Create seroprevalence table

Create seroprevalence table

Usage

sero_table(df, pathogen)

Arguments

df

processed data with parameter information produced by data_param_table()

pathogen

name of pathogen

Value

returns flextable with a summary of seroprevalence data

Examples

df <- data_param_table(pathogen = "marburg", exclude = c(15, 17))
#> Rows: 70 Columns: 55
#> ── Column specification ────────────────────────────────────────────────────────
#> Delimiter: ","
#> chr (26): parameter_data_id, parameter_type, parameter_unit, parameter_value...
#> dbl (18): article_id, parameter_value, parameter_lower_bound, parameter_uppe...
#> lgl (11): distribution_type, distribution_par1_value, distribution_par1_type...
#> 
#> 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.
sero_table(df = df, pathogen = "marburg")
Article
Country
Parameter type*
Seroprevalence (%)
Uncertainty type
Number Seropositive
Sample size
Population Group
Timing of survey
Disaggregated data
available
Gonzalez1989
Cameroon,Central African Republic,Chad,Republic of the Congo,Equatorial Guinea,Gabon
Unspecified
0.39
20
5,070
General population
Region
Johnson1993
Central African Republic
IFA
3
427
Outdoor workers
Johnson1993
Central African Republic
IFA
3.20
Range
137
4,295
General population
Pre outbreak
Age, Region, Sex
Gonzalez2000
Central African Republic
IgG
2.40
Range
33
1,340
Borchert2005
Democratic Republic of the Congo
IFA
0.00
Range
0
300
Post outbreak
Bausch2003
Democratic Republic of the Congo
IgG
2.00
15
912
Mid outbreak
Borchert2006
Democratic Republic of the Congo
IgG
1.65
CI95%
Household contacts of survivors
Post outbreak
Borchert2007
Democratic Republic of the Congo
IgG
2.10
Healthcare workers
Post outbreak
Ivanoff1982
Gabon
IFA
0.00
0
197
Ivanoff1982
Gabon
IFA
0.00
0
28
Pregnant women
Ivanoff1982
Gabon
IFA
0.00
0
28
Other
Becker1992
Germany
IgG
2.60
Other
Johnson1983
Kenya
IFA
8
1,899
Region
Johnson1983
Kenya
IFA
0.00
0
741
General population
Post outbreak
Martini1973
Kenya
Unspecified
0
79
Other
Post outbreak
Smith1982
Kenya
Unspecified
2
186
Persons under investigation
Post outbreak
Smith1982
Kenya
Unspecified
3
100
Healthcare workers
Post outbreak
Smith1982
Kenya
Unspecified
0
224
General population
Post outbreak
Smith1982
Kenya
Unspecified
0
63
Other
Post outbreak
Smith1982
Kenya
Unspecified
0
79
Other
Post outbreak
Smith1982
Kenya
Unspecified
0
44
Outdoor workers
Post outbreak
Van der Waals1986
Liberia
IFA
1.30
3
225
Other
Other
Other, Region
Mathiot1989
Madagascar
Unspecified
0.00
0
381
Other
Region
Tomori1988
Nigeria
IFA
1.70
29
1,677
General population
Moyen2015
Republic of the Congo
IgG
0.50
Pre outbreak
Schoepp2014
Sierra Leone
IgM
3.60
Persons under investigation
Other
Rugarabamu2022
Tanzania
IgM
0.30
1
308
Other
Region
Rodhain1989
Uganda
HAI/HI
4.50
6
132
Evans2018
Uganda
IgG
0
331
Other
*HAI/HI: Hemagglutination Inhibition Assay;
                     IFA: Indirect Fluorescent Antibody assay;
                     IgG: Immunoglobulin G;
                     IgM: Immunoglobulin M; Unspecified assay.