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Merge pull request #8 from jread-usgs/master
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update PBMTL,PGTML,PB0(bads),resample obs
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Jordan S Read authored Jun 26, 2020
2 parents 0be06c0 + 08cb82d commit f33438f
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Showing 17 changed files with 563 additions and 70 deletions.
1 change: 1 addition & 0 deletions .gitignore
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Expand Up @@ -24,6 +24,7 @@
vignettes/*.html
vignettes/*.pdf

in_data/mtl_outputs2_jared/*
tmp/*
rc.local
out_data/*
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21 changes: 17 additions & 4 deletions 1_spatial.yml
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Expand Up @@ -37,14 +37,21 @@ targets:
# would also have pb_target, pg_source, pg_target
# model_export_ids:
# command: list(pb0 = modeled_lake_ids, pb_source = calibrated_lake_ids)

source_ids:
command: extract_csv_column(filepath = '../lake-temperature-process-models/3_run/out/RMSE_transfer_glm.csv',
column = I('source_id'))

target_test_ids:
command: extract_id_pbmtl('../lake-temperature-process-models/3_run/out/transfer_tasks.rds.ind')

target_expansion_ids:
command: extract_expansion_ids('tmp/filtered_observations.rds',
target_ids = target_test_ids,
source_ids = source_ids)

target_ids:
command: extract_csv_column(filepath = 'in_data/pgdtl_rmse__2233Test_ens9 - pgdtl_rmse_pball_2300_ens9.csv',
column = I('target_id'))
command: c(target_test_ids, target_expansion_ids)

superset_release_ids:
command: c(source_ids, target_ids)
Expand Down Expand Up @@ -84,7 +91,13 @@ targets:
meteo_fl_info = xwalk_meteo_fl_names,
gnis_names_fl = '../lake-temperature-model-prep/2_crosswalk_munge/out/gnisname_nhdhr_xwalk.rds')


out_data/modeling_domain_map.png:
command: plot_domain_map(target_name,
lakes_sf_fl = "../lake-temperature-model-prep/1_crosswalk_fetch/out/canonical_lakes_sf.rds",
source_ids = source_ids, target_test_ids = target_test_ids, target_expansion_ids = target_expansion_ids,
us_counties_sf = us_counties_sf,
plot_crs = I("+init=epsg:2811"))

spatial_metadata:
command: extract_feature(modeled_lakes_sf)

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20 changes: 16 additions & 4 deletions 2_observations.yml
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Expand Up @@ -26,10 +26,22 @@ targets:
# in_data/hyperscales_temperature_observations.csv was downloaded from https://www.sciencebase.gov/catalog/item/5db81985e4b0b0c58b5a4c41
# as the "03_temperature_observations.zip" file on 2020-05-22. We're locking this file because it is what was used to train/calibrate. No
# changes to this file should be allowed without a really good reason.
# tmp/filtered_observations.rds:
# command: filter_csv_obs(target_name, site_ids = superset_release_ids,
# obs_start = export_start, obs_stop = export_stop,
# obs_csv = I('in_data/hyperscales_temperature_observations.csv'))

tmp/filtered_observations.rds:
command: filter_csv_obs(target_name, site_ids = superset_release_ids,
obs_start = export_start, obs_stop = export_stop,
obs_csv = I('in_data/hyperscales_temperature_observations.csv'))

command: filter_resample_obs(target_name, site_ids = filter_ids,
obs_start = export_start, obs_stop = export_stop,
sample_res = 0.5,
obs_feather = '../lake-temperature-model-prep/7b_temp_merge/out/merged_temp_data_daily.feather')

filter_ids:
command: c(source_ids, possible_target_ids)

possible_target_ids:
command: extract_csv_column(filepath = 'in_data/pgdtl_rmse__2233Test_ens9 - pgdtl_rmse_pball_2300_ens9.csv', column = I('target_id'))

out_data/temperature_observations.zip:
command: zip_filter_obs(target_name, 'tmp/filtered_observations.rds')
5 changes: 2 additions & 3 deletions 4_inputs.yml
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Expand Up @@ -35,9 +35,8 @@ targets:
groups = spatial_groups)

ice_flags_df:
command: export_pb_df(site_ids = superset_release_ids,
exp_prefix = I('pb0'), exp_suffix = I('ice_flags'),
file_template = I('../lake-temperature-process-models/3_run/sync/pb0_%s_temperatures.feather'))
command: export_from_table(model_out_fl = '../lake-temperature-process-models/3_run/out/pb0_src_trg_tasks.rds.ind',
exp_prefix = I('pb0'), exp_suffix = I('ice_flags'))

out/4_inputs_zips.yml:
command: zip_meteo_groups(target_name,
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52 changes: 48 additions & 4 deletions 5_predictions.yml
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Expand Up @@ -27,22 +27,58 @@ targets:
- out_data/predict_lakes.png
- out/5_pb0_predict_zips.yml
- out/5_pball_predict_zips.yml
- out/5_pgmtl_predict_zips.yml
- out/5_pgmtl9_predict_zips.yml
- out/5_pbmtl_predict_zips.yml

