📊 antimicrobial resistance: MICROBE dataset - neonatal deaths - total

dag/health.yml

@@ -926,3 +926,32 @@ steps:
     - data://meadow/antibiotics/2024-11-15/testing_coverage
   data://grapher/antibiotics/2024-11-15/testing_coverage:
     - data://garden/antibiotics/2024-11-15/testing_coverage
+
+  # IHME Neonatal all infectious syndromes
+  data-private://meadow/antibiotics/2024-11-20/microbe:
+    - snapshot-private://antibiotics/2024-11-20/microbe.zip
+  data-private://garden/antibiotics/2024-11-20/microbe:
+    - data-private://meadow/antibiotics/2024-11-20/microbe
+  data-private://grapher/antibiotics/2024-11-20/microbe:
+    - data-private://garden/antibiotics/2024-11-20/microbe
+  # IHME Neonatal bloodstream infections by pathogen
+  data-private://meadow/antibiotics/2024-11-20/pathogen_bloodstream:
+    - snapshot-private://antibiotics/2024-11-20/pathogen_bloodstream.csv
+  data-private://garden/antibiotics/2024-11-20/pathogen_bloodstream:
+    - data-private://meadow/antibiotics/2024-11-20/pathogen_bloodstream
+  data-private://grapher/antibiotics/2024-11-20/pathogen_bloodstream:
+    - data-private://garden/antibiotics/2024-11-20/pathogen_bloodstream
+  # IHME Neonatal bloodstream infections by resistance
+  data-private://meadow/antibiotics/2024-11-20/bloodstream_amr:
+    - snapshot-private://antibiotics/2024-11-20/bloodstream_amr.csv
+  data-private://garden/antibiotics/2024-11-20/bloodstream_amr:
+    - data-private://meadow/antibiotics/2024-11-20/bloodstream_amr
+  data-private://grapher/antibiotics/2024-11-20/bloodstream_amr:
+    - data-private://garden/antibiotics/2024-11-20/bloodstream_amr
+  # IHME Neonatal infections by syndrome
+  data-private://meadow/antibiotics/2024-11-24/total_syndrome:
+    - snapshot-private://antibiotics/2024-11-24/total_syndrome.csv
+  data-private://garden/antibiotics/2024-11-24/total_syndrome:
+    - data-private://meadow/antibiotics/2024-11-24/total_syndrome
+  data-private://grapher/antibiotics/2024-11-24/total_syndrome:
+    - data-private://garden/antibiotics/2024-11-24/total_syndrome

