R package for weekly notified dengue cases in Sri Lanka
You can install mozzie from CRAN with:
install.packages("mozzie")You can install mozzie from github with:
# install.packages("devtools")
devtools::install_github("thiyangt/mozzie")This is a basic example which shows you how to solve a common problem:
## basic example code
library(mozzie)
head(mozzie)
#> ID Year Week Colombo Gampaha Kalutara Kandy Matale Nuwara Eliya Galle
#> 1 1 2008 52 15 7 1 11 4 0 0
#> 2 2 2009 1 44 23 5 16 21 2 0
#> 3 3 2009 2 39 19 11 42 9 1 2
#> 4 4 2009 3 57 23 12 28 3 2 1
#> 5 5 2009 4 53 24 19 32 20 2 2
#> 6 6 2009 5 29 17 10 21 6 0 3
#> Hambantota Matara Jaffna Kilinochchi Mannar Vavuniya Mulative Batticalo
#> 1 6 22 0 0 8 0 0 1
#> 2 5 18 1 0 0 0 0 0
#> 3 3 18 1 0 0 0 0 0
#> 4 4 15 0 0 1 0 0 2
#> 5 7 15 0 0 1 2 0 1
#> 6 3 8 0 0 0 0 0 4
#> Ampara Trincomalee Kurunagala Puttalam Anuradhapura Polonnaruwa Badulla
#> 1 0 0 2 1 2 0 1
#> 2 1 1 10 5 0 0 1
#> 3 0 0 10 2 0 0 1
#> 4 3 0 5 2 2 3 4
#> 5 11 0 25 0 2 1 3
#> 6 14 6 17 1 2 2 2
#> Monaragala Ratnapura Kegalle
#> 1 1 2 16
#> 2 0 1 25
#> 3 0 2 21
#> 4 1 5 15
#> 5 2 2 14
#> 6 1 7 17summary(mozzie)
#> ID Year Week Colombo
#> Min. : 1.0 Min. :2008 Min. : 1.00 Min. : 0.0
#> 1st Qu.: 70.5 1st Qu.:2010 1st Qu.:12.00 1st Qu.: 57.0
#> Median :140.0 Median :2011 Median :24.00 Median : 99.0
#> Mean :140.0 Mean :2011 Mean :25.37 Mean :115.6
#> 3rd Qu.:209.5 3rd Qu.:2012 3rd Qu.:39.00 3rd Qu.:154.0
#> Max. :279.0 Max. :2014 Max. :53.00 Max. :475.0
#> Gampaha Kalutara Kandy Matale
#> Min. : 0.0 Min. : 0.00 Min. : 0.00 Min. : 0.00
#> 1st Qu.: 26.5 1st Qu.:11.00 1st Qu.: 11.00 1st Qu.: 3.50
#> Median : 46.0 Median :21.00 Median : 25.00 Median : 7.00
#> Mean : 56.2 Mean :22.52 Mean : 30.72 Mean : 12.21
#> 3rd Qu.: 80.0 3rd Qu.:33.00 3rd Qu.: 39.00 3rd Qu.: 13.00
#> Max. :256.0 Max. :75.00 Max. :217.00 Max. :130.00
#> Nuwara Eliya Galle Hambantota Matara
#> Min. : 0.000 Min. : 0.00 Min. : 0.000 Min. : 0.00
#> 1st Qu.: 1.000 1st Qu.: 5.00 1st Qu.: 3.000 1st Qu.: 5.00
#> Median : 3.000 Median :11.00 Median : 6.000 Median :10.00
#> Mean : 4.147 Mean :13.75 Mean : 9.423 Mean :14.86
#> 3rd Qu.: 5.500 3rd Qu.:19.50 3rd Qu.:11.500 3rd Qu.:19.00
#> Max. :24.000 Max. :70.00 Max. :87.000 Max. :76.00
#> Jaffna Kilinochchi Mannar Vavuniya
#> Min. : 0.00 Min. :0.000 Min. : 0.000 Min. : 0.000
#> 1st Qu.: 2.50 1st Qu.:0.000 1st Qu.: 0.000 1st Qu.: 0.000
#> Median : 8.00 Median :0.000 Median : 1.000 Median : 1.000
#> Mean : 14.82 Mean :0.509 Mean : 2.789 Mean : 6.638
#> 3rd Qu.: 16.00 3rd Qu.:1.000 3rd Qu.: 3.000 3rd Qu.: 2.000
#> Max. :329.00 Max. :9.000 Max. :84.000 Max. :209.000
#> Mulative Batticalo Ampara Trincomalee
#> Min. :0.0000 Min. : 0.00 Min. : 0.000 Min. : 0.00
#> 1st Qu.:0.0000 1st Qu.: 4.00 1st Qu.: 2.000 1st Qu.: 1.00
#> Median :0.0000 Median : 9.00 Median : 4.000 Median : 3.00
#> Mean :0.5484 Mean : 15.16 Mean : 6.272 Mean : 5.33
#> 3rd Qu.:0.0000 3rd Qu.: 19.00 3rd Qu.: 8.000 3rd Qu.: 6.00
#> Max. :8.0000 Max. :134.00 Max. :61.000 Max. :81.00
#> Kurunagala Puttalam Anuradhapura Polonnaruwa
#> Min. : 1.00 Min. : 0.00 Min. : 0.000 Min. : 0.000
#> 1st Qu.: 13.00 1st Qu.: 3.00 1st Qu.: 3.000 1st Qu.: 1.000
#> Median : 22.00 Median : 8.00 Median : 5.000 Median : 3.000
#> Mean : 30.43 Mean : 12.67 Mean : 8.606 Mean : 4.337
#> 3rd Qu.: 36.00 3rd Qu.: 16.00 3rd Qu.: 10.000 3rd Qu.: 6.000
#> Max. :228.00 Max. :123.00 Max. :112.000 Max. :23.000
#> Badulla Monaragala Ratnapura Kegalle
#> Min. : 0.00 Min. : 0.000 Min. : 0.00 Min. : 0.00
#> 1st Qu.: 3.00 1st Qu.: 2.000 1st Qu.: 8.00 1st Qu.: 9.00
#> Median : 6.00 Median : 3.000 Median : 17.00 Median : 18.00
#> Mean : 8.48 Mean : 5.695 Mean : 24.74 Mean : 23.62
#> 3rd Qu.: 10.00 3rd Qu.: 6.000 3rd Qu.: 33.00 3rd Qu.: 28.00
#> Max. :112.00 Max. :95.000 Max. :128.00 Max. :250.00library(ggplot2)
library(forecast)
autoplot(as.ts(mozzie$Colombo))+labs(x="time index", y="counts", title="Time series plot of dengue cases in Colombo")