# pb0 predictions are here: 3_run/sync/pb0_{site_id}_temperatures.feather
# pball predictions are here: 3_run/sync/pball_{site_id}_temperatures.feather
# calibrated params were cd, sw_factor, and coef_mix_hyp
# pball configs are here: 2_prep/sync/pball_{site_id}.nml

pb0_predictions_df:
command: export_pb_df(site_ids = superset_release_ids,
exp_prefix = I('pb0'), exp_suffix = I('temperatures'),
file_template = I('../lake-temperature-process-models/3_run/sync/pb0_%s_temperatures.feather'))
command: export_from_table(model_out_fl = '../lake-temperature-process-models/3_run/out/pb0_src_trg_tasks.rds.ind',
exp_prefix = I('pb0'), exp_suffix = I('temperatures'))

# also need to extend depth!
pbmtl_predictions_df:
command: export_pbmtl_df(model_out_fl = '../lake-temperature-process-models/3_run/out/transfer_tasks.rds.ind',
exp_prefix = I('pbmtl'), exp_suffix = I('temperatures'))

mtl_predictions_df:
command: export_mtl_df(site_ids = target_ids,
dummy = I("2020-06-10"),
exp_prefix = I('pgmtl'), exp_suffix = I('temperatures'),
dir_template = I('in_data/mtl_outputs2_jared/%s'),
file_pattern = I('top_source0_nhdhr'))

mtl9_predictions_df:
command: export_mtl_df(site_ids = target_ids,
dummy = I("2020-06-10"),
exp_prefix = I('pgmtl9'), exp_suffix = I('temperatures'),
dir_template = I('in_data/mtl_outputs2_jared/%s'),
file_pattern = I('9source_ensemble_output'))

pball_ids:
command: c(source_ids, target_test_ids)

pball_predictions_df:
command: export_pb_df(site_ids = source_ids,
command: export_pb_df(site_ids = pball_ids,
exp_prefix = I('pball'), exp_suffix = I('temperatures'),
file_template = I('../lake-temperature-process-models/3_run/sync/pball_%s_temperatures.feather'))

out/5_pgmtl9_predict_zips.yml:
command: zip_mtl_export_groups(target_name,
file_info_df = mtl9_predictions_df,
site_groups = site_ids_grouped,
export = I('pgmtl9_predictions'))

out/5_pgmtl_predict_zips.yml:
command: zip_mtl_export_groups(target_name,
file_info_df = mtl_predictions_df,
site_groups = site_ids_grouped,
export = I('pgmtl_predictions'))

out/5_pb0_predict_zips.yml:
command: zip_pb_export_groups(target_name,
file_info_df = pb0_predictions_df,
Expand All @@ -59,6 +95,14 @@ targets:
export_stop = export_stop,
export = I('pball_predictions'))

out/5_pbmtl_predict_zips.yml:
command: zip_pb_export_groups(target_name,
file_info_df = pbmtl_predictions_df,
site_groups = site_ids_grouped,
export_start = export_start,
export_stop = export_stop,
export = I('pbmtl_predictions'))

out_data/predict_lakes.png:
command: plot_grouped_lakes_preview(target_name,
spatial_groups, site_ids_grouped,
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36 changes: 36 additions & 0 deletions 6_evaluation.yml
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Expand Up @@ -17,6 +17,9 @@ targets:
depends:
- out_data/pb0_evaluation.csv
- out_data/pball_evaluation.csv
- out_data/pbmtl_evaluation.csv
- out_data/pgmtl9_evaluation.csv
- out_data/pgmtl_evaluation.csv

obs_for_eval:
command: readRDS('tmp/filtered_observations.rds')
Expand All @@ -43,6 +46,39 @@ targets:
command: compare_as_rmse(target_name,
matched_preds = pball_matched_to_observations)

pgmtl9_matched_to_observations:
command: match_pgmtl_obs(target_name, eval_data = obs_for_eval,
predict_df = mtl9_predictions_df)

out_data/pgmtl9_matched_to_observations.zip:
command: zip_this(target_name, pgmtl9_matched_to_observations)

out_data/pgmtl9_evaluation.csv:
command: compare_as_rmse(target_name,
matched_preds = pgmtl9_matched_to_observations)

pgmtl_matched_to_observations:
command: match_pgmtl_obs(target_name, eval_data = obs_for_eval,
predict_df = mtl_predictions_df)

