Set up, use, and interpret the results of the VERSE Equity Tool
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As low and middle-income countries expand domestic investment in vaccines, data on the economic value of these investments can help decisionmakers compare the benefits of vaccination with other health and non-health investments. These data can also provide advocates with rigorous evidence to demonstrate the impact of vaccines in terms that are comparable with other sectors. Additionally, it is crucial to understand inequities in access and coverage and how inequitable vaccine coverage may impede full the realization of the benefits of vaccines at the national level.
The toolkit was officially launched on May 25, 2022. You can watch a full presentation and demonstration of the toolkit in the video below:
Attendees received a post-webinar folio with useful links, accessible here.
Learn more about the VERSE project »
This repository contains the most up-to-date generic VERSE Equity Tool for DHS data analysis. It can be used, edited, and shared with proper credit, following the MIT license.
Customizable versions of the VERSE Equity Tool exist in other repositories. Please contact Mr. Gatien de Broucker to access or set up a separate repository: [email protected]
You must have R, R-Studio and Git-for-Windows installed on your computer and up-to-date.
- Download R
- Download R-Studio · Note: the free open-source license is enough
- Download Git-for-Windows
- In R-Studio, create a new project (File >> New Project...)
- In the New Project Wizard in R-Studio, select Version Control >> Git
- Paste the following URL to Repository URL and designate a folder where the VERSE program will be copied to
https://github.com/VERSE-Equity/VERSE-DHS.git - Open VERSE.R (you can type the following code in R-Studio)
file.edit("VERSE.R") - Install the necessary R packages
install.packages("ggrepel") install.packages("prevR") install.packages("sf") install.packages("matchmaker") install.packages("rmapshaper") install.packages("PHEindicatormethods") install.packages("radiant") install.packages("StatMeasures") devtools::install_github("ropensci/rdhs")
Read more about using Git and GitHub here »
Once the VERSE.R program is opened in R-Studio, you must specify several model inputs based on your analysis query and as appropriate for the country of interest:
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What is your working directory? The working directory determines where you want the VERSE outputs to be stored on your computer. It should be different from the clone repository, which only stores the program.
setwd("C:/YOUR DIRECTORY HERE") -
Which country do you want to analyze? And for what year of the DHS? For both questions above, you should review the availability of DHS data.
COUNTRY <- "Uganda" YEAR <- 2016
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Which vaccines to include? A list of available vaccines is displayed below. Only select vaccines that were included in the national immunization schedule the year the DHS survey was performed.
VACCINES <- c("BCG","DTP1","DTP2","DTP3","OPV1","OPV2","OPV3","ZERO","FULL","COMPLETE")
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Do you want to generate maps? Maps convey excellent insights on geographic disparities, but they add to the analysis time. You can deactivate them to make the program run faster.
MAP = "YES"
You can also search for ACTION NEEDED in VERSE.R to review where these inputs are needed.
The VERSE Equity Toolkit generates the following metrics:
- Coverage ("efficiency") metric: Coverage
- Equity metrics:
- Wagstaff concentration index (composite ranking): CI
- Wagstaff concentration index (wealth ranking)A: CI_Wealth
- Erreyger concentration index (composite ranking): CI_E
- Erreyger concentration index (wealth ranking)A: CI_E_Wealth
- Absolute Equity Gap: AEG
- Relative Equity Gap: REG
- Slope Index of Inequity: SII
- Relative Index of Inequity: RII
Notes:
A. The common concentration index based on socioeconomic status ("wealth") only is also generated.
After successfully running the toolkit, the coverage and equity metrics can be called using the following code:
results$[ENTER DESIRED METRIC AND SPECIFICATION HERE]The code for the metrics are presented in the list above (in italics). The codes for the specifications (national or subnational level, vaccine, and factor of inequity) are detailed in the VERSE Equity Toolkit User Guide.
Examples:
# National estimates for the Wagstaff concentration index
# (composite ranking) by vaccine
results$CI_Results
# Subnational estimates for the Wagstaff concentration index
# (composite ranking) for a specific vaccine (here, MCV1) by region
results$CI_GEO_MCV1Consult the VERSE Equity Toolkit User Guide for more details.
