Weekly forecast, score, and plot pipeline additions

e3bo · Jul 26, 2021 · 4db87de · 4db87de · github-actions · Aug 2, 2021
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diff --git a/dvc.lock b/dvc.lock
@@ -3154,3 +3154,65 @@ visualize-forecast-2021-07-19-and-data-2021-07-19:
     md5: 6c9fb32ad2dc62637578e3757822d465
   - path: visuals/fdt2021-07-19-ddt2021-07-19-inc-death-forecasts.png
     md5: d74661a10515ac21ac58923a3b2589e0
+hopkins-2021-07-26:
+  cmd: fdt=2021-07-26 ./pull-hopkins-ts-from-date.R
+  deps:
+  - path: pull-hopkins-ts-from-date.R
+    md5: d350b3ca9b344dea811f07232d0ec8d8
+  outs:
+  - path: hopkins/2021-07-26
+    md5: c17513f23bc43cedbfcbd5eb4adcbe99.dir
+forecast-2021-07-26:
+  cmd: fdt=2021-07-26 Rscript forecast-package-covidhub-forecast.R
+  deps:
+  - path: covidhub-common.R
+    md5: 1f55c954eadf100d55b57cabf1cf6403
+  - path: forecast-package-covidhub-forecast.R
+    md5: 335f9d16ef43206dbf928be515e11480
+  - path: hopkins/2021-07-26
+    md5: c17513f23bc43cedbfcbd5eb4adcbe99.dir
+  - path: model.ini
+    md5: 3fdf49b0ef1f5242fd059e6e11f64034
+  outs:
+  - path: forecasts/2021-07-26-CEID-Walk.csv
+    md5: 5243c5907079dd82fab1492ff245f708
+  - path: metrics/2021-07-26-forecast-calc-time.json
+    md5: 1dcacd83247ddac86b86a7d34d174a2c
+score-2021-07-26:
+  cmd: ddt=2021-07-26 ./quantile-score.R
+  deps:
+  - path: covidhub-common.R
+    md5: 1f55c954eadf100d55b57cabf1cf6403
+  - path: forecasts
+    md5: f8ba9ea98fc250f42d4dc80d9054c975.dir
+  - path: hopkins/2021-07-26
+    md5: c17513f23bc43cedbfcbd5eb4adcbe99.dir
+  - path: quantile-score.R
+    md5: 77eda0648caa45d816d5725ec07ae05b
+  outs:
+  - path: metrics/2021-07-26-residuals.rds
+    md5: 0830f9ff528378611ef9268a058bef23
+  - path: metrics/2021-07-26-score-by-loc-type-targ-type-forecast-date.csv
+    md5: 8eba2762080d169035696dc39bcc3eca
+  - path: metrics/2021-07-26-score-by-loc-type-targ-type.csv
+    md5: 7d05f9cd16e3bdc684e9a8f52a75ef49
+  - path: metrics/2021-07-26-score-by-loc-type.csv
+    md5: 58506f55d5b88f68b9704fd1a08774aa
+visualize-forecast-2021-07-26-and-data-2021-07-26:
+  cmd: ddt=2021-07-26 fdt=2021-07-26 ./forecast-vis.R
+  deps:
+  - path: covidhub-common.R
+    md5: 1f55c954eadf100d55b57cabf1cf6403
+  - path: forecast-vis.R
+    md5: 0ae631494af9e58254c85498876fc0eb
+  - path: forecasts/2021-07-26-CEID-Walk.csv
+    md5: 5243c5907079dd82fab1492ff245f708
+  - path: hopkins/2021-07-26
+    md5: c17513f23bc43cedbfcbd5eb4adcbe99.dir
+  outs:
+  - path: visuals/fdt2021-07-26-ddt2021-07-26-cum-death-forecasts.png
+    md5: 9470f9df3e129ae2be6af471f11810b8
+  - path: visuals/fdt2021-07-26-ddt2021-07-26-inc-case-forecasts.pdf
+    md5: cf782a837624ae6c22d9a51fcbc90055
+  - path: visuals/fdt2021-07-26-ddt2021-07-26-inc-death-forecasts.png
+    md5: 0b8acfb9e8d62ec2d7d327da3e4288a3
diff --git a/dvc.yaml b/dvc.yaml
@@ -2794,3 +2794,58 @@ stages:
         cache: false
     - visuals/fdt2021-07-19-ddt2021-07-19-inc-death-forecasts.png:
         cache: false
+  hopkins-2021-07-26:
+    cmd: fdt=2021-07-26 ./pull-hopkins-ts-from-date.R
+    deps:
+    - pull-hopkins-ts-from-date.R
+    outs:
+    - hopkins/2021-07-26
+  forecast-2021-07-26:
+    cmd: fdt=2021-07-26 Rscript forecast-package-covidhub-forecast.R
+    deps:
+    - covidhub-common.R
+    - forecast-package-covidhub-forecast.R
+    - hopkins/2021-07-26
+    - model.ini
+    outs:
+    - forecasts/2021-07-26-CEID-Walk.csv
+    metrics:
+    - metrics/2021-07-26-forecast-calc-time.json:
+        cache: false
+  score-2021-07-26:
+    cmd: ddt=2021-07-26 ./quantile-score.R
+    deps:
+    - covidhub-common.R
+    - forecasts
+    - hopkins/2021-07-26
+    - quantile-score.R
+    outs:
+    - metrics/2021-07-26-residuals.rds
+    plots:
+    - metrics/2021-07-26-score-by-loc-type-targ-type-forecast-date.csv:
+        cache: false
+        template: lqs-loctype-targtype-panels
+        x: forecast_date
+    - metrics/2021-07-26-score-by-loc-type-targ-type.csv:
+        cache: false
+        template: lqs-loctype-panel
+        x: target_type
+    - metrics/2021-07-26-score-by-loc-type.csv:
+        cache: false
+        template: lqs
+        x: loc_type
+        x_label: Location type
+  visualize-forecast-2021-07-26-and-data-2021-07-26:
+    cmd: ddt=2021-07-26 fdt=2021-07-26 ./forecast-vis.R
+    deps:
+    - covidhub-common.R
+    - forecast-vis.R
+    - forecasts/2021-07-26-CEID-Walk.csv
+    - hopkins/2021-07-26
+    outs:
+    - visuals/fdt2021-07-26-ddt2021-07-26-cum-death-forecasts.png:
+        cache: false
+    - visuals/fdt2021-07-26-ddt2021-07-26-inc-case-forecasts.pdf:
+        cache: false
+    - visuals/fdt2021-07-26-ddt2021-07-26-inc-death-forecasts.png:
+        cache: false
diff --git a/metrics/.gitignore b/metrics/.gitignore
@@ -47,3 +47,4 @@
 /2021-07-05-residuals.rds
 /2021-07-12-residuals.rds
 /2021-07-19-residuals.rds
+/2021-07-26-residuals.rds
diff --git a/metrics/2021-07-26-forecast-calc-time.json b/metrics/2021-07-26-forecast-calc-time.json
@@ -0,0 +1 @@
+{"wall":695.881}