diff --git a/auxiliary-data/README.md b/auxiliary-data/README.md index c979187..4d50c55 100644 --- a/auxiliary-data/README.md +++ b/auxiliary-data/README.md @@ -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 @@ -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 @@ -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] @@ -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 @@ -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. diff --git a/auxiliary-data/rsv/archive/extract_rsv.py b/auxiliary-data/archive/extract_rsv.py similarity index 100% rename from auxiliary-data/rsv/archive/extract_rsv.py rename to auxiliary-data/archive/extract_rsv.py diff --git a/auxiliary-data/rsv/archive/nrevss/rsv_antigen_3_week_average.csv b/auxiliary-data/archive/nrevss/rsv_antigen_3_week_average.csv similarity index 100% rename from auxiliary-data/rsv/archive/nrevss/rsv_antigen_3_week_average.csv rename to auxiliary-data/archive/nrevss/rsv_antigen_3_week_average.csv diff --git a/auxiliary-data/rsv/archive/nrevss/rsv_data_us.csv b/auxiliary-data/archive/nrevss/rsv_data_us.csv similarity index 100% rename from auxiliary-data/rsv/archive/nrevss/rsv_data_us.csv rename to auxiliary-data/archive/nrevss/rsv_data_us.csv diff --git a/auxiliary-data/rsv/archive/nrevss/rsv_numerator_data_5_week_average.csv b/auxiliary-data/archive/nrevss/rsv_numerator_data_5_week_average.csv similarity index 100% rename from auxiliary-data/rsv/archive/nrevss/rsv_numerator_data_5_week_average.csv rename to auxiliary-data/archive/nrevss/rsv_numerator_data_5_week_average.csv diff --git a/auxiliary-data/rsv/archive/nrevss/rsv_numerator_data_us.csv b/auxiliary-data/archive/nrevss/rsv_numerator_data_us.csv similarity index 100% rename from auxiliary-data/rsv/archive/nrevss/rsv_numerator_data_us.csv rename to auxiliary-data/archive/nrevss/rsv_numerator_data_us.csv diff --git a/auxiliary-data/rsv/archive/nrevss/rsv_pcr_3_week_average.csv b/auxiliary-data/archive/nrevss/rsv_pcr_3_week_average.csv similarity index 100% rename from auxiliary-data/rsv/archive/nrevss/rsv_pcr_3_week_average.csv rename to auxiliary-data/archive/nrevss/rsv_pcr_3_week_average.csv diff --git a/auxiliary-data/rsv/archive/nssp/resp_ed_count_weekly_national.csv b/auxiliary-data/archive/nssp/resp_ed_count_weekly_national.csv similarity index 100% rename from auxiliary-data/rsv/archive/nssp/resp_ed_count_weekly_national.csv rename to auxiliary-data/archive/nssp/resp_ed_count_weekly_national.csv diff --git a/auxiliary-data/rsv/archive/nssp/resp_ed_percent_weekly_national.csv b/auxiliary-data/archive/nssp/resp_ed_percent_weekly_national.csv similarity index 100% rename from auxiliary-data/rsv/archive/nssp/resp_ed_percent_weekly_national.csv rename to auxiliary-data/archive/nssp/resp_ed_percent_weekly_national.csv diff --git a/auxiliary-data/rsv/archive/nssp/resp_ed_percent_weekly_state.csv b/auxiliary-data/archive/nssp/resp_ed_percent_weekly_state.csv similarity index 100% rename from auxiliary-data/rsv/archive/nssp/resp_ed_percent_weekly_state.csv rename to auxiliary-data/archive/nssp/resp_ed_percent_weekly_state.csv diff --git a/auxiliary-data/vaccine_coverage/RSV_round1_Coverage_2023_2024.csv b/auxiliary-data/archive/vaccine_coverage/RSV_round1_Coverage_2023_2024.csv similarity index 100% rename from auxiliary-data/vaccine_coverage/RSV_round1_Coverage_2023_2024.csv rename to auxiliary-data/archive/vaccine_coverage/RSV_round1_Coverage_2023_2024.csv diff --git a/auxiliary-data/vaccine_coverage/add_doses.R b/auxiliary-data/archive/vaccine_coverage/add_doses.R similarity index 100% rename from auxiliary-data/vaccine_coverage/add_doses.R rename to auxiliary-data/archive/vaccine_coverage/add_doses.R