| Vaccine | Code (birth dose) | Code (dose 1) | Code (dose 2) | Code (dose 3) |
|---|---|---|---|---|
| Bacillus Calmette–Guérin | BCG | |||
| Diphtheria-Tetanus-Pertussis | DTP1 | DTP2 | DTP3 | |
| Polio (any) | PolioBD | POLIO1 A | POLIO2 A | POLIO3 A |
| Oral Polio only | OPV1 | OPV2 | OPV3 | |
| Inactivated Polio only | IPV1 | IPV2 | IPV3 | |
| Pentavalent | Penta1 | Penta2 | Penta3 | |
| Measles | MCV1 B | MCV2 B | ||
| Pneumococcal conjugate | PCV1 | PCV2 | PCV3 | |
| Rotavirus | ROTA1 | ROTA2 | ROTA3 | |
| Hepatitis B | HEPBBD | HEPB1 | HEPB2 | HEPB3 |
| Haemophilus influenzae type b | HIB1 | HIB2 | HIB3 |
In addition to individual vaccines, the following health outcomes should always be specified as inputs:
| Health outcome | Code | Description |
|---|---|---|
| Zero-dose status | ZERO | A child has a zero-dose status if they did not receive either BCG, DTP1, or OPV1 by 12 months of age |
| Fully-immunized for age status | FULL C | A child is considered fully immunized for age if they received all scheduled vaccines for their age (in the model, this applies to BCG, DTP1-3, OPV1-3, and any other specified vaccine) |
| Completed immunization schedule status | COMPLETE | TBD |
Notes:
A. Users should choose to use POLIO1-3 in the VACCINES() input unless they are sure that either OPV or IPV is exclusively given in the country of interest.
B. MCV1 and MCV2 are excluded in the calculation if supplemental immunization activity (or vaccine campaign) for measles took place in the two years preceding the analyzed DHS survey.
C. These vaccines and health outcomes must be included in the VACCINES() input.
We are aware of a common issue where the program stops running and you receive the following error message in the R Console:
Error in download.file(url, tf2, quiet = quiet_download) :
cannot open URL 'https://gis.dhsprogram.com/arcgis/rest/directories/arcgisjobs/tools
downloadsubnationaldata_gpserver/j3d3334c368334492902fa8a86a81666e/scratch
sdr_subnational_boundaries_2022-02-11.zip'To resolve it, run the following code directly in your R Console and re-execute the VERSE Equity Toolkit:
get_available_datasets(clear_cache=TRUE)This procedure will clear your cache and allow you to download another DHS dataset.
Most errors can be resolved by restarting R-Studio and ensuring that all necessary packages are installed. The VERSE Equity Toolkit requires the latest version of R and R-Studio to be installed, as well as several R packages listed above.
If this does not resolve the error, you can report it on the dedicated GitHub page. While the toolkit is designed to accommodate many deviations in the DHS data coding, it may be missing recent updates to the data.
Finally, the VERSE Equity Toolkit does not currently run (or requires additional inputs) for the following countries:
| Country (year) | Reason | Resolution |
|---|---|---|
| Any country prior to 2010 | VERSE Equity Toolkit not yet tested on pre-2010 data | We may update the tool to include these data (let us know if you are interested in using specific pre-2010 surveys) |
| Equatorial Guinea (2011) | DHS dataset is not available to the public | None |
| Sri Lanka (2016) | DHS dataset is not available to the public | None |
| Yemen (2013) | There are no map-shape files for Yemen, and there is no data on maternal education (the level will appear as 0% in the pie charts) | Set MAP = "NO" |
| Colombia (2015) | Colombia did not collect any immunization data in the 2015 DHS | None |
| Peru (2014) | DHS dataset is not available to the public | 2012 DHS dataset is available for Peru |
Report issues with the outputs or the program on the dedicated GitHub page. Others may have encountered the same issue and any resolution will be posted there.
The VERSE Equity Toolkit operates under the MIT License.
The license allows for many types of use of the VERSE Equity Toolkit. To provide credit, we recommend using the following reference:
Patenaude, B., Odihi, D., Sriudomporn, S., Mak, J., Watts, E., & de Broucker, G. (2022). A standardized approach for measuring multivariate equity in vaccination coverage, cost-of-illness, and health outcomes: Evidence from the Vaccine Economics Research for Sustainability & Equity (VERSE) project. Social Science & Medicine, 302, 114979. doi:https://doi.org/10.1016/j.socscimed.2022.114979
- Dr. Bryan Patenaude (he/him) at [email protected] to discuss applications of the VERSE Equity Toolkit on primary healthcare outcomes or other health outcomes, or on alternative data sources.
- Mr. Gatien de Broucker at [email protected] to learn about learning opportunities and VERSE-related courses.
Learn more about the VERSE project: ImmunizationEconomics.Org/verse-home
Read the news release about the VERSE Equity Toolkit: Measuring equity in vaccination coverage beyond socioeconomic status: Launch of the VERSE Equity Toolkit (27 April 2022)
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