From c17a9112b8ba8f3f2ba1be1b53fdaf02764a87bf Mon Sep 17 00:00:00 2001 From: Emma Mendelsohn Date: Fri, 29 Mar 2024 16:50:30 -0400 Subject: [PATCH] closes #83 --- R/aggregate_augmented_data_by_adm.R | 18 +- _targets.R | 34 +- _targets/meta/meta | 869 ++++++++++++++-------------- 3 files changed, 475 insertions(+), 446 deletions(-) diff --git a/R/aggregate_augmented_data_by_adm.R b/R/aggregate_augmented_data_by_adm.R index 9b4d3ed..9f34f94 100644 --- a/R/aggregate_augmented_data_by_adm.R +++ b/R/aggregate_augmented_data_by_adm.R @@ -9,19 +9,27 @@ #' @author Emma Mendelsohn #' @export aggregate_augmented_data_by_adm <- function(augmented_data, - rsa_polygon, - model_dates_selected) { + rsa_polygon, + model_dates_selected) { + # Read augmented data, convert to raster r <- arrow::read_parquet(glue::glue("{augmented_data}/date={model_dates_selected}/part-0.parquet")) |> rast() crs(r) <- crs(rast()) + + # Mask raster to polygon r <- mask(r, rsa_polygon) - p <- terra::extract(r, rsa_polygon, mean, na.rm = TRUE, weights = TRUE) # weighted mean + # Get the mean value by polygons + p <- terra::extract(r, rsa_polygon, mean, na.rm = TRUE, weights = FALSE, ID = FALSE) + + + # spatially weight in fitting - probability per unit area - per size of the district + # probability of it happening in the district is the spatial weighting bind_cols(rsa_polygon, p) |> as_tibble() |> mutate(date = model_dates_selected) |> - select(date, shapeName, ID, names(p)) - + select(date, shapeName, names(p)) + } diff --git a/_targets.R b/_targets.R index 4a0b8c5..93dc67a 100644 --- a/_targets.R +++ b/_targets.R @@ -519,29 +519,47 @@ model_targets <- tar_plan( rsa_polygon, model_dates_selected), pattern = model_dates_selected, - cue = tar_cue(tar_cue_general) + cue = tar_cue("thorough") ), + tar_target(rsa_polygon_spatial_weights, rsa_polygon |> + mutate(area = st_area(rsa_polygon)) |> + as_tibble() |> + select(shapeName, area)), + tar_target(model_data, left_join(aggregated_data_rsa, rvf_outbreaks, by = join_by(date, shapeName)) |> - mutate(outbreak_30 = replace_na(outbreak_30, FALSE)) + mutate(outbreak_30 = replace_na(outbreak_30, FALSE)) |> + left_join(rsa_polygon_spatial_weights, by = "shapeName") ), - # Train/test -------------------------------------------------- - - # Training and Testing (holdout dataset) - tar_target(model_data_split, initial_split(model_data, prop = 0.8, strata = outbreak_30)), + # Splitting -------------------------------------------------- + # Initial train and test (ie holdout) + tar_target(model_data_split, initial_split(model_data, prop = 0.8)), # pick random days left out of the training tar_target(training_data, training(model_data_split)), - tar_target(training_splits, vfold_cv(training_data, strata = outbreak_30)), # subsplit training analysis/assessment tar_target(holdout_data, testing(model_data_split)), + + # CV splits + # Mask from the training set the three months following the holdout dates for the given district and the surrounding districts. + # Should this be on the whole training set, or just the analysis portion of the training set? + # In other words, it doesn't have to be masked from the model's assessments in the CV routine, we can use that data to assess performance + tar_target(masked_data, get_masks_for_training(holdout_data)), + tar_target(training_splits, vfold_cv(training_data)), # subsplit training analysis/assessment + tar_target(training_splits_masked, 1), # subsplit training analysis/assessment + + # Define formula and model tar_target(model_workflow, build_workflow(training_data)), + + # Run tuning tar_target(tuned_parameters, tune_parameters(model_workflow, training_splits, grid_size = 10, n_cores = 4)) - + # Fit final model + # Generate predictions + ) # Deploy ----------------------------------------------------------- diff --git a/_targets/meta/meta b/_targets/meta/meta index 9dd27e0..38276be 100644 --- a/_targets/meta/meta +++ b/_targets/meta/meta @@ -1,433 +1,433 @@ 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@@ -6436,6 +6438,7 @@ readme|stem|61211399f70244f9|2419a0f44a0792be|4745aa592080ea1d|-165896733|README report_targets|object|ef46db3751d8e999||||||||||||||| rolling_box|function|1195d491d98c697b||||||||||||||| rsa_polygon|stem|85ff22f3d5abbfa8|97f9cfc42c3dc72d|c3b5fc02cdc369c1|-869273323|bucket=open-rvfcast-data*region=us-east-1*key=_targets/rsa_polygon*endpoint=TlVMTA*version=|t19755.8641201865s||12072624|qs|aws|vector|||0.33|| +rsa_polygon_spatial_weights|stem|4e52c40d5de9ca53|eca702e31bb932c0|df9ca22b8462ec4f|-361496493|bucket=open-rvfcast-data*region=us-east-1*key=_targets/rsa_polygon_spatial_weights*endpoint=TlVMTA*version=|t19811.8543717756s||1397|qs|aws|vector|||0.606|| rvf_outbreaks|stem|d0ef19afedc038a3|28f37c22047a2c01|a0dfd7fa96dd2384|1816028906|bucket=open-rvfcast-data*region=us-east-1*key=_targets/rvf_outbreaks*endpoint=TlVMTA*version=|t19786.9268302828s||4064|qs|aws|vector|||1.425|| save_transform_ecmwf_grib|function|6a76f13bf2e8bad9||||||||||||||| save_transform_grib|function|820e4c12a3d3a749||||||||||||||| @@ -6960,7 +6963,7 @@ submit_modis_ndvi_task_request_continent|function|cd3db23261baafe9|||||||||||||| tar_cue_general|object|a973f11a0f57f835||||||||||||||| tar_cue_upload_aws|object|a973f11a0f57f835||||||||||||||| test_targets|object|ef46db3751d8e999||||||||||||||| -training_data|stem|e52f9f6a24db66d5|ffa58e26f03cdc30|9b41524f1feaec79|-408453539|bucket=open-rvfcast-data*region=us-east-1*key=_targets/training_data*endpoint=TlVMTA*version=|t19787.8261746947s||7753199|qs|aws|vector|||0.004|| +training_data|stem|d245bf14bb92e2b8|ffa58e26f03cdc30|292188f40c4fe75b|-408453539|bucket=open-rvfcast-data*region=us-east-1*key=_targets/training_data*endpoint=TlVMTA*version=|t19811.867884918s||7893235|qs|aws|vector|||0.005|| training_data_splits|stem|d40a744f483dba4e|3b8941c5a92a5db2|1359cc8a778bc2e2|599471119|bucket=open-rvfcast-data*region=us-east-1*key=_targets/training_data_splits*endpoint=TlVMTA*version=|t19787.834269089s||78231646|qs|aws|vector|||0.018|| training_splits|stem|e22a0668b844ebc0|3b8941c5a92a5db2|1359cc8a778bc2e2|1412968132|bucket=open-rvfcast-data*region=us-east-1*key=_targets/training_splits*endpoint=TlVMTA*version=|t19787.8360909985s||78231430|qs|aws|vector|||0.029|| transform_ecmwf_forecasts|function|648667cbb23058c3|||||||||||||||