etl/steps/data/garden/antibiotics/2024-11-20/bloodstream_amr.countries.json

@@ -0,0 +1,3 @@
+{
+  "Global": "World"
+}

etl/steps/data/garden/antibiotics/2024-11-20/bloodstream_amr.meta.yml

@@ -0,0 +1,74 @@
+definitions:
+  common:
+    presentation:
+      topic_tags:
+        - Antibiotics
+    display:
+      numSignificantFigures: 3
+
+  pathogen_type:
+    <%- if pathogen_type == "Fungi" -%>
+    fungus
+    <%- elif pathogen_type == "Viruses" -%>
+    virus
+    <%- else  -%>
+    << pathogen_type.lower() >>
+    <%- endif -%>
+  counterfactual:
+    <% if counterfactual == "Associated" %>
+    where the death was associated with antibiotic resistance
+    <% elif counterfactual == "Susceptible" %>
+    where the bacteria causing the death were susceptible to antibiotics
+    <% elif counterfactual == "Untested" %>
+    where the pathogen was not tested for antibiotic resistance
+    <% endif %>
+
+
+
+# Learn more about the available fields:
+# http://docs.owid.io/projects/etl/architecture/metadata/reference/
+dataset:
+  update_period_days: 365
+
+
+tables:
+  bloodstream_amr:
+    variables:
+      value:
+        title: Neonatal deaths from << pathogen >> infections {definitions.counterfactual}
+        unit: deaths
+        description_short: Estimated number of [neonates](#dod:neonatal) – newborns under 28 days of age –  who die each year from << pathogen >> infections, {definitions.counterfactual} << pathogen >> is a {definitions.pathogen_type}.
+        display:
+          name: << pathogen >> - << counterfactual >>
+      upper:
+        title: Upper bound of neonatal deaths from << pathogen >> infections {definitions.counterfactual}
+        unit: deaths
+        description_short: Estimated number of [neonates](#dod:neonatal) – newborns under 28 days of age –  who die each year from << pathogen >> infections, {definitions.counterfactual}. << pathogen >> is a {definitions.pathogen_type}.
+        display:
+          name: << pathogen >> - << counterfactual >>
+      lower:
+        title: Lower bound of neonatal deaths from << pathogen >> infections {definitions.counterfactual}
+        unit: deaths
+        description_short: Estimated number of [neonates](#dod:neonatal) – newborns under 28 days of age –  who die each year from << pathogen >> infections, {definitions.counterfactual}. << pathogen >> is a {definitions.pathogen_type}.
+        display:
+          name: << pathogen >> - << counterfactual >>
+  amr_entity:
+    variables:
+      value:
+        title: Global neonatal deaths from bloodstream infections, by pathogen {definitions.counterfactual}
+        unit: deaths
+        description_short: Estimated number of [neonates](#dod:neonatal) – newborns under 28 days of age –  who die each year from bloodstream infections, {definitions.counterfactual}.
+        display:
+          name: << counterfactual >>
+      upper:
+        title: Upper bound of global neonatal deaths from bloodstream infections, by pathogen {definitions.counterfactual}
+        unit: deaths
+        description_short: Estimated number of [neonates](#dod:neonatal) – newborns under 28 days of age –  who die each year from bloodstream infections, {definitions.counterfactual}.
+        display:
+          name: << counterfactual >>
+      lower:
+        title: Lower bound of global neonatal deaths from bloodstream infections, by pathogen {definitions.counterfactual}
+        unit: deaths
+        description_short: Estimated number of [neonates](#dod:neonatal) – newborns under 28 days of age –  who die each year from bloodstream infections, {definitions.counterfactual}.
+        display:
+          name: << counterfactual >>

etl/steps/data/garden/antibiotics/2024-11-20/bloodstream_amr.py

@@ -0,0 +1,38 @@
+"""Load a meadow dataset and create a garden dataset."""
+
+from etl.data_helpers import geo
+from etl.helpers import PathFinder, create_dataset
+
+# Get paths and naming conventions for current step.
+paths = PathFinder(__file__)
+
+
+def run(dest_dir: str) -> None:
+    #
+    # Load inputs.
+    #
+    # Load meadow dataset.
+    ds_meadow = paths.load_dataset("bloodstream_amr")
+
+    # Read table from meadow dataset.
+    tb = ds_meadow.read("bloodstream_amr")
+
+    #
+    # Process data.
+    #
+    tb = geo.harmonize_countries(df=tb, countries_file=paths.country_mapping_path)
+    tb = tb.drop(columns=["age", "sex", "measure", "metric", "infectious_syndrome"])
+    tb_amr = tb.drop(columns=["country", "pathogen_type"]).rename(columns={"pathogen": "country"})
+    tb_amr = tb_amr.format(["country", "year", "counterfactual"], short_name="amr_entity")
+    tb = tb.format(["country", "year", "pathogen", "pathogen_type", "counterfactual"])
+
+    #
+    # Save outputs.
+    #
+    # Create a new garden dataset with the same metadata as the meadow dataset.
+    ds_garden = create_dataset(
+        dest_dir, tables=[tb, tb_amr], check_variables_metadata=True, default_metadata=ds_meadow.metadata
+    )
+
+    # Save changes in the new garden dataset.
+    ds_garden.save()

