==

version

f5191731 Location:

Variable Format: character

Notes: UNF:6:D4YZ9N1Qz+MVqV5CEs1eFA==

pangolin_version

f5191731 Location:

Variable Format: character

Notes: UNF:6:uoXB/y7jpu8kGk0+IFmAwQ==

pangoLEARN_version

f5191731 Location:

Variable Format: character

Notes: UNF:6:3sXlsupXK5Fyw6RgEd9HDw==

pango_version

f5191731 Location:

Variable Format: character

Notes: UNF:6:HdZFwssDccTJOP6WP1OzCw==

status

f5191731 Location:

Variable Format: character

Notes: UNF:6:qDjsUIMkqyC7dYwEr40HnQ==

note

f5191731 Location:

Variable Format: character

Notes: UNF:6:aJ6VYd/x4Ir1/gAdtOOtJw==

date

f5191734 Location:

Variable Format: character

Notes: UNF:6:Ge9v06vMYRbXgA7s3VEO0Q==

Kwale

f5191734 Location:

Summary Statistics: Mean 1.7636372549019603; Min. 0.0; Valid 306.0; StDev 2.176325078730757; Max. 11.536;

Variable Format: numeric

Notes: UNF:6:kgXt9VPkgVNAhTknANuEEA==

Kilifi

f5191734 Location:

Summary Statistics: Max. 53.555; Mean 5.720124260355029; Valid 338.0; Min. 0.0; StDev 10.025538716114553

Variable Format: numeric

Notes: UNF:6:czGJdZxVGuIoPiQKEzJTwA==

TanaRiver

f5191734 Location:

Summary Statistics: Max. 11.756; Min. 0.0; Mean 1.4311294642857133; StDev 2.3518153175997036; Valid 224.0;

Variable Format: numeric

Notes: UNF:6:dPzBs+z37xtYVOpZQk8TuQ==

Lamu

f5191734 Location:

Summary Statistics: Min. 0.0; Valid 244.0; Max. 53.601; Mean 8.810803278688526; StDev 11.191005595977837

Variable Format: numeric

Notes: UNF:6:b8rdgq1+vCvN7KlpA3pivA==

TaitaTaveta

f5191734 Location:

Summary Statistics: StDev 7.689295920625914; Min. 0.0; Valid 285.0; Max. 32.709; Mean 6.8540456140350905

Variable Format: numeric

Notes: UNF:6:WgEX4nk20EttKJavzOWiTg==

Mombasa

f5191734 Location:

Summary Statistics: StDev 25.494855168950167; Min. 1.3; Mean 22.798967164179107; Max. 121.301; Valid 335.0

Variable Format: numeric

Notes: UNF:6:QBq3oJB0o2ejCk8Uua3irA==

Coast

f5191734 Location:

Summary Statistics: Mean 9.211686390532543; StDev 11.068138564821153; Max. 56.457; Valid 338.0; Min. 0.297

Variable Format: numeric

Notes: UNF:6:elTGQM97oXcOIiG4nEL7xg==

seqName

f5191773 Location:

Variable Format: character

Notes: UNF:6:3OGJSiRdyhaOt5GUMEEKBg==

insertions

f5191773 Location:

Variable Format: character

Notes: UNF:6:Q69aVmOdJoQopWVoQm7euA==

taxa_name

f5191733 Location:

Variable Format: character

Notes: UNF:6:pie1J5dDpUUzbVZ/yD+pBg==

actualseq

f5191733 Location:

Variable Format: character

Notes: UNF:6:I8j90I2KAOZ45ExcB/kJLA==

datetested

f5191735 Location:

Variable Format: character

Notes: UNF:6:hVBTG+l1b6lSfmJGksS5Fg==

daily_summ

f5191735 Location:

Summary Statistics: Mean 286.24315068493144; StDev 191.7646192521236; Max. 1130.0; Valid 292.0; Min. 1.0;

Variable Format: numeric

Notes: UNF:6:ypmdMO6UIGnbISuo6ybBiw==

daily_positive

f5191735 Location:

Summary Statistics: Min. 0.0; Valid 292.0; Mean 21.88356164383561; StDev 24.33938453422309; Max. 170.0;

Variable Format: numeric

Notes: UNF:6:sIdhBPrrmywzQxpeZW6k4A==

daily_retest

f5191735 Location:

Summary Statistics: StDev 4.787214206190547; Max. 40.0; Mean 2.489726027397262; Valid 292.0; Min. 0.0

Variable Format: numeric

Notes: UNF:6:GQjDiJtOEJzLVsK78fNc8Q==

daily_unique

f5191735 Location:

Summary Statistics: Mean 19.393835616438384; Max. 149.0; StDev 21.71430466678334; Min. 0.0; Valid 292.0;

Variable Format: numeric

Notes: UNF:6:b6B5dkia8EcEKvYyjT1rrA==

prop_uniq_pos

f5191735 Location:

Summary Statistics: Max. 0.9; StDev 0.09591652238898007; Min. 0.0; Mean 0.08028092157534247; Valid 292.0

Variable Format: numeric

Notes: UNF:6:6sS/AmN8FfLCEyLOchO17Q==

daily_kajiado

f5191735 Location:

Summary Statistics: Min. 0.0; Max. 46.0; Valid 292.0; Mean 0.9349315068493166; StDev 5.122473796514696

Variable Format: numeric

Notes: UNF:6:sxUoq8d5Q2cKmMuWPhcdUQ==

daily_pos_kajiado

f5191735 Location:

Summary Statistics: Max. 12.0; StDev 1.0682748815358136; Valid 292.0; Min. 0.0; Mean 0.1746575342465755

Variable Format: numeric

Notes: UNF:6:sYdoMshT7T04TPsyj/jemQ==

daily_r_kajiado

f5191735 Location:

Summary Statistics: Min. 0.0; StDev 0.3192427371859278; Mean 0.034246575342465814; Valid 292.0; Max. 5.0;

Variable Format: numeric

Notes: UNF:6:gDDfOHYeDpq9fPhB+S8+Ew==

unique_pos_kajiado

f5191735 Location:

Summary Statistics: Mean 0.14041095890410993; Min. 0.0; Valid 292.0; StDev 0.9760766382453174; Max. 12.0

Variable Format: numeric

Notes: UNF:6:uRDra7oUm+/L3f3H57FSew==

prop_pos_kajiado

f5191735 Location:

Summary Statistics: Min. 0.0; Valid 18.0; Max. 0.4166667; StDev 0.15000933494482532; Mean 0.13176100555555556;

Variable Format: numeric

Notes: UNF:6:aWV5l3XAoDTmmdx+U3fd3Q==

daily_kilifi

f5191735 Location:

Summary Statistics: Min. 0.0; StDev 45.01735714254262; Mean 44.205479452054796; Valid 292.0; Max. 257.0

