clinicedc 2.0.11__py3-none-any.whl → 2.0.13__py3-none-any.whl

edc_analytics/custom_tables/fasting.py

@@ -0,0 +1,126 @@
+import pandas as pd
+from edc_constants.constants import FEMALE, MALE
+
+from ..constants import MEDIAN_IQR, N_ONLY, N_WITH_COL_PROP, N_WITH_ROW_PROP
+from ..row import RowDefinition, RowDefinitions
+from ..table import Table
+
+
+class FastingFbgTable(Table):
+    def __init__(
+        self,
+        main_df: pd.DataFrame = None,
+        colname: str | None = None,
+        title: str | None = None,
+    ):
+        colname = colname or "fasting_fbg_hrs"
+        title = title or "Fasting duration (hrs)"
+        super().__init__(colname=colname, main_df=main_df, title=title)
+
+    @property
+    def row_definitions(self) -> RowDefinitions:
+        df_tmp = self.main_df.copy()
+        row_defs = RowDefinitions(reverse_rows=False)
+        row0 = RowDefinition(
+            title=self.title,
+            label=self.default_sublabel,
+            condition=(df_tmp["gender"].notna()),
+            columns={FEMALE: (N_ONLY, 2), MALE: (N_ONLY, 2), "All": (N_ONLY, 2)},
+            drop=False,
+        )
+        row_defs.add(row0)
+        columns = {
+            FEMALE: (MEDIAN_IQR, 2),
+            MALE: (MEDIAN_IQR, 2),
+            "All": (MEDIAN_IQR, 2),
+        }
+        row_defs.add(
+            RowDefinition(
+                colname=self.colname,
+                label="FBG fasted (hours), median (IQR)",
+                condition=(self.main_df[self.colname].notna()),
+                columns=columns,
+                drop=False,
+            )
+        )
+        columns = {
+            FEMALE: (N_WITH_COL_PROP, 2),
+            MALE: (N_WITH_COL_PROP, 2),
+            "All": (N_WITH_ROW_PROP, 2),
+        }
+        row_defs.add(
+            RowDefinition(
+                colname=self.colname,
+                label="FBG Fasted <8.0 hrs",
+                condition=(self.main_df[self.colname] < 8.0),
+                columns=columns,
+                drop=False,
+            )
+        )
+        row_defs.add(
+            RowDefinition(
+                colname=self.colname,
+                label="not measured",
+                condition=(self.main_df[self.colname].isna()),
+                columns=columns,
+                drop=False,
+            )
+        )
+        return row_defs
+
+
+class FastingOgttTable(Table):
+    def __init__(self, main_df: pd.DataFrame = None):
+        super().__init__(colname="fasting_ogtt_hrs", main_df=main_df, title="")
+
+    @property
+    def row_definitions(self) -> RowDefinitions:
+        row_defs = RowDefinitions(reverse_rows=False)
+        columns = {
+            FEMALE: (MEDIAN_IQR, 2),
+            MALE: (MEDIAN_IQR, 2),
+            "All": (MEDIAN_IQR, 2),
+        }
+        row_defs.add(
+            RowDefinition(
+                colname=self.colname,
+                label="OGTT fasted (hours), median (IQR)",
+                condition=(self.main_df[self.colname].notna()),
+                columns=columns,
+                drop=False,
+            )
+        )
+        columns = {
+            FEMALE: (N_WITH_COL_PROP, 2),
+            MALE: (N_WITH_COL_PROP, 2),
+            "All": (N_WITH_ROW_PROP, 2),
+        }
+        row_defs.add(
+            RowDefinition(
+                colname=self.colname,
+                label="OGTT Fasted <8.0 hrs",
+                condition=(self.main_df[self.colname] < 8.0),
+                columns=columns,
+                drop=False,
+            )
+        )
+        row_defs.add(
+            RowDefinition(
+                colname=self.colname,
+                label="not measured",
+                condition=(self.main_df[self.colname].isna()),
+                columns=columns,
+                drop=False,
+            )
+        )
+        return row_defs
+
+
+class FastingTable(Table):
+    def __init__(self, main_df: pd.DataFrame = None):
+        super().__init__(main_df=main_df, title="Fasting duration (hrs)")
+
+    def build_table_df(self) -> None:
+        df1 = FastingFbgTable(main_df=self.main_df).table_df
+        df2 = FastingOgttTable(main_df=self.main_df).table_df
+        self.table_df = pd.concat([df1, df2])

