Last updated: 2022-10-02

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Knit directory: Vaccination_COVID/

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File	Version	Author	Date	Message
Rmd	9de46e5	thinhong	2022-09-29	optimise code for coverage: create a big table then filter to plot
Rmd	11694c5	thinhong	2022-08-30	change x axis labels to 3 months
html	11694c5	thinhong	2022-08-30	change x axis labels to 3 months
Rmd	74070b7	thinhong	2022-08-30	update Hai Duong vaccine coverage for 2017, 2018, 2 doses; clarify axis titles
html	74070b7	thinhong	2022-08-30	update Hai Duong vaccine coverage for 2017, 2018, 2 doses; clarify axis titles
Rmd	3b8e1fa	thinhong	2022-08-25	add coverage for mr and mmr
html	3b8e1fa	thinhong	2022-08-25	add coverage for mr and mmr
Rmd	8629620	thinhong	2022-08-25	add vaccine coverage and confidence interval
html	8629620	thinhong	2022-08-25	add vaccine coverage and confidence interval

knitr::opts_chunk$set(echo = F, warning = F, message = F, out.width = "100%")

library(data.table)
library(dplyr)


Attaching package: 'dplyr'

The following objects are masked from 'package:data.table':

    between, first, last

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

library(tidyr)
library(lubridate)


Attaching package: 'lubridate'

The following objects are masked from 'package:data.table':

    hour, isoweek, mday, minute, month, quarter, second, wday, week,
    yday, year

The following objects are masked from 'package:base':

    date, intersect, setdiff, union

library(ggplot2)
library(gtsummary)
library(ggsci)
library(plotly)


Attaching package: 'plotly'

The following object is masked from 'package:ggplot2':

    last_plot

The following object is masked from 'package:stats':

    filter

The following object is masked from 'package:graphics':

    layout

pv_name <- "Hai Duong"
pv_filename <- "haiduong"

datap <- file.path("~", "Downloads", "updated_dataset")
dtoutp <- file.path("~", "Dropbox", "github", "vaccine_registry_data", pv_filename)

covidvc <- readRDS(file.path(datap, "Combined_VAC_COVID19_2022-02-17.rds"))
measle_all <- readRDS(file.path(datap, "measles_haiduong.rds"))
measle_all <- data.table(measle_all)

hepb <- readRDS(file.path(datap, "hepb_haiduong.rds"))
hepb <- data.table(hepb)
hepb <- hepb[which(hepb$shot == 1),]

time_step <- "month"
measle_all$vacym <- floor_date(measle_all$vacdate, time_step)
measle_all$vacname2 <- factor(measle_all$vacname2, levels = c("Measles", "MR", "MMR"))

hepb$dob_ym <- floor_date(hepb$dob, time_step)
measle_all$dob_ym <- floor_date(measle_all$dob, time_step)
measle_all$vac_ym <- floor_date(measle_all$vacdate, time_step)

Measles and COVID-19 vaccination per month

Version	Author	Date
74070b7	thinhong	2022-08-30

High peak of MR shots in Nov 2019
No disruption in Apr 2020
Disruptions in Aug 2020 and Feb 2021

Vaccination campaign in Nov 2019

An MR vaccination campaign is triggered during this time in Hai Duong, focusing on children 1-5 year-old

Version	Author	Date
74070b7	thinhong	2022-08-30
8629620	thinhong	2022-08-25

No disruption in Apr 2020 but in Aug 2020 and Feb 2021

The monthly vaccination date at public clinics is usually at the end of the month. In Mar 2020: right before lockdown they vaccinate children and right after lockdown they came back to vaccinate children

Hai Duong had a Hai Duong city-wide lockdown from 14/8-28/8, this time looks like they only organised the vaccination day in Sep so all children scheduled in Aug miss the shot

Version	Author	Date
74070b7	thinhong	2022-08-30
8629620	thinhong	2022-08-25

Zoom in 2021

Hai Duong had a province-wide lockdown from 28/1/2021 - 15/2 (Directive 15), 16/2 - 2/3 (Directive 16), 3/3 - 17/3 (Directive 15), 18/3 - 31/3 (Directive 19)

Directive 16 > 15 > 19

Version	Author	Date
74070b7	thinhong	2022-08-30
8629620	thinhong	2022-08-25

Public vs private

First let decide how a shot is public or private


hospital    other  private   public  unknown 
     389     2171    36149   353342    12616

Extract children who get 2 shots

Some received the same vaccine in the same day, filter them out and continue

Some received 3 shots, filtered them out.

Change dataset from long to wide format

Aggregate them by month

Line plot

Version	Author	Date
11694c5	thinhong	2022-08-30
74070b7	thinhong	2022-08-30

# A tibble: 6 × 10
    pid denom low_ci high_ci vyear_1st vmonth_1st shot1   shot2  pct2 vacdate_…¹
  <dbl> <dbl>  <dbl>   <dbl>     <dbl>      <dbl> <fct>   <chr> <dbl> <date>    
1    11    26   23.4    63.1      2020          1 private priv…  42.3 2020-01-01
2    51   106   38.3    58.0      2020          1 public  priv…  48.1 2020-01-01
3    33    46   56.5    84.0      2020          8 private priv…  71.7 2020-08-01
4    56   132   33.9    51.3      2020          8 public  priv…  42.4 2020-08-01
5    11    17   38.3    85.8      2021          2 private priv…  64.7 2021-02-01
6    32    68   34.8    59.6      2021          2 public  priv…  47.1 2021-02-01
# … with abbreviated variable name ¹vacdate_1st