Variable Format: numeric

Notes: UNF:6:EcmOKNPn89l0b1eT1Gy6dA==

daily_pos_kilifi

f5191735 Location:

Summary Statistics: Valid 292.0; Mean 4.93835616438357; Min. 0.0; Max. 114.0; StDev 12.526108872035463;

Variable Format: numeric

Notes: UNF:6:nUsmeqBTREjxvsFicJzNIA==

daily_r_kilifi

f5191735 Location:

Summary Statistics: Valid 292.0; StDev 2.8509721462336373; Max. 37.0; Min. 0.0; Mean 0.8082191780821896;

Variable Format: numeric

Notes: UNF:6:Q8m5UzXlKVJQfFKGUrUDPQ==

unique_pos_kilifi

f5191735 Location:

Summary Statistics: Max. 97.0; Min. 0.0; StDev 10.52228118592831; Mean 4.130136986301369; Valid 292.0;

Variable Format: numeric

Notes: UNF:6:fvOURl5dEAyrASpEHAFcyQ==

prop_pos_kilifi

f5191735 Location:

Summary Statistics: StDev 0.1344931882249256; Valid 274.0; Mean 0.08296138832116785; Min. 0.0; Max. 0.8888889;

Variable Format: numeric

Notes: UNF:6:6eePr1SQlUCT1abQCgCVxw==

daily_kwale

f5191735 Location:

Summary Statistics: Mean 18.804794520547944; StDev 26.45997257660867; Min. 0.0; Valid 292.0; Max. 125.0;

Variable Format: numeric

Notes: UNF:6:ZQ63szYn6ucI2JPEydBgCQ==

daily_pos_kwale

f5191735 Location:

Summary Statistics: Max. 31.0; Valid 292.0; Min. 0.0; Mean 1.4965753424657549; StDev 3.885383914452838

Variable Format: numeric

Notes: UNF:6:np5Gc10bNSrUKVYknaKO+Q==

daily_r_kwale

f5191735 Location:

Summary Statistics: Valid 292.0; Max. 3.0; Mean 0.034246575342465814; StDev 0.25990702968095825; Min. 0.0

Variable Format: numeric

Notes: UNF:6:qcOsag0dmbRT7tMn7gzBdg==

unique_pos_kwale

f5191735 Location:

Summary Statistics: StDev 3.8603569874086734; Mean 1.4623287671232887; Max. 31.0; Min. 0.0; Valid 292.0;

Variable Format: numeric

Notes: UNF:6:Kw4WszaNGpmwjVDshyvqtA==

prop_pos_kwale

f5191735 Location:

Summary Statistics: Valid 161.0; Max. 1.0; StDev 0.1509510215171258; Mean 0.07992038509316772; Min. 0.0;

Variable Format: numeric

Notes: UNF:6:xz/b6IrYynjYEGdQquWTfg==

daily_laikipia

f5191735 Location:

Summary Statistics: Min. 0.0; Mean 0.18150684931506866; Valid 292.0; StDev 2.5815763698208816; Max. 43.0

Variable Format: numeric

Notes: UNF:6:7rbroiRTUmpMgk6Q7Trf/A==

daily_pos_laikipia

f5191735 Location:

Summary Statistics: Max. 2.0; StDev 0.11704114719613103; Min. 0.0; Valid 292.0; Mean 0.00684931506849313;

Variable Format: numeric

Notes: UNF:6:kKu4rQEoWiPZ8/uDASQOow==

daily_r_laikipia

f5191735 Location:

Summary Statistics: Valid 292.0; Min. 0.0; Max. 0.0; Mean 0.0; StDev 0.0

Variable Format: numeric

Notes: UNF:6:FRQOZMwUF+S+0hD1zQau7Q==

unique_pos_laikipia

f5191735 Location:

Summary Statistics: Valid 292.0; Mean 0.00684931506849313; StDev 0.11704114719613103; Min. 0.0; Max. 2.0

Variable Format: numeric

Notes: UNF:6:kKu4rQEoWiPZ8/uDASQOow==

prop_pos_laikipia

f5191735 Location:

Summary Statistics: Min. 0.0; Valid 2.0; Mean 0.0232558; Max. 0.0465116; StDev 0.03288866776383623

Variable Format: numeric

Notes: UNF:6:D1NZUX6xrjErHULNfl4JuA==

daily_lamu

f5191735 Location:

Summary Statistics: Min. 0.0; Max. 135.0; Valid 292.0; StDev 20.72066138015096; Mean 9.431506849315081;

Variable Format: numeric

Notes: UNF:6:RBa2LqqbNZfAvY9tDIUGfQ==

daily_pos_lamu

f5191735 Location:

Summary Statistics: Max. 41.0; Mean 1.1952054794520535; StDev 3.6183349855422073; Min. 0.0; Valid 292.0;

Variable Format: numeric

Notes: UNF:6:wgMHfkLGopQXdQdJq50IDw==

daily_r_lamu

f5191735 Location:

Summary Statistics: Mean 0.1335616438356166; StDev 0.8924869610075116; Min. 0.0; Max. 13.0; Valid 292.0

Variable Format: numeric

Notes: UNF:6:PKywo0Hdw1k4Lyc7xPgVuw==

unique_pos_lamu

f5191735 Location:

Summary Statistics: StDev 2.991907993191191; Min. 0.0; Valid 292.0; Mean 1.06164383561644; Max. 28.0

Variable Format: numeric

Notes: UNF:6:AIm7HVnLXp41Wxxp9rV5HQ==

prop_pos_lamu

f5191735 Location:

Summary Statistics: Valid 114.0; Mean 0.11558979210526317; StDev 0.16212220250480183; Max. 1.0; Min. 0.0

Variable Format: numeric

Notes: UNF:6:k2O/UWAfWopEvoO4kHCtAw==

daily_mombasa

f5191735 Location:

Summary Statistics: Valid 292.0; Max. 898.0; StDev 143.49899519736078; Mean 158.02397260273983; Min. 0.0

Variable Format: numeric

Notes: UNF:6:l7eGrYdD4QPL1hoxdJaF6Q==

daily_pos_mombasa

f5191735 Location:

Summary Statistics: Mean 10.743150684931516; Min. 0.0; Max. 87.0; Valid 292.0; StDev 12.700588007786843

Variable Format: numeric

Notes: UNF:6:mKFqzaKThi7aJGAbz23NaQ==

daily_r_mombasa

f5191735 Location:

Summary Statistics: Valid 292.0; StDev 3.1240269397817255; Min. 0.0; Max. 27.0; Mean 1.0821917808219195

Variable Format: numeric

Notes: UNF:6:X+PKt7ew3iC5E6mor9EWcQ==

unique_pos_mombasa

f5191735 Location:

Summary Statistics: Mean 9.660958904109593; Min. 0.0; StDev 11.483655639371381; Max. 75.0; Valid 292.0

