Create table with all outbreak data for a particular pathogen

Create table with all outbreak data for a particular pathogen

Usage

outbreak_table(df, pathogen)

Arguments

df

processed data with outbreak information produced by data_outbreak_table()

pathogen

name of pathogen

Value

returns flextable summarising all extracted outbreaks for the specified pathogen

Examples

df <- data_outbreak_table(pathogen = "marburg")
#> Rows: 23 Columns: 24
#> ── Column specification ────────────────────────────────────────────────────────
#> Delimiter: ","
#> chr  (8): outbreak_start_month, outbreak_end_month, outbreak_country, outbre...
#> dbl (15): outbreak_id, article_id, outbreak_start_day, outbreak_start_year, ...
#> lgl  (1): outbreak_size
#> 
#> ℹ Use `spec()` to retrieve the full column specification for this data.
#> ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
#> Rows: 58 Columns: 25
#> ── Column specification ────────────────────────────────────────────────────────
#> Delimiter: ","
#> chr  (8): pathogen, first_author_first_name, article_title, doi, journal, no...
#> dbl (16): article_id, covidence_id, year_publication, volume, issue, page_fi...
#> lgl  (1): paper_copy_only
#> 
#> ℹ Use `spec()` to retrieve the full column specification for this data.
#> ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
outbreak_table(df = df, pathogen = "marburg")
#> Adding missing grouping variables: `outbreak_start_year`
Country
Location
Article
Start
End
Deaths
Confirmed
Suspected
Asymptomatic
Severe/hospitalised
Confirmation Method
Angola
Carroll2013
2005
2005
227
252
0
Not specified
Angola
Palvin2014
2004
2005
227
252
Angola
Uige Province
Towner2006
Oct2004
Jul2005
227
252
0
Democratic Republic of the Congo
Durba and Watsa
Borchert2002
Oct1998
May1999
61
73
0
Symptoms
Democratic Republic of the Congo
Durba and Watsa
Bausch2006
Oct1998
Sep2000
125
48
106
0
Molecular  
Democratic Republic of the Congo
Durba and Watsa villages
Borchert2006
Oct1998
Aug2000
76
33
0
Molecular  
Democratic Republic of the Congo
Palvin2014
1998
2000
128
154
Germany
Marburg, Frankfurt am Main
Albarino2013
18Aug1968
13Nov1968
5
23
1
Symptoms
Germany,Yugoslavia
Marburg (23), Frankfurt am Main (6), Belgrade (2)
Martini1973
Aug1968
Nov1968
7
31
1
Symptoms
Germany,Yugoslavia
Pavlin2014
1967
7
31
Kenya
Pavlin2014
1980
1
2
Kenya
Pavlin2014
1987
1
1
Netherlands
Pavlin2014
2008
1
1
Russian Federation
Pavlin2014
1988
1
1
Russian Federation
Pavlin2014
1990
0
1
South Africa,Zimbabwe
Johannesburg
Conrad1978
12Feb1975
1
3
1
Molecular  
Uganda
Kamwenge and Ibanda
Adjemian2011
10Jun2007
14Sep2007
1
4
0
Molecular  
Uganda
Kabale; Ibanda; Mbarara; Kampala
Albarino2013
18Oct2012
7Nov2012
4
15
Molecular  
Uganda
Ibanda, Kabale and Kamwenge Districts
Knust2015
Jul2012
10Nov2012
15
15
11
Molecular  
Uganda
Ibanda and Kabale
Mbonye2012
Sep2012
13Nov2012
7
9
5
Molecular  
Uganda
Kampala
Nyakarahuka2017
17Sep2014
28Sep2014
1
1
1
Molecular  
Uganda
Pavlin2014
2007
2
4
United States
Colorado
Pavlin2014
2008
0
1