# A tibble: 18 × 10
     pid denom low_ci high_ci vyear_1st vmonth_1st shot1  shot2  pct2 vacdate_…¹
   <dbl> <dbl>  <dbl>   <dbl>     <dbl>      <dbl> <fct>  <chr> <dbl> <date>    
 1    31    62   37.0    63.0      2021          3 priva… priv…  50   2021-03-01
 2   445  2897   14.1    16.7      2021          3 public priv…  15.4 2021-03-01
 3    25    54   32.6    60.4      2021          4 priva… priv…  46.3 2021-04-01
 4   304  1711   16.0    19.7      2021          4 public priv…  17.8 2021-04-01
 5    18    50   22.9    50.8      2021          5 priva… priv…  36   2021-05-01
 6   266  1664   14.3    17.8      2021          5 public priv…  16.0 2021-05-01
 7    29    44   50.1    79.5      2021          6 priva… priv…  65.9 2021-06-01
 8   354  2065   15.5    18.8      2021          6 public priv…  17.1 2021-06-01
 9    26    48   39.2    68.6      2021          7 priva… priv…  54.2 2021-07-01
10   364  2030   16.3    19.7      2021          7 public priv…  17.9 2021-07-01
11    25    35   53.7    85.4      2021          8 priva… priv…  71.4 2021-08-01
12   372  1697   20.0    24.0      2021          8 public priv…  21.9 2021-08-01
13    11    27   22.4    61.2      2021          9 priva… priv…  40.7 2021-09-01
14   258  1281   18.0    22.4      2021          9 public priv…  20.1 2021-09-01
15    17    28   40.6    78.5      2021         10 priva… priv…  60.7 2021-10-01
16   237   694   30.6    37.8      2021         10 public priv…  34.1 2021-10-01
17    10    14   41.9    91.6      2021         11 priva… priv…  71.4 2021-11-01
18   156   276   50.4    62.5      2021         11 public priv…  56.5 2021-11-01
# … with abbreviated variable name ¹vacdate_1st

Population level

Version	Author	Date
74070b7	thinhong	2022-08-30

Children who got 2 shots

Version	Author	Date
74070b7	thinhong	2022-08-30
8629620	thinhong	2022-08-25

Vaccine coverage

Measles

2017

2018

2019

2020

Compare cohorts between years

Measles or MR

2017

2018

2019

2020

Compare cohorts between years

Measles, MR or MMR

2017

2018

2019

2020

Compare cohorts between years

2 shots

Public vaccines only (Measles, MR)

Any vaccine (Measles, MR, MMR)

R version 4.2.1 (2022-06-23)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Big Sur ... 10.16

Matrix products: default
BLAS:   /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] plotly_4.10.0     ggsci_2.9         gtsummary_1.6.1   ggplot2_3.3.6    
[5] lubridate_1.8.0   tidyr_1.2.1       dplyr_1.0.10      data.table_1.14.2

loaded via a namespace (and not attached):
 [1] tidyselect_1.1.2    xfun_0.33           bslib_0.4.0        
 [4] purrr_0.3.4         colorspace_2.0-3    vctrs_0.4.2        
 [7] generics_0.1.3      viridisLite_0.4.1   htmltools_0.5.3    
[10] yaml_2.3.5          utf8_1.2.2          rlang_1.0.6        
[13] jquerylib_0.1.4     later_1.3.0         pillar_1.8.1       
[16] glue_1.6.2          withr_2.5.0         RColorBrewer_1.1-3 
[19] lifecycle_1.0.2     stringr_1.4.1       munsell_0.5.0      
[22] gtable_0.3.1        workflowr_1.7.0     htmlwidgets_1.5.4  
[25] evaluate_0.16       labeling_0.4.2      knitr_1.40         
[28] fastmap_1.1.0       crosstalk_1.2.0     httpuv_1.6.6       
[31] fansi_1.0.3         highr_0.9           Rcpp_1.0.9         
[34] promises_1.2.0.1    scales_1.2.1        cachem_1.0.6       
[37] jsonlite_1.8.0      farver_2.1.1        fs_1.5.2           
[40] digest_0.6.29       stringi_1.7.8       rprojroot_2.0.3    
[43] grid_4.2.1          cli_3.4.1           tools_4.2.1        
[46] magrittr_2.0.3      sass_0.4.2          lazyeval_0.2.2     
[49] tibble_3.1.8        whisker_0.4         pkgconfig_2.0.3    
[52] ellipsis_0.3.2      broom.helpers_1.9.0 httr_1.4.4         
[55] gt_0.7.0            rmarkdown_2.16      rstudioapi_0.14    
[58] R6_2.5.1            git2r_0.30.1        compiler_4.2.1

Hai Duong: Measles

Duc Du, Thinh Ong

2020-01-29 (update: 2022-10-02)

Measles and COVID-19 vaccination per month

Vaccination campaign in Nov 2019

No disruption in Apr 2020 but in Aug 2020 and Feb 2021

Zoom in 2021

Public vs private

Population level

Children who got 2 shots

Vaccine coverage

Measles

2017

2018

2019

2020

Compare cohorts between years

Measles or MR

2017

2018

2019

2020

Compare cohorts between years

Measles, MR or MMR

2017

2018

2019

2020

Compare cohorts between years

2 shots

Public vaccines only (Measles, MR)

Any vaccine (Measles, MR, MMR)