Variable Format: numeric

Notes: UNF:6:XsgRVzoxO+OAXIS5AuSpwQ==

prop_pos_mombasa

f5191735 Location:

Summary Statistics: StDev 0.14728791065403066; Valid 277.0; Mean 0.09358629133574008; Min. 0.0; Max. 1.0

Variable Format: numeric

Notes: UNF:6:/A1a0FyJi4IVUhfkAOz1HQ==

daily_nairobi

f5191735 Location:

Summary Statistics: Valid 292.0; StDev 27.71967355050296; Max. 472.0; Min. 0.0; Mean 1.8527397260273986;

Variable Format: numeric

Notes: UNF:6:cEjJkJGevmCrO/Ox86uL6g==

daily_pos_nairobi

f5191735 Location:

Summary Statistics: Valid 292.0; Mean 0.034246575342465814; Min. 0.0; StDev 0.35004925645827956; Max. 5.0

Variable Format: numeric

Notes: UNF:6:uyXbHuH0AH35CqDeDibaLw==

daily_r_nairobi

f5191735 Location:

Summary Statistics: Valid 292.0; Min. 0.0; Max. 0.0; Mean 0.0; StDev 0.0

Variable Format: numeric

Notes: UNF:6:FRQOZMwUF+S+0hD1zQau7Q==

unique_pos_nairobi

f5191735 Location:

Summary Statistics: Mean 0.034246575342465814; Max. 5.0; Min. 0.0; Valid 292.0; StDev 0.35004925645827956

Variable Format: numeric

Notes: UNF:6:uyXbHuH0AH35CqDeDibaLw==

prop_pos_nairobi

f5191735 Location:

Summary Statistics: Min. 0.0; Valid 9.0; StDev 0.16315999207400775; Mean 0.07453884444444445; Max. 0.5;

Variable Format: numeric

Notes: UNF:6:DwDADI6VOScbbT+keSH0Mw==

daily_taita_taveta

f5191735 Location:

Summary Statistics: Max. 323.0; StDev 60.151237608783156; Valid 292.0; Min. 0.0; Mean 49.80479452054788

Variable Format: numeric

Notes: UNF:6:eXYvNPNa1Dss058VQaG+vw==

daily_pos_taita_taveta

f5191735 Location:

Summary Statistics: StDev 6.646644426015044; Max. 52.0; Min. 0.0; Valid 292.0; Mean 2.9349315068493116;

Variable Format: numeric

Notes: UNF:6:gSAIwMjYfKvK38H+HQoMjA==

daily_r_taita_taveta

f5191735 Location:

Summary Statistics: Mean 0.3493150684931511; StDev 1.6312770522976507; Min. 0.0; Max. 21.0; Valid 292.0

Variable Format: numeric

Notes: UNF:6:XAmFCoxfco2EUPLa0/kL7Q==

unique_pos_taita_taveta

f5191735 Location:

Summary Statistics: StDev 5.757666214470464; Mean 2.585616438356161; Valid 292.0; Min. 0.0; Max. 51.0

Variable Format: numeric

Notes: UNF:6:/BQc43aq4iizYifMWUqNkg==

prop_pos_taita_taveta

f5191735 Location:

Summary Statistics: Valid 217.0; Min. 0.0; StDev 0.12842247349220146; Mean 0.068742399078341; Max. 1.0

Variable Format: numeric

Notes: UNF:6:BoDgovJcrYmBf1BZOHLdLw==

daily_tana_river

f5191735 Location:

Summary Statistics: Min. 0.0; StDev 9.005724902245388; Mean 3.0034246575342416; Valid 292.0; Max. 62.0

Variable Format: numeric

Notes: UNF:6:uzxSAWa5qj5Q+GoA1hnCuQ==

daily_pos_tana_river

f5191735 Location:

Summary Statistics: Valid 292.0; StDev 1.502853129260115; Min. 0.0; Max. 13.0; Mean 0.3595890410958914

Variable Format: numeric

Notes: UNF:6:dlnYTdd3oaDKOyHl/wbyMg==

daily_r_tana_river

f5191735 Location:

Summary Statistics: Mean 0.04794520547945198; StDev 0.3281142995220061; Min. 0.0; Valid 292.0; Max. 3.0;

Variable Format: numeric

Notes: UNF:6:DKCvr6GwxADg7xt+mgq1qQ==

unique_pos_tana_river

f5191735 Location:

Summary Statistics: StDev 1.2905157749886336; Max. 11.0; Mean 0.31164383561643944; Min. 0.0; Valid 292.0

Variable Format: numeric

Notes: UNF:6:CvT4SJYbC20KRthTLNHIig==

prop_pos_tana_river

f5191735 Location:

Summary Statistics: Max. 1.0; Mean 0.08856566781609203; Min. 0.0; Valid 87.0; StDev 0.19397216216566587;

Variable Format: numeric

Notes: UNF:6:wOKeMSdoXlblmKWqZudULQ==

dups

f5191735 Location:

Summary Statistics: Mean 0.4863013698630134; Max. 1.0; Min. 0.0; Valid 292.0; StDev 0.5006703598254437

Variable Format: numeric

Notes: UNF:6:2+j5uvTgYyoMQKRxEGLchg==

strain

f5191752 Location:

Variable Format: character

Notes: UNF:6:92EyqNj730hpW+RovZg4wQ==

date

f5191752 Location:

Summary Statistics: StDev 0.23653261676751802; Valid 1661.0; Mean 2020.480195063215; Max. 2021.153; Min. 2020.208

Variable Format: numeric

Notes: UNF:6:iUek3bNP1m8T9gLPiGAIEw==

id

f5191752 Location:

Variable Format: character

Notes: UNF:6:3kKZLZnh5fSwHLH5yoPYEQ==

lineage

f5191752 Location:

Variable Format: character

Notes: UNF:6:2iJhY/YWY6nwx2xhTUuklw==

location

f5191752 Location:

Variable Format: character

Notes: UNF:6:GZxDllOAN65zHwfKUVfm3Q==

sample_id

f5191752 Location:

Variable Format: character

Notes: UNF:6:mfwh5KSCuaJKJHcUESgZOQ==

date_collection

f5191752 Location:

Variable Format: character

Notes: UNF:6:/QpRod6haWQPsY9FhjqmUw==

datecollection

f5191752 Location:

Variable Format: character

Notes: UNF:6:/QpRod6haWQPsY9FhjqmUw==

county_origin

f5191752 Location:

Variable Format: character

Notes: UNF:6:8BY/PiM3SlZccSTx8K8e/Q==

country

f5191752 Location:

Variable Format: character

Notes: UNF:6:ukPJnIu9+Jh7UdVDbxxWXg==

kenya_or_global

f5191752 Location:

Variable Format: character

Notes: UNF:6:zyws4F2MY9K9QwbQoH9opA==

strain

f5191755 Location:

Variable Format: character

Notes: UNF:6:wzhn5Y60Zu3k/LHkIVGvJA==

date

f5191755 Location:

