In JensXII/MCVCovLoc: Measles containing vaccine coverage
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
{width="6.0in" height="3.0in"}
Figure 2. Structure on disk
{width="2.0in" height="4.0in"}
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,
AdministrativeMCVFile = 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
{width="6.4in" height="3.6in"}
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
{width="6.4in" height="3.6in"}
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
{width="6.4in" height="3.6in"}
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:
{width="6.4in" height="3.6in"}
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 | Character |
| | identifier that | |
| | allows linking the | |
| | individual population | |
| | and individual | |
| | vaccination files | |
+-----------------------+-----------------------+-----------------------+
| NUTS | NUTS Id for where the | Character |
| | person had residence | |
| | at date of data | |
| | extraction | |
+-----------------------+-----------------------+-----------------------+
| BirthDate | Date of birth | YYYY-MM-DD |
+-----------------------+-----------------------+-----------------------+
Minimal individual vaccination file
+-----------------------+-----------------------+-----------------------+
| Variable name | Meaning | Format |
+=======================+=======================+=======================+
| PersonID | Unique person | Character |
| | identifier that | |
| | allows linking the | |
| | individual population | |
| | and individual | |
| | vaccination files | |
+-----------------------+-----------------------+-----------------------+
| VacDate | Date of vaccination | YYYY-MM-DD |
+-----------------------+-----------------------+-----------------------+
| DoseRecorded | Dose received | 1 -- first dose |
| | | |
| | | 2 -- second dose |
+-----------------------+-----------------------+-----------------------+
Minimal aggregated population file
+-----------------------+-----------------------+-----------------------+
| Variable name | Meaning | Format |
+=======================+=======================+=======================+
| NUTS | NUTS Id for where the | Character |
| | person had residence | |
| | at date of data | |
| | extraction | |
+-----------------------+-----------------------+-----------------------+
| 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 | Character |
| | person had residence | |
| | at date of data | |
| | extraction | |
+-----------------------+-----------------------+-----------------------+
| BirthYear | Year of birth | Integer(4) |
+-----------------------+-----------------------+-----------------------+
| VacAgeMonth | Age in months, when | Integer |
| | vaccinated | |
+-----------------------+-----------------------+-----------------------+
| DoseRecorded | Dose received | 1 -- first dose |
| | | |
| | | 2 -- second dose |
+-----------------------+-----------------------+-----------------------+
| Count | Number of vaccinated | Integer |
| | persons | |
+-----------------------+-----------------------+-----------------------+
APPENDIX 2
Combined R data
+-----------------------+-----------------------+-----------------------+
| Variable name | Meaning | Format |
+=======================+=======================+=======================+
| StatusDate | Date of inventory | YYYY-MM-DD |
+-----------------------+-----------------------+-----------------------+
| NUTS | NUTS Id for where the | Character |
| | person had residence | |
| | at StatusDate | |
+-----------------------+-----------------------+-----------------------+
| BirthYear | Year of birth | Integer(4) |
+-----------------------+-----------------------+-----------------------+
| VacAgeMonth | Age in months, when | Integer |
| | vaccinated | |
+-----------------------+-----------------------+-----------------------+
| DoseRecorded | Dose received | 1 -- first dose |
| | | |
| | | 2 -- second dose |
+-----------------------+-----------------------+-----------------------+
| Count | Number of vaccinated | Integer |
| | persons | |
+-----------------------+-----------------------+-----------------------+
JensXII/MCVCovLoc documentation built on Dec. 13, 2020, 1:47 p.m.
R Package Documentation
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Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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
{width="6.0in" height="3.0in"}
Figure 2. Structure on disk
{width="2.0in" height="4.0in"}
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, AdministrativeMCVFile = 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
{width="6.4in" height="3.6in"}
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
{width="6.4in" height="3.6in"}
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
{width="6.4in" height="3.6in"}
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:
{width="6.4in" height="3.6in"}
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 | Character | | | identifier that | | | | allows linking the | | | | individual population | | | | and individual | | | | vaccination files | | +-----------------------+-----------------------+-----------------------+ | NUTS | NUTS Id for where the | Character | | | person had residence | | | | at date of data | | | | extraction | | +-----------------------+-----------------------+-----------------------+ | BirthDate | Date of birth | YYYY-MM-DD | +-----------------------+-----------------------+-----------------------+
Minimal individual vaccination file
+-----------------------+-----------------------+-----------------------+ | Variable name | Meaning | Format | +=======================+=======================+=======================+ | PersonID | Unique person | Character | | | identifier that | | | | allows linking the | | | | individual population | | | | and individual | | | | vaccination files | | +-----------------------+-----------------------+-----------------------+ | VacDate | Date of vaccination | YYYY-MM-DD | +-----------------------+-----------------------+-----------------------+ | DoseRecorded | Dose received | 1 -- first dose | | | | | | | | 2 -- second dose | +-----------------------+-----------------------+-----------------------+
Minimal aggregated population file
+-----------------------+-----------------------+-----------------------+ | Variable name | Meaning | Format | +=======================+=======================+=======================+ | NUTS | NUTS Id for where the | Character | | | person had residence | | | | at date of data | | | | extraction | | +-----------------------+-----------------------+-----------------------+ | 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 | Character | | | person had residence | | | | at date of data | | | | extraction | | +-----------------------+-----------------------+-----------------------+ | BirthYear | Year of birth | Integer(4) | +-----------------------+-----------------------+-----------------------+ | VacAgeMonth | Age in months, when | Integer | | | vaccinated | | +-----------------------+-----------------------+-----------------------+ | DoseRecorded | Dose received | 1 -- first dose | | | | | | | | 2 -- second dose | +-----------------------+-----------------------+-----------------------+ | Count | Number of vaccinated | Integer | | | persons | | +-----------------------+-----------------------+-----------------------+
APPENDIX 2
Combined R data
+-----------------------+-----------------------+-----------------------+ | Variable name | Meaning | Format | +=======================+=======================+=======================+ | StatusDate | Date of inventory | YYYY-MM-DD | +-----------------------+-----------------------+-----------------------+ | NUTS | NUTS Id for where the | Character | | | person had residence | | | | at StatusDate | | +-----------------------+-----------------------+-----------------------+ | BirthYear | Year of birth | Integer(4) | +-----------------------+-----------------------+-----------------------+ | VacAgeMonth | Age in months, when | Integer | | | vaccinated | | +-----------------------+-----------------------+-----------------------+ | DoseRecorded | Dose received | 1 -- first dose | | | | | | | | 2 -- second dose | +-----------------------+-----------------------+-----------------------+ | Count | Number of vaccinated | Integer | | | persons | | +-----------------------+-----------------------+-----------------------+
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