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🔨 Fixing IGME under 15 table #1927

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Nov 8, 2023
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41 changes: 16 additions & 25 deletions etl/steps/data/garden/un/2023-08-16/igme.py
Original file line number Diff line number Diff line change
Expand Up @@ -26,7 +26,9 @@ def run(dest_dir: str) -> None:
tb_vintage = ds_vintage["igme"].reset_index()
tb_youth = tb_vintage[tb_vintage["indicator_name"].isin(["Deaths age 5 to 14", "Mortality rate age 5 to 14"])]
tb_youth = process_vintage_data(tb_youth)

tb_youth = tb_youth.rename(
columns={"Observation value": "obs_value", "Lower bound": "lower_bound", "Upper bound": "upper_bound"}
)
# Process current data.
#
tb = fix_sub_saharan_africa(tb)
Expand Down Expand Up @@ -60,7 +62,7 @@ def run(dest_dir: str) -> None:
tb_com = calculate_under_fifteen_mortality_rates(tb_com)
tb_com = tb_com.set_index(
["country", "year", "indicator", "sex", "wealth_quintile", "unit_of_measure"], verify_integrity=True
).drop(columns=["source"])
)

# Calculate post neonatal deaths
tb = add_post_neonatal_deaths(tb)
Expand Down Expand Up @@ -192,27 +194,16 @@ def calculate_under_fifteen_mortality_rates(tb: Table) -> Table:
tb_merge = pr.merge(
u5_mortality,
mortality_5_14,
on=["country", "year", "wealth_quintile", "sex", "source"],
on=["country", "year", "wealth_quintile", "sex"],
suffixes=("_u5", "_5_14"),
)
tb_merge["adjusted_5_14_mortality_rate"] = (100 - tb_merge["obs_value_u5"]) / 100 * tb_merge["obs_value_5_14"]
tb_merge["obs_value"] = tb_merge["obs_value_u5"] + tb_merge["adjusted_5_14_mortality_rate"]
tb_merge["indicator"] = "Under-fifteen mortality rate"
tb_merge["unit_of_measure"] = "Deaths per 1,000 live births"

result_tb = tb_merge[
[
"country",
"year",
"indicator",
"sex",
"unit_of_measure",
"wealth_quintile",
"obs_value",
"source",
]
]
result_tb = result_tb[result_tb["indicator"].isin(["Under-fifteen mortality rate", "Under-fifteen deaths"])]
result_tb = tb_merge[["country", "year", "indicator", "sex", "unit_of_measure", "wealth_quintile", "obs_value"]]
result_tb = result_tb[result_tb["indicator"].isin(["Under-fifteen mortality rate"])]
result_tb.metadata.short_name = "igme_under_fifteen_mortality"

return result_tb
Expand Down Expand Up @@ -264,9 +255,9 @@ def calculate_under_fifteen_deaths(tb: Table) -> Table:
.drop(columns="indicator")
.rename(
columns={
"Observation value": "under_five_mortality",
"Lower bound": "under_five_mortality_lb",
"Upper bound": "under_five_mortality_ub",
"obs_value": "under_five_mortality",
"lower_bound": "under_five_mortality_lb",
"upper_bound": "under_five_mortality_ub",
}
)
)
Expand All @@ -275,9 +266,9 @@ def calculate_under_fifteen_deaths(tb: Table) -> Table:
.drop(columns="indicator")
.rename(
columns={
"Observation value": "five_to_fourteen_mortality",
"Lower bound": "five_to_fourteen_mortality_lb",
"Upper bound": "five_to_fourteen_mortality_ub",
"obs_value": "five_to_fourteen_mortality",
"lower_bound": "five_to_fourteen_mortality_lb",
"upper_bound": "five_to_fourteen_mortality_ub",
}
)
)
Expand All @@ -299,9 +290,9 @@ def calculate_under_fifteen_deaths(tb: Table) -> Table:
]
).rename(
columns={
"under_fifteen_mortality": "Observation value",
"under_fifteen_mortality_lb": "Lower bound",
"under_fifteen_mortality_ub": "Upper bound",
"under_fifteen_mortality": "obs_value",
"under_fifteen_mortality_lb": "lower_bound",
"under_fifteen_mortality_ub": "upper_bound",
}
)
tb_u15["indicator"] = "Under-fifteen deaths"
Expand Down