Summary Statistics: Max. 2021.526; Mean 2020.4950719079577; StDev 0.37897360323010243; Min. 2020.178; Valid 1043.0

Variable Format: numeric

Notes: UNF:6:z5qdyk41IAJzcAm7xw1bpA==

id

f5191755 Location:

Variable Format: character

Notes: UNF:6:wzhn5Y60Zu3k/LHkIVGvJA==

lineage

f5191755 Location:

Variable Format: character

Notes: UNF:6:ih0NAuSlMKVZV2ZMEL8T1Q==

location

f5191755 Location:

Variable Format: character

Notes: UNF:6:+Er7A/P7KeaoUQVLRyTxoA==

sample_id

f5191755 Location:

Variable Format: character

Notes: UNF:6:RdMnWWqQSFhFC9FgqHfpeg==

date_collection

f5191755 Location:

Variable Format: character

Notes: UNF:6:gWR22geyUEf/CANewAv9SA==

datecollection

f5191755 Location:

Variable Format: character

Notes: UNF:6:gWR22geyUEf/CANewAv9SA==

county_origin

f5191755 Location:

Variable Format: character

Notes: UNF:6:R4OTvRYHrzlSrPyfongRDg==

country

f5191755 Location:

Variable Format: character

Notes: UNF:6:rCTJ6TJYgEHEbA7NnF7DqQ==

kenya_or_global

f5191755 Location:

Variable Format: character

Notes: UNF:6:npSjpYewXdrC2LXG5+Whag==

strain

f5191757 Location:

Variable Format: character

Notes: UNF:6:Z3tp/u4yRhqnH5teDONm2g==

date

f5191757 Location:

Summary Statistics: Min. 2020.705; StDev 0.1175848144808422; Valid 57.0; Mean 2020.9929122807018; Max. 2021.345

Variable Format: numeric

Notes: UNF:6:tbMLt9Mty4vOYIF0Tt3RrQ==

id

f5191757 Location:

Variable Format: character

Notes: UNF:6:cfJfl6cOO4Zbxg3nTEP08g==

lineage

f5191757 Location:

Variable Format: character

Notes: UNF:6:F0+1AiipuErVEZsbma7nPw==

location

f5191757 Location:

Variable Format: character

Notes: UNF:6:QEkBD4ovLRsL0h1HJVHxiA==

sample_id

f5191757 Location:

Variable Format: character

Notes: UNF:6:i6JHQMTF5KGQbvP9FlWJ2w==

date_collection

f5191757 Location:

Variable Format: character

Notes: UNF:6:5b19qQtmWpXvpkXRdwG4ww==

datecollection

f5191757 Location:

Variable Format: character

Notes: UNF:6:5b19qQtmWpXvpkXRdwG4ww==

county_origin

f5191757 Location:

Variable Format: character

Notes: UNF:6:DoZy0KT4sffdFDHq5tlEpg==

country

f5191757 Location:

Variable Format: character

Notes: UNF:6:4oNd9LVytZVOphh7L5icPQ==

kenya_or_global

f5191757 Location:

Variable Format: character

Notes: UNF:6:GjIOFhIW9PMhoCRWcqXMEQ==

strain

f5191758 Location:

Variable Format: character

Notes: UNF:6:FYcWiog18odKCz71p1qXkg==

date

f5191758 Location:

Summary Statistics: StDev 0.328923964955065; Valid 1964.0; Max. 2021.422; Min. 2020.15; Mean 2020.9697362525458;

Variable Format: numeric

Notes: UNF:6:i0pIHViuuDm2Tkm+KwLXHA==

id

f5191758 Location:

Variable Format: character

Notes: UNF:6:IM0W7AJ036TY/I2ajA4/ow==

lineage

f5191758 Location:

Variable Format: character

Notes: UNF:6:2FLI4slfH0vhDT4sty/HJw==

location

f5191758 Location:

Variable Format: character

Notes: UNF:6:7RMdLl2XjD8rwyA3qpc9ng==

sample_id

f5191758 Location:

Variable Format: character

Notes: UNF:6:lSz451Q8qYzNDc/S/ECFKg==

date_collection

f5191758 Location:

Variable Format: character

Notes: UNF:6:jCJDIN77cGbHXXeHTR9iKQ==

datecollection

f5191758 Location:

Variable Format: character

Notes: UNF:6:jCJDIN77cGbHXXeHTR9iKQ==

county_origin

f5191758 Location:

Variable Format: character

Notes: UNF:6:ioFjCscZZy0kNM7ACj0Frw==

country

f5191758 Location:

Variable Format: character

Notes: UNF:6:vXWp4qCpn5jk7B5WKMlUIw==

kenya_or_global

f5191758 Location:

Variable Format: character

Notes: UNF:6:epp/St/K/MNTTvt/isbrXg==

strain

f5191761 Location:

Variable Format: character

Notes: UNF:6:E4OnfmkpGGg9Ueqtv1MQYA==

date

f5191761 Location:

Summary Statistics: Valid 56.0; Min. 2020.541; Max. 2021.052; StDev 0.07849835592620158; Mean 2020.8694107142858

Variable Format: numeric

Notes: UNF:6:ImPob4Lan5WFJQQYZLuLJQ==

id

f5191761 Location:

Variable Format: character

Notes: UNF:6:OtzRlPfy1H8mCNUfrRYIpw==

lineage

f5191761 Location:

Variable Format: character

Notes: UNF:6:wza+mhg6OoeW/JHH4vvhTg==

location

f5191761 Location:

Variable Format: character

Notes: UNF:6:4+JTBzGaDD9eK6uHyRtOhg==

sample_id

f5191761 Location:

Variable Format: character

Notes: UNF:6:FoKg0emWYl5kFrOzoDGy2w==

date_collection

f5191761 Location:

Variable Format: character

Notes: UNF:6:BX8I2pd7HOM2tPIV4FlqPA==

datecollection

f5191761 Location:

Variable Format: character

Notes: UNF:6:BX8I2pd7HOM2tPIV4FlqPA==

county_origin

f5191761 Location:

Variable Format: character

Notes: UNF:6:YX1nc31tuVtx8q03RGK/vA==

country

f5191761 Location:

Variable Format: character

Notes: UNF:6:fG/rHtiV4couYsgPx+VhUA==

kenya_or_global

f5191761 Location:

Variable Format: character

Notes: UNF:6:Agm00DsaflkfZuDPftjcxg==

strain

f5191763 Location:

Variable Format: character

Notes: UNF:6:0MfIRLX6OpgodCpde/eYAA==

date

f5191763 Location:

Summary Statistics: Mean 2020.9909019607844; Valid 51.0; Min. 2020.587; Max. 2021.189; StDev 0.18069690145677825

Variable Format: numeric

Notes: UNF:6:e7V9cl+qt6JniwfR0CA32Q==

id

f5191763 Location:

