Sri Lanka

District-wise weekly Dengue cases from 2006 to 2023-present

library(denguedatahub)
library(tsibble)
srilanka_weekly_data

# A tibble: 25,766 × 6
    year  week start.date end.date   district    cases
   <dbl> <dbl> <chr>      <chr>      <chr>       <dbl>
 1  2006    52 12/23/2006 12/29/2006 Colombo        71
 2  2006    52 12/23/2006 12/29/2006 Gampaha        12
 3  2006    52 12/23/2006 12/29/2006 Kalutara       12
 4  2006    52 12/23/2006 12/29/2006 Kandy          20
 5  2006    52 12/23/2006 12/29/2006 Matale          4
 6  2006    52 12/23/2006 12/29/2006 NuwaraEliya     1
 7  2006    52 12/23/2006 12/29/2006 Galle           1
 8  2006    52 12/23/2006 12/29/2006 Hambanthota     1
 9  2006    52 12/23/2006 12/29/2006 Matara         11
10  2006    52 12/23/2006 12/29/2006 Jaffna          0
# ℹ 25,756 more rows

srilanka_weekly_data$start.date <- as.Date(
  srilanka_weekly_data$start.date,
  format = "%d/%m/%Y"
)
srilanka_weekly_data$end.date <- as.Date(
  srilanka_weekly_data$end.date,
  format = "%d/%m/%Y"
)

Identification of dengue serotypes circulating in Sri Lanka

head(sl_dengue_serotype)

# A tibble: 6 × 2
  reporting.year dengue.serotype
           <dbl> <chr>          
1           1965 DENV-1, DENV-2 
2           1968 DENV-1, DENV-2 
3           1978 DENV-4         
4           1980 DENV (IIIA)    
5           1990 DENV (IIIA)    
6           1992 DENV-4         

Type and proportion of breeding habitats positive for Aedes aegypti mosquitoes, across provinces in Sri Lanka, 2017

head(sl_sites)

# A tibble: 6 × 7
  Province     Discarded_items Water_storage_containers…¹ Ponds_and_ornamental…²
  <chr>                  <dbl>                      <dbl>                  <dbl>
1 Western                 50.9                       10                      3.7
2 Eastern                 33.9                       22.9                    3  
3 Sabaragamuwa            55.6                        5.1                    5.1
4 Northern                18.8                       55                      2.9
5 Central                 21.9                       42.9                    1.8
6 Southern                41.6                       23.7                    4.8
# ℹ abbreviated names: ¹​Water_storage_containers_and_tanks,
#   ²​Ponds_and_ornamental_items
# ℹ 3 more variables: Wells_and_tube_wells <dbl>,
#   Natural_water_collections <dbl>, Other_miscellaneous_items <dbl>

Annual reported dengue cases in Sri Lanka

head(sl_annual)

# A tibble: 6 × 3
   year dengue.cases epidemic
  <dbl>        <dbl>    <dbl>
1  1989          203        0
2  1990         1350        0
3  1991         1048        0
4  1992          656        0
5  1993          756        0
6  1994          582        0

Tutorial: Visualisation of Data

Visualize srilanka_weekly_data

visdat::vis_dat(srilanka_weekly_data)

Time series visualization

library(plotly)
library(viridis)

#  Visualizing colombo district cases
number_ticks <- function(n) {function(limits) pretty(limits, n)}
srilanka_weekly_data %>%  
ggplot(aes(x=start.date, y=cases)) + geom_line()  + 
  scale_x_date(date_breaks = "1 year", date_labels = "%Y") + 
  theme(axis.text.x = element_text(angle = 90, vjust = 0.5, hjust=1)) +
  facet_wrap(vars(district), scales = "free_y", ncol=5)