Merge pull request #6 from ihmeuw/all-v2

All of the changes for the climate and cgf paper first submission.

Author: Moloq

notebooks/2024_06_25_compare_to_GBD.ipynb

@@ -34,6 +34,27 @@
     "    gbd.to_parquet(output_path / f'{measure}.parquet')\n"
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": 3,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "for measure, rei_id in [('stunting', 241), ('wasting', 240)]:\n",
+    "    sev = db_queries.get_outputs(\n",
+    "        'rei',\n",
+    "        rei_id=rei_id,\n",
+    "        release_id=9,\n",
+    "        measure_id=29,\n",
+    "        metric_id=3,\n",
+    "        location_id='all',\n",
+    "        year_id='all',\n",
+    "        age_group_id='all',\n",
+    "        sex_id='all',\n",
+    "    )\n",
+    "    sev.to_parquet(output_path / f'{measure}_sev.parquet')\n"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": 3,

notebooks/2024_07_03_save_gbd_prevalence.ipynb

@@ -32,8 +32,8 @@ packages = [
 [tool.poetry.dependencies]
 python = ">=3.10, <3.13"
 click = "*"
-numpy = "^1.26.0"
-pandas = "^1.5"
+numpy = "^2.1.2"
+pandas = "^2.2.3"
 pymer4 = "^0.8.2"
 scikit-learn = "^1.5.0"
 matplotlib = "^3.9.0"
@@ -70,8 +70,8 @@ requires = ["poetry-core>=1.0.0"]
 build-backend = "poetry.core.masonry.api"
 
 [tool.poetry.scripts]
-strun = "spatial_temp_cgf.cli:strun"
-sttask = "spatial_temp_cgf.cli:sttask"
+strun = "rra_climate_health.cli:strun"
+sttask = "rra_climate_health.cli:sttask"
 
 [tool.ruff]
 target-version = "py310" # The lowest supported version

notebooks/2024_10_20_sev_shift.ipynb

@@ -1,31 +1,53 @@
-version:
-  training_data: "2024_07_01.01"
-measure: "stunting"
+extra_terms:
+- any_days_over_30C * ldi_pc_pd
+grid_predictors: null
 holdout:
-  type: "no_holdout"
+  proportion: 0.2
+  seed: 42
+  type: no_holdout
+measure: stunting
 predictors:
-  - name: "intercept"
-    random_effect: "ihme_loc_id"
-  - name: "days_over_30C"
-    transform:
-      type: 'scaling'
-      strategy: 'inner_ninety_five'
-  - name: "ldi_pc_pd"
-    transform:
-      type: 'scaling'
-      strategy: 'inner_ninety_five'
-  - name: "elevation"
-    transform:
-      type: 'scaling'
-      strategy: 'inner_ninety_five'
-  - name: "mean_temperature"
-    transform:
-      type: 'scaling'
-      strategy: 'inner_ninety_five'
-  - name: "any_days_over_30C"
-    transform:
-      type: 'masking'
-      from_column: 'days_over_30C'
-      threshold: 0
-extra_terms:
-  - "any_days_over_30C * ldi_pc_pd"
+- name: intercept
+  random_effect: ihme_loc_id
+  transform:
+    strategy: identity
+    type: scaling
+- name: sex_id
+  random_effect: ''
+  transform:
+    strategy: identity
+    type: categorical
+- name: age_group_id
+  random_effect: ''
+  transform:
+    strategy: identity
+    type: categorical
+- name: days_over_30C
+  random_effect: ''
+  transform:
+    strategy: inner_ninety_five
+    type: scaling
+- name: ldi_pc_pd
+  random_effect: ''
+  transform:
+    strategy: inner_ninety_five
+    type: scaling
+- name: elevation
+  random_effect: ''
+  transform:
+    strategy: inner_ninety_five
+    type: scaling
+- name: mean_temperature
+  random_effect: ''
+  transform:
+    strategy: inner_ninety_five
+    type: scaling
+- name: any_days_over_30C
+  random_effect: ''
+  transform:
+    from_column: days_over_30C
+    threshold: 0.0
+    type: masking
+submodel_vars: null
+version:
+  training_data: '2024_09_05.01'

notebooks/_sandbox.ipynb

@@ -0,0 +1,53 @@
+extra_terms:
+- any_days_over_30C * ldi_pc_pd
+grid_predictors: null
+holdout:
+  proportion: 0.2
+  seed: 42
+  type: no_holdout
+measure: wasting
+predictors:
+- name: intercept
+  random_effect: ihme_loc_id
+  transform:
+    strategy: identity
+    type: scaling
+- name: sex_id
+  random_effect: ''
+  transform:
+    strategy: identity
+    type: categorical
+- name: age_group_id
+  random_effect: ''
+  transform:
+    strategy: identity
+    type: categorical
+- name: days_over_30C
+  random_effect: ''
+  transform:
+    strategy: inner_ninety_five
+    type: scaling
+- name: ldi_pc_pd
+  random_effect: ''
+  transform:
+    strategy: inner_ninety_five
+    type: scaling
+- name: elevation
+  random_effect: ''
+  transform:
+    strategy: inner_ninety_five
+    type: scaling
+- name: mean_temperature
+  random_effect: ''
+  transform:
+    strategy: inner_ninety_five
+    type: scaling
+- name: any_days_over_30C
+  random_effect: ''
+  transform:
+    from_column: days_over_30C
+    threshold: 0.0
+    type: masking
+submodel_vars: null
+version:
+  training_data: '2024_09_05.01'

poetry.lock

@@ -14,7 +14,7 @@
 _P = ParamSpec("_P")
 
 
-VALID_MEASURES = ["wasting", "stunting"]
+VALID_MEASURES = ["wasting", "stunting", "underweight"]
 
 
 def get_choice_callback(
@@ -62,12 +62,12 @@ def with_source_type(
 
 
 VALID_CMIP6_SCENARIOS = [
-    "ssp119",
-    # "ssp126",
+    #"ssp119",
+    "ssp126",
     "ssp245",
     # "ssp370",
     "ssp585",
-    "constant_climate",
+    #"constant_climate",
 ]
 
 
@@ -104,7 +104,7 @@ def with_sex_id(
     )
 
 
-VALID_AGE_GROUP_IDS = ["4", "5"]
+VALID_AGE_GROUP_IDS = ['388', '389', '238', '34']
 
 
 def with_age_group_id(
@@ -178,6 +178,33 @@ def with_model_version() -> ClickOption[_P, _T]:
         help="The model version to run.",
     )
 
+def with_wealth_version() -> ClickOption[_P, _T]:
+    return click.option(
+        "--wealth-version",
+        "-w",
+        type=str,
+        required=True,
+        help="The version of wealth (income/consumption) to use.",
+    )
+
+def with_n_draws() -> ClickOption[_P, _T]:
+    return click.option(
+        "--draws",
+        "-d",
+        type=int,
+        default=1,
+        required=True,
+        help="The number of draws to run.",
+    )
+
+def with_draw() -> ClickOption[_P, _T]:
+    return click.option(
+        "--draw",
+        "-d",
+        type=int,
+        required=True,
+        help="The draw to run.",
+    )
 
 __all__ = [
     "VALID_MEASURES",
@@ -197,4 +224,5 @@ def with_model_version() -> ClickOption[_P, _T]:
     "with_results_version",
     "with_model_version",
     "with_queue",
+    "with_wealth_version"
 ]