Merge pull request #234 from jgehrcke/jp/value-evolution

tools: add specific-day-value-evolution-plot.py/sh

tools/specific-day-value-evolution-plot.py

@@ -0,0 +1,57 @@
+import sys
+import pandas as pd
+import matplotlib.pyplot as plt
+from matplotlib import dates
+
+plt.style.use("ggplot")
+
+csv_filepath = sys.argv[1]
+day_of_interest = sys.argv[2]
+
+df = pd.read_csv(
+    csv_filepath,
+    index_col=["commit_time_iso8601"],
+    parse_dates=["commit_time_iso8601"],
+    date_parser=lambda col: pd.to_datetime(col, utc=True),
+)
+df.index.name = "time"
+
+# There may be duplicate rows / samples (for commits to the repo that did not
+# change the file in question). Remove duplicates, and also make it so that
+# that there is one data point per day (this drops many rows, and forward-fills
+# for some days).
+df = df.drop_duplicates().resample("1D").pad()
+
+title = f"Deaths (all Germany) on {day_of_interest}, evolution in RKI database"
+
+df["deaths_sum"].plot(
+    title=title, marker="x", grid=True, figsize=[12, 9], color="black"
+)
+
+plt.xlabel("date of RKI database query")
+plt.ylabel("sum_deaths_germany_2020-03-30")
+plt.tight_layout()
+# plt.show()
+plt.savefig(f"sum_deaths_germany_{day_of_interest}_evolution_rki_db.png", dpi=90)
+
+
+# Get time differences (unit: seconds) in the df's datetimeindex. `dt`
+# is a magic accessor that yields an array of time deltas.
+dt_seconds = pd.Series(df.index).diff().dt.total_seconds()
+# Construct new series with original datetimeindex as index and time
+# differences (unit: days) as values.
+dt_days = pd.Series(dt_seconds) / 86400.0
+dt_days.index = df.index
+change_per_day = df["deaths_sum"].diff().div(dt_days)
+df["deaths_sum_change_per_day"] = change_per_day
+
+plt.figure()
+df["deaths_sum_change_per_day"].plot(
+    title="", linewidth=0, marker="x", figsize=[12, 9], color="black", logy=True
+)
+plt.xlabel("date")
+plt.ylabel("daily change of sum_deaths_germany_2020-03-30")
+plt.tight_layout()
+plt.savefig(
+    f"sum_deaths_germany_{day_of_interest}_evolution_rki_db_changeperday.png", dpi=90
+)

tools/specific-day-value-evolution-plot.sh

@@ -0,0 +1,32 @@
+#!/usr/bin/env bash
+set -o errexit
+set -o errtrace
+set -o nounset
+set -o pipefail
+
+INFILE="deaths-rki-by-state.csv"
+DAY_OF_INTEREST="2020-03-30"
+OUTFILENAME="rki-deaths-on-${DAY_OF_INTEREST}-evolution.csv"
+
+echo "commit_time_iso8601,deaths_sum" > ${OUTFILENAME}
+
+# Iterate through commit hashes. Order: past -> future.
+for commit in $(git rev-list --reverse master)
+do
+    COMMIT_TIME_ISO8601=$(git show -s --format=%ci "${commit}")
+
+    # Get last column (known to be sum_deaths) for the row on day of interest.
+    set +e
+    DEATHS_SUM=$(git show "${commit}:${INFILE}" | grep "${DAY_OF_INTEREST}" | awk -F, '{print $NF}')
+    set -e
+
+    # https://unix.stackexchange.com/a/146945/13256
+    if [[ ! -z "${DEATHS_SUM// }" ]]; then
+        echo "sum(deaths) in ${INFILE} at ${COMMIT_TIME_ISO8601}: ${DEATHS_SUM}"
+    else
+        echo "no data point extracted for commit $commit: emtpy val"
+        continue
+    fi
+
+    echo "${COMMIT_TIME_ISO8601},${DEATHS_SUM}" >> ${OUTFILENAME}
+done