edc_analytics/custom_tables/fbg.py

@@ -0,0 +1,98 @@
+import pandas as pd
+from edc_constants.constants import FEMALE, MALE
+
+from ..constants import MEAN_95CI, N_ONLY, N_WITH_COL_PROP, N_WITH_ROW_PROP
+from ..row import RowDefinition, RowDefinitions
+from ..table import Table
+
+
+class FbgTable(Table):
+    def __init__(self, main_df: pd.DataFrame = None):
+        super().__init__(colname="fbg", main_df=main_df, title="FBG (mmol/L) categories")
+
+    @property
+    def row_definitions(self) -> RowDefinitions:
+        df_tmp = self.main_df.copy()
+        row_defs = RowDefinitions(reverse_rows=False)
+        row0 = RowDefinition(
+            title=self.title,
+            label=self.default_sublabel,
+            condition=(df_tmp["gender"].notna()),
+            columns={FEMALE: (N_ONLY, 2), MALE: (N_ONLY, 2), "All": (N_ONLY, 2)},
+            drop=False,
+        )
+        row_defs.add(row0)
+
+        columns = {
+            FEMALE: (N_WITH_COL_PROP, 2),
+            MALE: (N_WITH_COL_PROP, 2),
+            "All": (N_WITH_ROW_PROP, 2),
+        }
+        row_defs.add(
+            RowDefinition(
+                colname=self.colname,
+                label="Not fasted",
+                condition=(self.main_df["fasting_fbg_hrs"] < 8.0),
+                columns=columns,
+                drop=True,
+            )
+        )
+
+        columns = {
+            FEMALE: (MEAN_95CI, 2),
+            MALE: (MEAN_95CI, 2),
+            "All": (MEAN_95CI, 2),
+        }
+        row_mean = RowDefinition(
+            colname=self.colname,
+            label="Mean (95% CI)",
+            condition=(self.main_df[self.colname].notna()),
+            columns=columns,
+            drop=False,
+        )
+        columns = {
+            FEMALE: (N_WITH_COL_PROP, 2),
+            MALE: (N_WITH_COL_PROP, 2),
+            "All": (N_WITH_ROW_PROP, 2),
+        }
+
+        row_defs.add(
+            RowDefinition(
+                colname=self.colname,
+                label="<6.1",
+                condition=(self.main_df[self.colname] < 6.1),
+                columns=columns,
+                drop=True,
+            )
+        )
+        row_defs.add(
+            RowDefinition(
+                colname=self.colname,
+                label="6.1-6.9",
+                condition=(self.main_df[self.colname] >= 6.1)
+                & (self.main_df[self.colname] < 7.0),
+                columns=columns,
+                drop=True,
+            )
+        )
+        row_defs.add(
+            RowDefinition(
+                colname=self.colname,
+                label="7.0 and above",
+                condition=(self.main_df[self.colname] >= 7.0),
+                columns=columns,
+                drop=True,
+            )
+        )
+        row_defs.add(
+            RowDefinition(
+                colname=self.colname,
+                label="not measured",
+                condition=(self.main_df[self.colname].isna()),
+                columns=columns,
+                drop=True,
+            )
+        )
+
+        row_defs.add(row_mean)
+        return row_defs

