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

2. press ‘Clone and download’

3. press ‘Download ZIP’

4. unzip and save the downloaded to a designeded folder

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

6. run:

devtools::install(build_vignettes = TRUE)

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

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

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

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

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

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

APPENDIX 1

APPENDIX 2

Combined R data