data-raw/demo-subnational-pjnz/README.md
In mrc-ide/naomi: Naomi Model for Subnational HIV Estimates
These files are alternative testing and demonstration files representing subnational
Spectrum files. Three Spectrum PJNZ files werecreated based on the Malawi 2019 PJNZ file.
Update 22 August 2024: Updated files were created with the Malawi 2024 PJNZ file
using Sepctrum 6.36. Saved in folder mwi2024_v6.36/.
Region codes in .PJN files manually changed as follows:
- Northern Region: code 10
- Central Region: code 11
- Southern Region: code 12
Datasets are also created for zone-level programme data inputs for efficient model testing.
Area hierarchy
The spectrum_region_code field was updated from 0 to the values 10, 11, 12.
Spectrum files
Base population
The base population and net migration were scaled in each file based on the proportions:
| Region | Proportion |
|: --------|------------|
| Northern | 13% |
| Central | 43% |
| Southern | 44% |
No other changes were made to demographic inputs. Fertility and non-HIV mortality rates were retained at national values.
Update 22 August 2024: Same proportion applied for HIV tests conducted in Shiny90.
Number on ART
The number on ART was scaled by the proportions:
| Region | Proportion |
|: --------|------------|
| Northern | 10% |
| Central | 29% |
| Southern | 61% |
The same proportions were used for adults on ART, children on ART, and children receiving cotrimoxazole.
Update 22 August 2024: Same proportion applied for ART initiations and HIV diagnoses in Shiny90.
PMTCT and ANC clients
PMTCT and ANC clients were scaled
| Region | Clients | Known Positive | ANC tested | Tested positive | PMTCT |
|: --------|------------|----------------|------------|-----------------|-------|
| Northern | 13% | 8% | 12% | 8% | 8% |
| Central | 43% | 26% | 42% | 28% | 27% |
| Southern | 44% | 66% | 46% | 64% | 65% |
EPP fitting
EPP was refit single region in each file.
For the 2024 Spectrum file: EPP by region was re-imported from the 2022 PJNZ files
Analysis was done using the Spectrum v5.87 and based from the 2019 Malawi Spectrum file.
mrc-ide/naomi documentation built on Jan. 6, 2025, 10:20 a.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
These files are alternative testing and demonstration files representing subnational Spectrum files. Three Spectrum PJNZ files werecreated based on the Malawi 2019 PJNZ file.
Update 22 August 2024: Updated files were created with the Malawi 2024 PJNZ file
using Sepctrum 6.36. Saved in folder mwi2024_v6.36/.
Region codes in .PJN files manually changed as follows:
- Northern Region: code 10
- Central Region: code 11
- Southern Region: code 12
Datasets are also created for zone-level programme data inputs for efficient model testing.
Area hierarchy
The spectrum_region_code field was updated from 0 to the values 10, 11, 12.
Spectrum files
Base population
The base population and net migration were scaled in each file based on the proportions:
| Region | Proportion | |: --------|------------| | Northern | 13% | | Central | 43% | | Southern | 44% |
No other changes were made to demographic inputs. Fertility and non-HIV mortality rates were retained at national values.
Update 22 August 2024: Same proportion applied for HIV tests conducted in Shiny90.
Number on ART
The number on ART was scaled by the proportions:
| Region | Proportion | |: --------|------------| | Northern | 10% | | Central | 29% | | Southern | 61% |
The same proportions were used for adults on ART, children on ART, and children receiving cotrimoxazole.
Update 22 August 2024: Same proportion applied for ART initiations and HIV diagnoses in Shiny90.
PMTCT and ANC clients
PMTCT and ANC clients were scaled
| Region | Clients | Known Positive | ANC tested | Tested positive | PMTCT | |: --------|------------|----------------|------------|-----------------|-------| | Northern | 13% | 8% | 12% | 8% | 8% | | Central | 43% | 26% | 42% | 28% | 27% | | Southern | 44% | 66% | 46% | 64% | 65% |
EPP fitting
EPP was refit single region in each file.
For the 2024 Spectrum file: EPP by region was re-imported from the 2022 PJNZ files
Analysis was done using the Spectrum v5.87 and based from the 2019 Malawi Spectrum file.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.