etl/steps/data/garden/antibiotics/2024-11-20/microbe.countries.json

@@ -0,0 +1,3 @@
+{
+  "Global": "World"
+}

etl/steps/data/garden/antibiotics/2024-11-20/microbe.meta.yml

@@ -0,0 +1,53 @@
+# NOTE: To learn more about the fields, hover over their names.
+definitions:
+  common:
+    presentation:
+      topic_tags:
+        - Global Health
+    display:
+      numSignificantFigures: 3
+  pathogen_type:
+    <%- if pathogen_type == "Fungi" -%>
+    fungus
+    <%- elif pathogen_type == "Viruses" -%>
+    virus
+    <%- else  -%>
+    << pathogen_type.lower() >>
+    <%- endif -%>
+
+
+# Learn more about the available fields:
+# http://docs.owid.io/projects/etl/architecture/metadata/reference/
+dataset:
+  update_period_days: 365
+
+
+tables:
+  microbe:
+    variables:
+      value:
+        title: Neonatal deaths from << pathogen >> infections
+        unit: deaths
+        description_short: Estimated number of [neonates](#dod:neonatal) – newborns under 28 days of age –  who die each year from << pathogen >> infections. << pathogen >> is a {definitions.pathogen_type}.
+      upper:
+        title: Upper bound of neonatal deaths from << pathogen >> infections
+        unit: deaths
+        description_short: Estimated number of [neonates](#dod:neonatal) – newborns under 28 days of age –  who die each year from << pathogen >> infections. << pathogen >> is a {definitions.pathogen_type}.
+      lower:
+        title: Lower bound of neonatal deaths from << pathogen >> infections
+        unit: deaths
+        description_short: Estimated number of [neonates](#dod:neonatal) – newborns under 28 days of age –  who die each year from << pathogen >> infections. << pathogen >> is a {definitions.pathogen_type}.
+  pathogen_entity:
+    variables:
+      value:
+        title: Global neonatal deaths from bloodstream infections, by pathogen
+        unit: deaths
+        description_short: Estimated number of [neonates](#dod:neonatal) – newborns under 28 days of age –  who die each year from bloodstream infections.
+      upper:
+        title: Upper bound of global neonatal deaths from bloodstream infections, by pathogen
+        unit: deaths
+        description_short: Estimated number of [neonates](#dod:neonatal) – newborns under 28 days of age –  who die each year from bloodstream infections.
+      lower:
+        title: Lower bound of global neonatal deaths from bloodstream infections, by pathogen
+        unit: deaths
+        description_short: Estimated number of [neonates](#dod:neonatal) – newborns under 28 days of age –  who die each year from bloodstream infections.

etl/steps/data/garden/antibiotics/2024-11-20/microbe.py

@@ -0,0 +1,39 @@
+"""Load a meadow dataset and create a garden dataset."""
+
+from etl.data_helpers import geo
+from etl.helpers import PathFinder, create_dataset
+
+# Get paths and naming conventions for current step.
+paths = PathFinder(__file__)
+
+
+def run(dest_dir: str) -> None:
+    #
+    # Load inputs.
+    #
+    # Load meadow dataset.
+    ds_meadow = paths.load_dataset("microbe")
+
+    # Read table from meadow dataset.
+    tb = ds_meadow.read("microbe")
+
+    #
+    # Process data.
+    #
+    tb = geo.harmonize_countries(df=tb, countries_file=paths.country_mapping_path)
+
+    tb = tb.drop(columns=["age", "sex", "measure", "metric", "counterfactual", "infectious_syndrome"])
+    # Create a table where the pathogen is the entity
+    tb_pathogen = tb.drop(columns=["country", "pathogen_type"]).rename(columns={"pathogen": "country"})
+    tb = tb.format(["country", "year", "pathogen_type", "pathogen"])
+    tb_pathogen = tb_pathogen.format(["country", "year"], short_name="pathogen_entity")
+    #
+    # Save outputs.
+    #
+    # Create a new garden dataset with the same metadata as the meadow dataset.
+    ds_garden = create_dataset(
+        dest_dir, tables=[tb, tb_pathogen], check_variables_metadata=True, default_metadata=ds_meadow.metadata
+    )
+
+    # Save changes in the new garden dataset.
+    ds_garden.save()

