EpiMundi

FMD outbreaks in Africa

Descriptive stats

$numeric_summary
        variable       min        max      mean  median
1       latitude 26.798000   37.27370 35.762338 36.1480
2      longitude -9.540806   13.48826  4.767517  4.7506
3      sumAtRisk  1.000000 2370.00000 89.957447 20.0000
4       sumCases  1.000000  663.00000 12.372340  4.0000
5      sumDeaths  0.000000  326.00000  4.623602  0.0000
6   sumDestroyed  0.000000  424.00000  3.132500  0.0000
7 sumSlaughtered  0.000000 1005.00000 11.787599  2.0000

$speciesDescription
# A tibble: 17 × 2
   speciesDescription                                                      Freq
   <chr>                                                                  <int>
 1 domestic, cattle                                                         510
 2 domestic, sheep                                                          126
 3 domestic, goat, domestic, sheep                                           96
 4 domestic, cattle, domestic, sheep                                         90
 5 domestic, cattle, domestic, goat, domestic, sheep                         40
 6 domestic, sheep, domestic, goat                                           19
 7 domestic, sheep, domestic, cattle                                         16
 8 domestic, cattle, domestic, sheep, domestic, goat                         11
 9 domestic, cattle, domestic, goat/sheep                                    10
10 domestic, goat                                                             9
11 domestic, cattle, domestic, goat                                           5
12 domestic, sheep, domestic, cattle, domestic, goat                          4
13 domestic, goat, domestic, cattle, domestic, sheep                          2
14 domestic, goat, domestic, sheep, domestic, cattle                          2
15 domestic, sheep, domestic, goat, domestic, cattle                          2
16 domestic, cattle, domestic, goat, domestic, sheep, domestic, camelidae     1
17 domestic, goat, domestic, cattle                                           1

$serotypes
# A tibble: 5 × 2
  serotypes      Freq
  <chr>         <int>
1 O               927
2 Not Specified     8
3 A                 7
4 A, O              1
5 <NA>              1

No humans affected as expected since FMD is non-zoonotic.

# A tibble: 3 × 5
  country events total_cases total_deaths avg_reporting_delay_days
  <fct>    <int>       <dbl>        <dbl>                    <dbl>
1 Algeria    727        9465         3209                    47.3 
2 Tunisia    159        1317           22                    17.8 
3 Morocco     40         113            3                     7.52

Spatial analysis

Figure 1 - Study areas

1. Map the outbreak intensity per country

2. Test different techniques for spatial distribution of disease outbreaks

3. Check lag between outbreak and reporting

Timeseries of date of outbreak and date of reporting lag (black for outbreak dates and red for reporting)

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