Variable Format: character

Notes: UNF:6:liYyIKoY6w7u0Wq2OQCy2w==

lineage

f5191763 Location:

Variable Format: character

Notes: UNF:6:shW27VFnyJZahtFqeVz/xA==

location

f5191763 Location:

Variable Format: character

Notes: UNF:6:NiGzacjw1ZEGfIAtYA6asw==

sample_id

f5191763 Location:

Variable Format: character

Notes: UNF:6:wZFSJvqrw7ScqqpR9vx1Sg==

date_collection

f5191763 Location:

Variable Format: character

Notes: UNF:6:P30fmkYLlVkpcQV9Z+pM5Q==

datecollection

f5191763 Location:

Variable Format: character

Notes: UNF:6:P30fmkYLlVkpcQV9Z+pM5Q==

county_origin

f5191763 Location:

Variable Format: character

Notes: UNF:6:mgmL7dkMbGYulivdFa60tA==

country

f5191763 Location:

Variable Format: character

Notes: UNF:6:G/AcO92T0S+2Zw1J52+r8w==

kenya_or_global

f5191763 Location:

Variable Format: character

Notes: UNF:6:7pl2HUC8UWY3XXPhlIoOfw==

strain

f5191750 Location:

Variable Format: character

Notes: UNF:6:OGZsRVX8HLFAmqGELjlcOA==

date

f5191750 Location:

Summary Statistics: Max. 2021.148; StDev 0.24292493995813175; Min. 2020.208; Mean 2020.4458664025926; Valid 2777.0

Variable Format: numeric

Notes: UNF:6:1pMXr3J8mF5X9cs1TqaDMw==

seq_len

f5191750 Location:

Summary Statistics: StDev 0.0; Valid 2777.0; Max. 29903.0; Mean 29903.0; Min. 29903.0;

Variable Format: numeric

Notes: UNF:6:vEqz86O2NYhABtgg3h8MCg==

Ns

f5191750 Location:

Summary Statistics: Mean 725.4241987756482; Max. 5927.0; Min. 0.0; Valid 2777.0; StDev 1231.413319643187

Variable Format: numeric

Notes: UNF:6:YZ/6eJDAAnb+xTAS4DNWPw==

dash

f5191750 Location:

Summary Statistics: StDev 166.1043881185681; Valid 2777.0; Max. 2755.0; Min. 0.0; Mean 112.05473532589113

Variable Format: numeric

Notes: UNF:6:30TCDnVfKVqWaCLHMUQIyQ==

id

f5191750 Location:

Variable Format: character

Notes: UNF:6:SS5hbTTsZXEdg4Fqr+ncYw==

lineage

f5191750 Location:

Variable Format: character

Notes: UNF:6:mft+GyGDORtAjjOBOop4Jg==

location

f5191750 Location:

Variable Format: character

Notes: UNF:6:rZuDVvmOdtGfdEkaVUGsuw==

sample_id

f5191750 Location:

Variable Format: character

Notes: UNF:6:2UFi8GNaGEBebp/BGBcUkg==

date_collection

f5191750 Location:

Variable Format: character

Notes: UNF:6:O58TOAvyzx3sOAvjxeQAZg==

datecollection

f5191750 Location:

Variable Format: character

Notes: UNF:6:O58TOAvyzx3sOAvjxeQAZg==

county_origin

f5191750 Location:

Variable Format: character

Notes: UNF:6:1PvKGre6CE6nmLFFvYGpAQ==

country

f5191750 Location:

Variable Format: character

Notes: UNF:6:HARZGTrs+MlGj9liwQoNTg==

kenya_or_global

f5191750 Location:

Variable Format: character

Notes: UNF:6:LoHJJU/fsRf74FreTfQMRQ==

strain

f5191764 Location:

Variable Format: character

Notes: UNF:6:bu5WADsbg9sSPEXaZMAWMQ==

date

f5191764 Location:

Summary Statistics: Valid 604.0; Max. 2021.148; Mean 2020.5299718543047; StDev 0.2112638762515525; Min. 2020.208;

Variable Format: numeric

Notes: UNF:6:qndiim9L1xPwoC11T2Aylw==

id

f5191764 Location:

Variable Format: character

Notes: UNF:6:bu5WADsbg9sSPEXaZMAWMQ==

lineage

f5191764 Location:

Variable Format: character

Notes: UNF:6:prpSlMkjofFYL8/VjdO3aQ==

location

f5191764 Location:

Variable Format: character

Notes: UNF:6:ZYMgYlVtPPjOTomgluNNdw==

sample_id

f5191764 Location:

Variable Format: character

Notes: UNF:6:ESTESI+ffGLZk0jIYPthEg==

date_collection

f5191764 Location:

Variable Format: character

Notes: UNF:6:GGxJhZV3URGPMAVwTMFLJA==

datecollection

f5191764 Location:

Variable Format: character

Notes: UNF:6:GGxJhZV3URGPMAVwTMFLJA==

county_origin

f5191764 Location:

Variable Format: character

Notes: UNF:6:vUoBlDTOpLvOdcpRd9pimg==

country

f5191764 Location:

Variable Format: character

Notes: UNF:6:fvn+gTsQOa4cr/ig+rHBRg==

kenya_or_global

f5191764 Location:

Variable Format: character

Notes: UNF:6:ZslxDdnBhioewLndRPbxWQ==

strain

f5191779 Location:

Variable Format: character

Notes: UNF:6:KU1vwFmY8Bf4QHo/oSMj5A==

date

f5191779 Location:

Summary Statistics: StDev 0.28557658921294415; Max. 2021.153; Valid 4748.0; Mean 2020.654457666386; Min. 2020.208

Variable Format: numeric

Notes: UNF:6:oF786PgSp5bxOZIMWTx9wQ==

seq_len

f5191779 Location:

Summary Statistics: Max. 29903.0; Valid 4748.0; StDev 0.0; Mean 29903.0; Min. 29903.0

Variable Format: numeric

Notes: UNF:6:OMivRhtEduQdJG77gkeYvg==

Ns

f5191779 Location:

Summary Statistics: Mean 656.9328138163601; Max. 5936.0; Valid 4748.0; StDev 1197.3261861819292; Min. 0.0;

Variable Format: numeric

Notes: UNF:6:JgJOEsivzPuGTuGjGYEbSA==

dash

f5191779 Location:

Summary Statistics: Mean 105.40754001684834; Max. 2755.0; Min. 0.0; StDev 118.09482146553462; Valid 4748.0;

Variable Format: numeric

Notes: UNF:6:oM1+BthlvmHJQ4RUMr86+Q==

id

f5191779 Location:

Variable Format: character

Notes: UNF:6:DGTUFyCdnRQZgIIVJNUL/A==

lineage

f5191779 Location:

Variable Format: character

Notes: UNF:6:PW/Ajr8MZq60VYS6Mps7EA==

location

f5191779 Location:

Variable Format: character

Notes: UNF:6:Hh1toDksDVCyvgwb2cHC5Q==

sample_id

f5191779 Location:

Variable Format: character

Notes: UNF:6:yjCltcuktoBRcga6td+5wQ==

date_collection

f5191779 Location:

Variable Format: character

Notes: UNF:6:hVamUT/EaosdrVTIC7u3dA==

datecollection

f5191779 Location:

Variable Format: character

Notes: UNF:6:XtqPAfzjyD9BqeEy2xJwNw==

origin

f5191779 Location:

Variable Format: character

Notes: UNF:6:G6Y0Z40RbPcGAWCzkFu32g==

country

f5191779 Location:

Variable Format: character

Notes: UNF:6:7OylzVt4zTTzygUct4gUBQ==

Monthly

f5191732 Location:

Variable Format: character

Notes: UNF:6:J6BqkfRRqvQ12WOiYNgY3g==

Tests

f5191732 Location:

Summary Statistics: Min. 94.0; StDev 4679.645771365023; Mean 6893.0; Valid 12.0; Max. 14560.0

Variable Format: numeric

Notes: UNF:6:VvKRBmMn1SLMeFbakwT6BQ==

Positive

f5191732 Location:

Summary Statistics: Max. 1156.0; Min. 7.0; StDev 385.69774435430656; Mean 527.25; Valid 12.0

Variable Format: numeric

Notes: UNF:6:DewqMP+VKF8YTot2ev4VAw==

Sequenced

f5191732 Location:

Summary Statistics: Valid 12.0; Max. 166.0; StDev 41.33088946831926; Min. 4.0; Mean 62.66666666666667

Variable Format: numeric

Notes: UNF:6:8jwJQupsFfBJIMC3u2JTlg==

Not_sequenced

f5191732 Location:

Summary Statistics: Mean 464.58333333333337; Min. 3.0; StDev 387.09957805884176; Valid 12.0; Max. 1107.0;

Variable Format: numeric

Notes: UNF:6:cCU/6sUJi6uaJ9MR/fGAZA==

Sequenced_prop

f5191732 Location:

Summary Statistics: Valid 12.0; Max. 77.44360902; Mean 23.152946723166664; Min. 4.238754325; StDev 23.312467144571965

Variable Format: numeric

Notes: UNF:6:/l4mI+0euthW6/0l/3v92Q==

Not_sequenced_prop

f5191732 Location:

Summary Statistics: Valid 12.0; Max. 95.76124567; Mean 76.84705327583333; Min. 22.55639098; StDev 23.312467143762976

Variable Format: numeric

Notes: UNF:6:Dz126zsKMwLTKP5ij6/x7g==

iso_code

f5191737 Location:

Variable Format: character

Notes: UNF:6:B4K1gDC6O0dld9vNQ9HWOA==

continent

f5191737 Location:

Variable Format: character

Notes: UNF:6:IHH+zfqM8diX6fINh8EsGw==

location

f5191737 Location:

Variable Format: character

Notes: UNF:6:jNTV++1kvM3WbyfreBkWIw==

date

f5191737 Location:

Variable Format: character

Notes: UNF:6:ZEsTp6LlLFUPraSeSuhfpA==

total_cases

f5191737 Location:

Summary Statistics: Min. 1.0; Mean 1005630.9568628552; Valid 92983.0; Max. 1.77040185E8; StDev 6916718.9758718265

Variable Format: numeric

Notes: UNF:6:ZKpXVQ/KW/LaU7SOnJAVMQ==

new_cases

f5191737 Location:

Summary Statistics: Min. -74347.0; StDev 37986.53962462477; Max. 906008.0; Valid 92980.0; Mean 6050.756420737139

Variable Format: numeric

Notes: UNF:6:QTIx+Bfg1Q5S3nTUE+R5fg==

new_cases_smoothed

f5191737 Location:

Summary Statistics: Valid 91965.0; Min. -6223.0; Mean 6081.882220116775; Max. 826389.571; StDev 37752.752621365646

Variable Format: numeric

Notes: UNF:6:kkP6jQ0fdhizyShmrIjS8w==

total_deaths

f5191737 Location:

Summary Statistics: Min. 1.0; Max. 3832997.0; Valid 82939.0; StDev 164125.89073169543; Mean 27539.00210997436

Variable Format: numeric

Notes: UNF:6:6BBQWmScnlMwFqozgT1Sig==

new_deaths

f5191737 Location:

Summary Statistics: Max. 18050.0; Min. -1918.0; Mean 147.2234911847371; Valid 83095.0; StDev 805.3707998570759;

Variable Format: numeric

Notes: UNF:6:CfGCkvBEE3GgMRffzLy/XA==

new_deaths_smoothed

f5191737 Location:

Summary Statistics: Min. -232.143; Max. 14737.0; Valid 91965.0; Mean 132.05334754529; StDev 746.2045338658065

Variable Format: numeric

Notes: UNF:6:rbGd7o6OGa3FtSuh0UAlmg==

total_cases_per_million

f5191737 Location:

Summary Statistics: Min. 0.001; Mean 12367.812646782791; Valid 92487.0; StDev 23011.73936805102; Max. 179072.025

Variable Format: numeric

Notes: UNF:6:0Q64LUHUbb1NiJpWQ/lf/g==

new_cases_per_million

f5191737 Location:

Summary Statistics: Mean 76.1224645776561; Valid 92484.0; Min. -2153.437; Max. 18293.675; StDev 199.1852365310752

Variable Format: numeric

Notes: UNF:6:5XfIHI5z/RV08FOxNBP/EQ==

new_cases_smoothed_per_million

f5191737 Location:

Summary Statistics: Mean 76.44938059995185; Max. 4083.5; Valid 91474.0; StDev 158.82972639089513; Min. -276.825

Variable Format: numeric

Notes: UNF:6:u2UNNkKDmx85TQGCBM/KeA==

total_deaths_per_million

f5191737 Location:

Summary Statistics: Max. 5740.079; StDev 503.2704932405009; Valid 82456.0; Mean 276.1735982948483; Min. 0.001;

Variable Format: numeric

Notes: UNF:6:VRRLSyyQUAaJRuMpyJ9bow==

new_deaths_per_million

f5191737 Location:

Summary Statistics: Mean 1.5601092940492838; Max. 218.329; Valid 82612.0; Min. -76.445; StDev 3.9829773559623534

Variable Format: numeric

Notes: UNF:6:5/Xm6XHfMgFyi0T9xwFC9g==

new_deaths_smoothed_per_million

f5191737 Location:

Summary Statistics: Min. -10.921; StDev 3.0467428429389174; Max. 63.14; Mean 1.4001197389422178; Valid 91474.0

Variable Format: numeric

Notes: UNF:6:VfV7/9RGHDESxKth/G+XMA==

reproduction_rate

f5191737 Location:

Summary Statistics: StDev 0.35225834569074377; Min. -0.01; Mean 1.0049775125968117; Valid 77599.0; Max. 5.79

Variable Format: numeric

Notes: UNF:6:pLHwMIAKZtXoylnJGriTDg==

icu_patients

f5191737 Location:

Summary Statistics: Max. 28889.0; StDev 2932.1048834288663; Valid 9647.0; Mean 1083.9175909609667; Min. 0.0

Variable Format: numeric

Notes: UNF:6:LDTzyFwcasqkLtGV26WuZQ==

icu_patients_per_million

f5191737 Location:

Summary Statistics: Min. 0.0; Max. 192.455; Mean 26.86629148958226; Valid 9647.0; StDev 27.37787020597021

Variable Format: numeric

Notes: UNF:6:Hslh8CRlFEOn5UuwHM5t9g==

hosp_patients

f5191737 Location:

Summary Statistics: StDev 12033.57060019555; Mean 4733.366107913996; Valid 11991.0; Min. 0.0; Max. 133214.0;

Variable Format: numeric

Notes: UNF:6:LJVUahj3AqC9t7pV1oNlhg==

hosp_patients_per_million

f5191737 Location:

Summary Statistics: Min. 0.0; StDev 212.67181921159815; Max. 1532.573; Mean 173.05536860979072; Valid 11991.0;

Variable Format: numeric

Notes: UNF:6:Jxph50EHXsdE0K3bijhh5g==

weekly_icu_admissions

f5191737 Location:

Summary Statistics: StDev 569.8492607213334; Max. 4002.456; Min. 0.0; Mean 273.4194439359266; Valid 874.0;

Variable Format: numeric

Notes: UNF:6:mVq5UOSqdXP343XMkD8oXg==

weekly_icu_admissions_per_million

f5191737 Location:

Summary Statistics: Mean 20.851954233409614; Max. 278.756; StDev 35.80804981055262; Min. 0.0; Valid 874.0

Variable Format: numeric

Notes: UNF:6:Jq9umGapUfI466Y3A0CuPw==

weekly_hosp_admissions

f5191737 Location:

Summary Statistics: Valid 1509.0; StDev 10946.389871735744; Mean 3631.120665341286; Min. 0.0; Max. 116323.0

Variable Format: numeric

Notes: UNF:6:L+0Xw+ZIn5PMv2ueWvy2wg==

weekly_hosp_admissions_per_million

f5191737 Location:

Summary Statistics: Min. 0.0; StDev 218.0502384642534; Mean 112.395436713055; Valid 1509.0; Max. 2656.911

Variable Format: numeric

Notes: UNF:6:18vK9mlSPy5hGDQ6TLp4ig==

new_tests

f5191737 Location:

Summary Statistics: Valid 43315.0; Mean 46967.41793836385; StDev 173383.06266530982; Max. 3740296.0; Min. -239172.0

Variable Format: numeric

Notes: UNF:6:YM14WC4BIHwbiP60uSVUmQ==

total_tests

f5191737 Location:

Summary Statistics: Min. 0.0; StDev 3.2037751354207687E7; Max. 4.5698287E8; Valid 43017.0; Mean 7291297.70943903

Variable Format: numeric

Notes: UNF:6:hlIMRGhd1sBBLDVjVuBKGQ==

total_tests_per_thousand

f5191737 Location:

Summary Statistics: StDev 686.1784999077665; Mean 292.1314212055699; Min. 0.0; Valid 43017.0; Max. 8713.886

Variable Format: numeric

Notes: UNF:6:tx0yBdCaDZbAvFFSNSQ5rw==

new_tests_per_thousand

f5191737 Location:

Summary Statistics: Mean 2.0973777675170253; Max. 327.086; Valid 43315.0; Min. -23.01; StDev 6.0787243715069925;

Variable Format: numeric

Notes: UNF:6:4qsySX57d8jeiPECgGsOzw==

new_tests_smoothed

f5191737 Location:

Summary Statistics: Valid 50297.0; Min. 0.0; Max. 3080396.0; Mean 44655.22814482007; StDev 158061.621286846

Variable Format: numeric

Notes: UNF:6:ww2ra54QOfzHHUard5NJ8w==

new_tests_smoothed_per_thousand

f5191737 Location:

Summary Statistics: StDev 5.128748790028705; Min. 0.0; Valid 50297.0; Mean 2.0041977652742697; Max. 92.104;

Variable Format: numeric

Notes: UNF:6:AYyzLwqKzRngMui4WDdtKQ==

positive_rate

f5191737 Location:

Summary Statistics: StDev 0.09758697445398755; Valid 47451.0; Max. 0.933; Min. 0.0; Mean 0.08887856947166595;

Variable Format: numeric

Notes: UNF:6:ZZqQN6XG2SSNkqN6y+XP3A==

tests_per_case

f5191737 Location:

Summary Statistics: StDev 885.308308006102; Valid 46852.0; Mean 162.461472295741; Max. 50000.0; Min. 1.1

Variable Format: numeric

Notes: UNF:6:mAr+DjHlH3UmSulkoc4s2g==

tests_units

f5191737 Location:

Variable Format: character

Notes: UNF:6:zhpI3BJOFdcyWQG0MhYuZw==

total_vaccinations

f5191737 Location:

Summary Statistics: StDev 1.3468099489587218E8; Mean 2.6291614665064294E7; Valid 14785.0; Min. 0.0; Max. 2.496809053E9;

Variable Format: numeric

Notes: UNF:6:M8alnAXy+eeijixJidtSkA==

people_vaccinated

f5191737 Location:

Summary Statistics: Max. 1.648384607E9; Mean 1.4454953689244254E7; Min. 0.0; StDev 7.065944459335177E7; Valid 14056.0

Variable Format: numeric

Notes: UNF:6:hp0Wx7fYD8Ei6olc5CoUSw==

people_fully_vaccinated

f5191737 Location:

Summary Statistics: StDev 3.695426393517802E7; Min. 1.0; Max. 7.48099346E8; Mean 8119206.29569076; Valid 11184.0;

Variable Format: numeric

Notes: UNF:6:2scAcjhEKJoxF0BaOwXjIQ==

new_vaccinations

f5191737 Location:

Summary Statistics: Mean 607004.5126356507; Min. 0.0; StDev 2774672.2482078066; Valid 12346.0; Max. 3.9679875E7;

Variable Format: numeric

Notes: UNF:6:GWRc8tjrqjIo3eszDTm3ww==

new_vaccinations_smoothed

f5191737 Location:

Summary Statistics: Max. 3.5636692E7; StDev 1855791.4498738968; Mean 293376.5299886192; Valid 25493.0; Min. 0.0

Variable Format: numeric

Notes: UNF:6:geTCQds2HJkAzBzR8V03gA==

total_vaccinations_per_hundred

f5191737 Location:

Summary Statistics: Valid 14785.0; Min. 0.0; Max. 231.01; StDev 28.49550062715189; Mean 21.294503889076765

Variable Format: numeric

Notes: UNF:6:KrRr3cFH0+8ciBIRE2nH+g==

people_vaccinated_per_hundred

f5191737 Location:

Summary Statistics: Min. 0.0; Mean 14.107832953898685; Max. 116.15; Valid 14056.0; StDev 17.36350759497746

Variable Format: numeric

Notes: UNF:6:yCHlf8Tg9CtMwROMtj0Wag==

people_fully_vaccinated_per_hundred

f5191737 Location:

Summary Statistics: Mean 8.55839145207439; Min. 0.0; Valid 11184.0; StDev 12.578760317322603; Max. 114.86;

Variable Format: numeric

Notes: UNF:6:SvXwHR0CV216895U5VFknw==

new_vaccinations_smoothed_per_million

f5191737 Location:

Summary Statistics: Valid 25493.0; Max. 118759.0; Mean 3155.8019848585395; Min. 0.0; StDev 4468.035647086802

Variable Format: numeric

Notes: UNF:6:23oxRLFhktYcpBH3pSMt4A==

stringency_index

f5191737 Location:

Summary Statistics: Valid 81239.0; Min. 0.0; Max. 100.0; Mean 58.46861027339091; StDev 21.15331085715357

Variable Format: numeric

Notes: UNF:6:JuT78qfnTJUMCnbebhxOzA==

population

f5191737 Location:

Summary Statistics: Max. 7.794798729E9; Mean 1.2540478449967714E8; Min. 47.0; Valid 95595.0; StDev 6.819571030725335E8;

Variable Format: numeric

Notes: UNF:6:8BNoA/dSs7LOvoENYrX6DA==

population_density

f5191737 Location:

Summary Statistics: Mean 383.96435280965665; StDev 1788.2718878823378; Valid 89442.0; Min. 0.137; Max. 20546.766

Variable Format: numeric

Notes: UNF:6:IYxmgD4rw+D5AhcXwIbn7Q==

median_age

f5191737 Location:

Summary Statistics: Mean 30.568878646806805; Max. 48.2; StDev 9.131405870667715; Min. 15.1; Valid 86137.0;

Variable Format: numeric

Notes: UNF:6:sSc++CEu+0AJJWJlDdCSMQ==

aged_65_older

f5191737 Location:

Summary Statistics: Mean 8.793553430319257; StDev 6.214068738814226; Valid 85167.0; Min. 1.144; Max. 27.049

Variable Format: numeric

Notes: UNF:6:aS0A5LBDizpR7cMxAApQ5w==

aged_70_older

f5191737 Location:

Summary Statistics: Max. 18.493; Valid 85660.0; Mean 5.567415759981291; Min. 0.526; StDev 4.239288487646081

Variable Format: numeric

Notes: UNF:6:J2/lLAhsRCrdgIMYRi8X6w==

gdp_per_capita

f5191737 Location:

Summary Statistics: Max. 116935.6; Valid 86454.0; Min. 661.24; StDev 19974.977581923496; Mean 19281.828714125477

Variable Format: numeric

Notes: UNF:6:08IhMrPA8iGR1mQkCGiBFw==

extreme_poverty

f5191737 Location:

Summary Statistics: Mean 13.39186213745154; Valid 58406.0; Max. 77.6; Min. 0.1; StDev 19.955113606866018;

Variable Format: numeric

Notes: UNF:6:JiuAH2FNhNsGBkizOZ4s9w==

cardiovasc_death_rate

f5191737 Location:

Summary Statistics: Min. 79.37; Max. 724.417; StDev 118.9678303530037; Valid 86522.0; Mean 258.3213998058296;

Variable Format: numeric

Notes: UNF:6:SEvyYrsKhRTrQJkE/CUz9Q==

diabetes_prevalence

f5191737 Location:

Summary Statistics: Valid 88676.0; Min. 0.99; Mean 7.915207158644958; StDev 4.128078329583089; Max. 30.53;

Variable Format: numeric

Notes: UNF:6:5FLQEVdX84r5N8/vgefscA==

female_smokers

f5191737 Location:

Summary Statistics: Min. 0.1; StDev 10.446175900451832; Mean 10.552849560658702; Valid 67715.0; Max. 44.0

Variable Format: numeric

Notes: UNF:6:i/yYnY1SZ+cfvl5r33ewJQ==

male_smokers

f5191737 Location:

Summary Statistics: Mean 32.68206222648537; Min. 7.7; StDev 13.48039115191064; Max. 78.1; Valid 66724.0

Variable Format: numeric

Notes: UNF:6:2Waq99iNYHTTUPgOYlhKrg==

handwashing_facilities

f5191737 Location:

Summary Statistics: StDev 31.760049837908493; Min. 1.188; Mean 50.8510629586178; Max. 100.0; Valid 43473.0

Variable Format: numeric

Notes: UNF:6:SkbqFJ2udbp/jBtDEgf/BA==

hospital_beds_per_thousand

f5191737 Location:

Summary Statistics: Min. 0.1; Valid 78863.0; Mean 3.0286547937562576; StDev 2.4597985440540806; Max. 13.8;

Variable Format: numeric

Notes: UNF:6:1p0U7cPkqA+YLb5w1dyD1g==

life_expectancy

f5191737 Location:

Summary Statistics: Min. 53.28; StDev 7.5590114704607965; Valid 91377.0; Mean 73.23326077678186; Max. 86.75

Variable Format: numeric

Notes: UNF:6:9AjsGhJ8R52hh8VVIrSjCw==

human_development_index

f5191737 Location:

Summary Statistics: Min. 0.394; StDev 0.15037086823725335; Mean 0.7275334732859638; Valid 86696.0; Max. 0.957

Variable Format: numeric

Notes: UNF:6:9v77gpYHg/wfxygeIuKjsw==

excess_mortality

f5191737 Location:

Summary Statistics: Valid 3406.0; Max. 409.69; Mean 18.247718731650036; Min. -95.59; StDev 36.2302941420511

Variable Format: numeric

Notes: UNF:6:4e6L0wRm3PzITC6cVgZdWg==

taxa_name

f5191744 Location:

Variable Format: character

Notes: UNF:6:5u7IJ2gMnnBnucrFFC4UEA==

actualseq

f5191744 Location:

Variable Format: character

Notes: UNF:6:6Ka1I33ZYgHbSFQlgj7mWA==

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annottated_tree_events.csv

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text/csv

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Fig. 6A.R

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Fig. 6B.R

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Fig. 6E.R

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Fig. 6F.R

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Fig. 6G.R

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Fig. G.R

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Fig.1A.R

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Fig.1B-D.R

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Fig.5B.R

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Fig.5C.R

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Fig.7.R

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Fig.8.R

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Global_Kenya_N.8.aligned.fasta

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