out_data/pgmtl_matched_to_observations.zip:
command: zip_this(target_name, pgmtl_matched_to_observations)

out_data/pgmtl_evaluation.csv:
command: compare_as_rmse(target_name,
matched_preds = pgmtl_matched_to_observations)

pbmtl_matched_to_observations:
command: match_extend_glm_obs(target_name, eval_data = obs_for_eval,
predict_df = pbmtl_predictions_df)

out_data/pbmtl_matched_to_observations.zip:
command: zip_this(target_name, pbmtl_matched_to_observations)

out_data/pbmtl_evaluation.csv:
command: compare_as_rmse(target_name,
matched_preds = pbmtl_matched_to_observations)

tmp/compare_rmses.png:
command: plot_rmses(
target_name,
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32 changes: 16 additions & 16 deletions out/4_ice_flags_zips.yml
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tmp/ice_flags_16_N41.25-43.00_W82.75-91.25.zip: 6c2187cde75af31f1d87355c7868c94b
tmp/ice_flags_15_N43.50-45.00_W91.50-93.50.zip: fec57136be5f70f8d00048b3efc4ced4
tmp/ice_flags_14_N43.00-45.00_W93.50-99.50.zip: 0841a4a868aecc96950765ffbd9d904c
tmp/ice_flags_13_N43.00-45.50_W83.50-91.50.zip: 1b783e218e578ac9b4409880e7eb9609
tmp/ice_flags_12_N45.00-45.50_W91.50-93.00.zip: dc4c3efc5586e336416456a96606b95e
tmp/ice_flags_11_N45.00-45.50_W93.00-94.50.zip: 6a9639782ceff69a615233f1aaaaea12
tmp/ice_flags_10_N45.00-46.00_W94.50-99.50.zip: 2b494f0384a9d0771de91d3bc94d6c8a
tmp/ice_flags_09_N45.50-47.00_W93.00-94.00.zip: ce059569780e1b7cd29d791e1e559c26
tmp/ice_flags_08_N45.50-47.00_W94.00-94.50.zip: ff220be73df9bec3b9c8fff756e4ea69
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tmp/ice_flags_06_N45.50-46.50_W84.50-92.00.zip: 7d91467d876ddd6e97ec7e6ff1c8938c
tmp/ice_flags_05_N46.50-48.00_W84.50-92.00.zip: f2a406f762e20d314d4d92fbff6039cf
tmp/ice_flags_04_N45.50-48.00_W92.00-93.00.zip: 0224c2186255686517d9749d6131b975
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tmp/ice_flags_10_N45.00-46.00_W94.50-99.50.zip: c570a1bdd45ff7cdf8b979ef6b590714
tmp/ice_flags_09_N45.50-47.00_W93.00-94.00.zip: bd6cdaffd2b165e27604699e0fdf56fd
tmp/ice_flags_08_N45.50-47.00_W94.00-94.50.zip: c35ebf05ad0ac0e2481254cdd06b9fcf
tmp/ice_flags_07_N46.00-47.00_W94.50-99.00.zip: fc93c72556d930e75a02e0716e521dc7
tmp/ice_flags_06_N45.50-46.50_W84.50-92.00.zip: b9f1bc967e03f696aa7acbdd275e15c1
tmp/ice_flags_05_N46.50-48.00_W84.50-92.00.zip: 454df6cc1d36b6b01801572e0e2b4792
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tmp/ice_flags_01_N48.00-49.00_W89.50-99.50.zip: b93382bbc4c5450440fd543e0fbabdcb

32 changes: 16 additions & 16 deletions out/5_pb0_predict_zips.yml
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tmp/pb0_predictions_16_N41.25-43.00_W82.75-91.25.zip: dea72e03b636915044a8be24362a7d2f
tmp/pb0_predictions_15_N43.50-45.00_W91.50-93.50.zip: daf6cd3d160fa2c9c1d5f9a617836491
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tmp/pb0_predictions_13_N43.00-45.50_W83.50-91.50.zip: df5d916abb7f752ace28848aed7f8b6d
tmp/pb0_predictions_12_N45.00-45.50_W91.50-93.00.zip: 3ef77c96b479ae1e38f2807ae173f717
tmp/pb0_predictions_11_N45.00-45.50_W93.00-94.50.zip: 1d1a02bcad5e8ba0fe2c5ca8a8328bee
tmp/pb0_predictions_10_N45.00-46.00_W94.50-99.50.zip: f7b648fd3ab75932d1ef3368514b537b
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30 changes: 15 additions & 15 deletions out/5_pball_predict_zips.yml
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tmp/pball_predictions_16_N41.25-43.00_W82.75-91.25.zip: 1b8fbaf9db2d80b7327b0165948898e5
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