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create/move archive folder
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LucieContamin committed Oct 10, 2024
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60 changes: 33 additions & 27 deletions auxiliary-data/README.md
Original file line number Diff line number Diff line change
Expand Up @@ -7,28 +7,13 @@ It contains multiple folders:
extract and update the data.
- one for location and population data
- one for birth rate data
- one archive for past version and past round associated files

## Vaccine Coverage

The folder [vaccine_coverage/](./vaccine_coverage/) provides weekly
state-specific cumulative coverage for specific rounds.

### Round 1 - 2023 / 2024

For round 1, the file
[vaccine_coverage/RSV_round1_Coverage_2023_2024.csv](./vaccine_coverage/RSV_round1_Coverage_2023_2024.csv)
provides vaccine coverage (percentage) from summer 2023 to the end of the
projection period to apply to infants 0-6 months (`rsv_cov_infants_pes` and
`resv_cov_infants_opt`) and seniors over 60 years (`rsv_cover_over_60_pes` and
`rsv_cov_over60_opt`). Values represent the optimistic and pessimistic
assumptions prescribed in RSV round 1

The `rsv_n_dose_infants_opt` is the cumulative weekly number of monoclonal
doses administered to infants 0-6 months during October through March in the
optimistic scenario. This includes birth doses and catch up doses.
`rsv_n_dose_infants_pes` is the same for the pessimistic scenario.


### Round 2 - 2024 / 2025

For round 2, the file
Expand All @@ -42,12 +27,6 @@ Coverage should be considered additive to that of last season. The same coverage
values apply to all intervention scenarios (A-D), while the counterfactual (F)
assumes no coverage.


### Associated code

The R code to generate the `rsv_n_dose_infants_` is also available in the
[vaccine_coverage/](./vaccine_coverage/) folder in an
[add_doses.R](./vaccine_coverage/add_doses.R) file.

## Location and Census Data

Expand Down Expand Up @@ -176,6 +155,33 @@ are downloaded weekly and output in PARQUET files:
For more information, please consult the
[NSSP homepage](https://www.cdc.gov/nssp/index.html)

----

## Archive

### Vaccine Coverage

#### Round 1 - 2023 / 2024

For round 1, the file
[vaccine_coverage/RSV_round1_Coverage_2023_2024.csv](./archive/vaccine_coverage/RSV_round1_Coverage_2023_2024.csv)
provides vaccine coverage (percentage) from summer 2023 to the end of the
projection period to apply to infants 0-6 months (`rsv_cov_infants_pes` and
`resv_cov_infants_opt`) and seniors over 60 years (`rsv_cover_over_60_pes` and
`rsv_cov_over60_opt`). Values represent the optimistic and pessimistic
assumptions prescribed in RSV round 1

The `rsv_n_dose_infants_opt` is the cumulative weekly number of monoclonal
doses administered to infants 0-6 months during October through March in the
optimistic scenario. This includes birth doses and catch up doses.
`rsv_n_dose_infants_pes` is the same for the pessimistic scenario.

### Associated code

The R code to generate the `rsv_n_dose_infants_` is also available in the
[vaccine_coverage/](./archive/vaccine_coverage/) folder in an
[add_doses.R](./archive/vaccine_coverage/add_doses.R) file.


### Past NREVSS and NSSP version data [ARCHIVED version]

Expand Down Expand Up @@ -237,9 +243,9 @@ The National RSV Trends were extracted from the
Two tables are extracted:

- Percent positive respiratory syncytial virus tests in the United States,
by week ([rsv/nrevss/rsv_data_us.csv](./rsv/archive/nrevss/rsv_data_us.csv))
by week ([rsv/nrevss/rsv_data_us.csv](./archive/nrevss/rsv_data_us.csv))
- RSV detections in the United States, by week
([rsv/nrevss/rsv_numerator_data_us.csv](./rsv/archive/nrevss/rsv_numerator_data_us.csv))
([rsv/nrevss/rsv_numerator_data_us.csv](./archive/nrevss/rsv_numerator_data_us.csv))

##### State

Expand All @@ -252,11 +258,11 @@ The National RSV Trends were extracted from the
For each state, three tables are extracted:

- Percent positive antigen detection RSV tests, by 3-week moving average
([rsv/nrevss/rsv_antigen_3_week_average.csv](./rsv/archive/nrevss/rsv_antigen_3_week_average.csv))
([rsv/nrevss/rsv_antigen_3_week_average.csv](./archive/nrevss/rsv_antigen_3_week_average.csv))
- Percent positive RSV PCR tests, by 3-week moving average
([rsv/nrevss/rsv_pcr_3_week_average.csv](./rsv/archive/nrevss/rsv_pcr_3_week_average.csv))
([rsv/nrevss/rsv_pcr_3_week_average.csv](./archive/nrevss/rsv_pcr_3_week_average.csv))
- RSV detections, by 5-week average
([rsv/nrevss/rsv_numerator_data_5_week_average.csv](./rsv/archive/nrevss/rsv_numerator_data_5_week_average.csv))
([rsv/nrevss/rsv_numerator_data_5_week_average.csv](./archive/nrevss/rsv_numerator_data_5_week_average.csv))

All the states data are compiled together into one file.

Expand Down
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