etl/steps/data/garden/antibiotics/2024-11-20/pathogen_bloodstream.countries.json

@@ -0,0 +1,3 @@
+{
+  "Global": "World"
+}

etl/steps/data/garden/antibiotics/2024-11-20/pathogen_bloodstream.meta.yml

@@ -0,0 +1,40 @@
+# NOTE: To learn more about the fields, hover over their names.
+definitions:
+  common:
+    presentation:
+      topic_tags:
+        - Antibiotics
+    display:
+      numSignificantFigures: 3
+      name: << pathogen >>
+
+  pathogen_type:
+    <% if pathogen_type == "Fungi" %>
+    fungus
+    <% elif pathogen_type == "Viruses" %>
+    virus
+    <% else  %>
+    << pathogen_type.lower() >>
+    <% endif %>
+
+# Learn more about the available fields:
+# http://docs.owid.io/projects/etl/architecture/metadata/reference/
+dataset:
+  update_period_days: 365
+
+
+tables:
+  pathogen_bloodstream:
+    variables:
+      value:
+        title: Neonatal deaths from << pathogen >> infections
+        unit: deaths
+        description_short: Estimated number of [neonates](#dod:neonatal) – newborns under 28 days of age –  who die each year from << pathogen >> infections. << pathogen >> is a {definitions.pathogen_type}.
+      upper:
+        title: Upper bound of neonatal deaths from << pathogen >> infections
+        unit: deaths
+        description_short: Estimated number of [neonates](#dod:neonatal) – newborns under 28 days of age –  who die each year from << pathogen >> infections. << pathogen >> is a {definitions.pathogen_type}.
+      lower:
+        title: Lower bound of neonatal deaths from << pathogen >> infections
+        unit: deaths
+        description_short: Estimated number of [neonates](#dod:neonatal) – newborns under 28 days of age –  who die each year from << pathogen >> infections. << pathogen >> is a {definitions.pathogen_type}.

etl/steps/data/garden/antibiotics/2024-11-20/pathogen_bloodstream.py

@@ -0,0 +1,37 @@
+"""Load a meadow dataset and create a garden dataset."""
+
+from etl.data_helpers import geo
+from etl.helpers import PathFinder, create_dataset
+
+# Get paths and naming conventions for current step.
+paths = PathFinder(__file__)
+
+
+def run(dest_dir: str) -> None:
+    #
+    # Load inputs.
+    #
+    # Load meadow dataset.
+    ds_meadow = paths.load_dataset("pathogen_bloodstream")
+
+    # Read table from meadow dataset.
+    tb = ds_meadow.read("pathogen_bloodstream")
+
+    #
+    # Process data.
+    #
+    tb = geo.harmonize_countries(df=tb, countries_file=paths.country_mapping_path)
+
+    tb = tb.drop(columns=["age", "sex", "measure", "metric", "counterfactual", "infectious_syndrome"])
+    tb = tb.format(["country", "year", "pathogen_type", "pathogen"])
+
+    #
+    # Save outputs.
+    #
+    # Create a new garden dataset with the same metadata as the meadow dataset.
+    ds_garden = create_dataset(
+        dest_dir, tables=[tb], check_variables_metadata=True, default_metadata=ds_meadow.metadata
+    )
+
+    # Save changes in the new garden dataset.
+    ds_garden.save()

etl/steps/data/garden/antibiotics/2024-11-24/total_syndrome.countries.json

@@ -0,0 +1,3 @@
+{
+  "Global": "World"
+}

etl/steps/data/garden/antibiotics/2024-11-24/total_syndrome.meta.yml

@@ -0,0 +1,42 @@
+# NOTE: To learn more about the fields, hover over their names.
+definitions:
+  common:
+    presentation:
+      topic_tags:
+        - Antibiotics
+
+
+# Learn more about the available fields:
+# http://docs.owid.io/projects/etl/architecture/metadata/reference/
+dataset:
+  update_period_days: 365
+
+
+tables:
+  total_syndrome:
+    variables:
+      value:
+        title: Global neonatal deaths from << infectious_syndrome.lower() >> infections
+        unit: deaths
+        description_short: Estimated number of [neonates](#dod:neonatal) – newborns under 28 days of age –  who die each year from << infectious_syndrome.lower() >>.
+        display:
+          roundingMode: significantFigures
+          numSignificantFigures: 3
+          name: << infectious_syndrome >>
+      upper:
+        title: Upper bound of global neonatal deaths from << infectious_syndrome.lower() >> infections
+        unit: deaths
+        description_short: Estimated number of [neonates](#dod:neonatal) – newborns under 28 days of age –  who die each year from << infectious_syndrome.lower() >>.
+        display:
+          roundingMode: significantFigures
+          numSignificantFigures: 3
+          name: << infectious_syndrome >>
+      lower:
+        title: Lower bound of global neonatal deaths from << infectious_syndrome.lower() >> infections
+        unit: deaths
+        description_short: Estimated number of [neonates](#dod:neonatal) – newborns under 28 days of age –  who die each year from << infectious_syndrome.lower() >>.
+        display:
+          numSignificantFigures: 3
+          roundingMode: significantFigures
+          name: << infectious_syndrome >>
+