### PROJECT

#### R-code project status and instructions

European Joint Action on Vaccination

# Installation Guide

## Install R-package

The package demand R 3.5.0 or later.

The project R package MCVCovLoc can be installed from GitHub:

To do this the package devtools are needed and can be installed from cran:

install.packages("devtools")

To install the MCVCovLoc package:

devtools::install_github("JensXII/MCVCovLoc", build_vignettes = TRUE)

For older version of R or devtools, this does not work e.g. the vignettes users_guide and install_guide are not build. Then try:

devtools::install_github("JensXII/MCVCovLoc", build_opts = c("--no-resave-data", "--no-manual"))

If this doesn’t work either, you can download the source-code and install this: - you may not be able to do this with Windows Explorer, but have to use Crome or another web-browser.

1. https://github.com/JensXII/MCVCovLoc

5. in the folder double-click the MCVCovLoc R-project file

6. run:

devtools::install(build_vignettes = TRUE)

# Users Guide

## Introduction

Data on coverage of measles containing vaccines are extracted at calender dates e.g. monthly or quarterly. Thus being cross sectional inventories of measles contaning vaccination coverages.

When more cross sectional coverage-data have been collected, it will be possible to follow coverage over calendar time.

The structural setup is shown in figure 1 and 2, input datasets and variables in appendix 1 and the combined output R data in appendix 2.

Figure 1. Setup

Figure 2. Structure on disk

## Input data

Both information on population and vaccinations are needed. Why input data always have to consist of a set of two data-files.

Valid sets of input data will be one of the following:

• Indiviudal population file + Individual vaccination file

• Indiviudal population file + Aggregated vaccination file

• Aggregated population file + Aggregated vaccination file

while the combination Aggregated population file + Individual vaccination file will not be a valid set of input data.

Data in a set of input data should be extracted simultanously or as close in time to one another as possible.
It is recommend to include date-of-extraction in the naming of the files.

Note:

• The input data csv-files must be semicolon-separated csv-files

• Persons with year of birth < 2005 should not be included in the input data

• For NUTS, minimum NUTS0 i.e. countrycode (two characters), must be included

• NUTS detailing can maximum be level 3

• If NUTS-levels more detailed that NUTS0 are used, then all NUTS must be at the same level – in both input files.

## Scripts

Initially, create a dedicated directory for this project (wdir), and a subdirectory in this call data. The later is where input ;-seperated input files must be located

Example:

• Project directory: S:/Data/MCVCovLoc_wdir_DK

• Subdirectory: S:/Data/MCVCovLoc_wdir_DK/data

### New data

For each inventory/status i.e. dates where a valid set of input data are available execute InputData.

Example, with an individual population and an individual vaccination file:

MCVCovLoc::InputData(
wdir = "S:/Data/MCVCovLoc_wdir_DK",
StatusDate = "2019-10-01",
IndividuelPopulationFile = "DKIndPop20191001.csv",
IndividuelMCVFile = "DKIndVac20191001.csv",
AggregatedPopulationFile = NA,
AggregatedMCVFile = NA,
)

This will create a subdirectory wdir/Status_20191010 containing three subdirectories:

• Inputdata – containing the inputdata used

• Data – containing the AggPop, AggVac and combined R files

• Output – containing coverage graphs on NUTS-level 0 for both doses.

### Coverage graphs by Birth cohort

Following the example above, to have a graph of dose 1 coverage by Birth cohort/year in the NUTS DK01 area:

MCVCovLoc::VacCovBd(
wdir = "S:/Data/MCVCovLoc_wdir_DK",
StatusDate = "2019-10-01",
NUTS = "DK01",
dose = 1,
save = TRUE
)

which creates this graph in the directory wdir/Status_20191001/Output

Do you only want to see the graph, but not store it on disk, use save = FALSE

### Coverage graphs by age of vaccination

Following the example above, to have a graph of dose 1 coverage by age in months at vaccination in the NUTS DK01 area:

MCVCovLoc::VacCovAge(
wdir = "S:/Data/MCVCovLoc_wdir",
StatusDate = "2019-10-01",
NUTS = "DK",
dose = 1,
save = TRUE
)

Which creates this graph in the directory wdir/Status_20191001/Output

Do you only want to see the graph, but not store it on disk, use save = FALSE

### Coverage maps

A map of the coverage in a birth-cohort may be drawn on different NUTS-levels.

Following the example above, for birth-cohort 2005 and dose 2:

MCVCovLoc::MapCov(
wdir = 'S:/Data/MCVCovLoc_wdir_DK',
StatusDate = '2019-12-01',
BirthCohort = 2005,
NUTS = 'DK01',
dose = 2,
save = TRUE
)

which creates this map in the directory wdir/Status_20191001/Output

Do you only want to see the map, but not store it on disk, use save = FALSE

### Shiny dashboard

To have a dashboard showing all your registered data:

MCVCovLoc::ShowCov(
wdir = "S:/Data/MCVCovLoc_wdir_DK"
)

This will start a Shiny daskboard:

## APPENDIX 1

### Inputdata

Minimal means that these variables must be in the files, with the specified names. There may also be other variables in data e.g. gender, but these are not included in the coverage calculations and output.

Minimal individual population file

Variable name Meaning Format
PersonID Unique person identifier that allows linking the individual population and individual vaccination files Character
NUTS NUTS Id for where the person had residence at date of data extraction Character
BirthDate Date of birth YYYY-MM-DD

Minimal individual vaccination file

Variable name Meaning Format
PersonID Unique person identifier that allows linking the individual population and individual vaccination files Character
VacDate Date of vaccination YYYY-MM-DD

1 – first dose

2 – second dose

Minimal aggregated population file

Variable name Meaning Format
NUTS NUTS Id for where the person had residence at date of data extraction Character
BirthYear Birth cohort YYYY - Integer(4)
Count Number of persons Integer

Minimal aggregated vaccination file

Variable name Meaning Format
NUTS NUTS Id for where the person had residence at date of data extraction Character
BirthYear Year of birth Integer(4)
VacAgeMonth Age in months, when vaccinated Integer

1 – first dose

2 – second dose

Count Number of vaccinated persons Integer

## APPENDIX 2

Combined R data

Variable name Meaning Format
StatusDate Date of inventory YYYY-MM-DD
NUTS NUTS Id for where the person had residence at StatusDate Character
BirthYear Year of birth Integer(4)
VacAgeMonth Age in months, when vaccinated Integer