edc_analytics/custom_tables/fbg_ogtt.py

@@ -0,0 +1,384 @@
+import pandas as pd
+from edc_constants.constants import FEMALE, MALE
+
+from ..constants import N_ONLY, N_WITH_COL_PROP, N_WITH_ROW_PROP
+from ..row import RowDefinition, RowDefinitions
+from ..table import Table
+
+
+class FbgOgttTable1(Table):
+
+    fbg_colname = "fbg"
+    ogtt_colname = "ogtt"
+
+    def __init__(self, main_df: pd.DataFrame = None):
+        super().__init__(
+            colname="",
+            main_df=main_df,
+            title="OGTT & FBG (mmol/L) categories",
+        )
+
+    @property
+    def row_definitions(self) -> RowDefinitions:
+        df_tmp = self.main_df.copy()
+        row_defs = RowDefinitions(reverse_rows=False)
+        row0 = RowDefinition(
+            title=self.title,
+            label=self.default_sublabel,
+            condition=(df_tmp["gender"].notna()),
+            columns={FEMALE: (N_ONLY, 2), MALE: (N_ONLY, 2), "All": (N_ONLY, 2)},
+            drop=False,
+        )
+        row_defs.add(row0)
+        columns = {
+            FEMALE: (N_WITH_COL_PROP, 2),
+            MALE: (N_WITH_COL_PROP, 2),
+            "All": (N_WITH_ROW_PROP, 2),
+        }
+
+        row_defs.add(
+            RowDefinition(
+                colname=self.colname,
+                label="Not fasted",
+                condition=(
+                    (self.main_df["fasting_fbg_hrs"] < 8.0)
+                    | (self.main_df["fasting_ogtt_hrs"] < 8.0)
+                ),
+                columns=columns,
+                drop=True,
+            )
+        )
+
+        condition = (
+            (self.main_df[self.ogtt_colname] >= 11.1)
+            & (self.main_df[self.fbg_colname] >= 7.0)
+            & (self.main_df[self.ogtt_colname].notna())
+            & (self.main_df[self.fbg_colname].notna())
+        )
+        row_defs.add(
+            RowDefinition(
+                colname=self.colname,
+                label="OGTT ≥11.1 and FBG ≥7.0",
+                condition=condition,
+                columns=columns,
+                drop=True,
+            )
+        )
+
+        condition = (
+            ((df_tmp[self.ogtt_colname] >= 11.1) | (df_tmp[self.fbg_colname] >= 7.0))
+            & (df_tmp[self.fbg_colname].notna())
+            & (df_tmp[self.ogtt_colname].notna())
+        )
+
+        row_defs.add(
+            RowDefinition(
+                colname=self.colname,
+                label="OGTT ≥11.1 or FBG ≥7.0",
+                condition=condition,
+                columns=columns,
+                drop=True,
+            )
+        )
+
+        condition = (
+            ((df_tmp[self.fbg_colname] >= 6.1) | (df_tmp[self.ogtt_colname] >= 7.8))
+            & (df_tmp[self.fbg_colname].notna())
+            & (df_tmp[self.ogtt_colname].notna())
+        )
+        row_defs.add(
+            RowDefinition(
+                colname=self.colname,
+                label="OGTT ≥7.8 or FBG ≥6.1",
+                condition=condition,
+                columns=columns,
+                drop=True,
+            )
+        )
+
+        condition = (
+            ((df_tmp[self.fbg_colname] < 6.1) | (df_tmp[self.ogtt_colname] < 7.8))
+            & (df_tmp[self.fbg_colname].notna())
+            & (df_tmp[self.ogtt_colname].notna())
+        )
+        row_defs.add(
+            RowDefinition(
+                colname=self.colname,
+                label="OGTT <7.8 or FBG <6.1",
+                condition=condition,
+                columns=columns,
+                drop=True,
+            )
+        )
+
+        condition = (df_tmp[self.fbg_colname].notna()) & (df_tmp[self.ogtt_colname].notna())
+        row_defs.add(
+            RowDefinition(
+                colname=self.colname,
+                label="Other",
+                condition=condition,
+                columns=columns,
+                drop=True,
+            )
+        )
+
+        condition = (df_tmp[self.fbg_colname].notna()) & (df_tmp[self.ogtt_colname].isna())
+        row_defs.add(
+            RowDefinition(
+                colname=self.colname,
+                label="OGTT not measured",
+                condition=condition,
+                columns=columns,
+                drop=True,
+            )
+        )
+        condition = (df_tmp[self.fbg_colname].isna()) & (df_tmp[self.ogtt_colname].notna())
+        row_defs.add(
+            RowDefinition(
+                colname=self.colname,
+                label="FBG not measured",
+                condition=condition,
+                columns=columns,
+                drop=True,
+            )
+        )
+        condition = (df_tmp[self.fbg_colname].isna()) & (df_tmp[self.ogtt_colname].isna())
+        row_defs.add(
+            RowDefinition(
+                colname=self.colname,
+                label="not measured",
+                condition=condition,
+                columns=columns,
+                drop=True,
+            )
+        )
+        return row_defs
+
+
+class FbgOgttTable2(Table):
+
+    fbg_colname = "fbg"
+    ogtt_colname = "ogtt"
+
+    def __init__(self, main_df: pd.DataFrame = None):
+        super().__init__(
+            colname="",
+            main_df=main_df,
+            title="OGTT & FBG (mmol/L) additional",
+        )
+
+    @property
+    def row_definitions(self) -> RowDefinitions:
+        df_tmp = self.main_df.copy()
+        row_defs = RowDefinitions(reverse_rows=False)
+        row0 = RowDefinition(
+            title=self.title,
+            label="Glucose levels, n (%)",
+            condition=(df_tmp["gender"].notna()),
+            columns={FEMALE: (N_ONLY, 2), MALE: (N_ONLY, 2), "All": (N_ONLY, 2)},
+            drop=False,
+        )
+        row_defs.add(row0)
+        columns = {
+            FEMALE: (N_WITH_COL_PROP, 2),
+            MALE: (N_WITH_COL_PROP, 2),
+            "All": (N_WITH_ROW_PROP, 2),
+        }
+
+        row_defs.add(
+            RowDefinition(
+                colname=self.colname,
+                label="Not fasted",
+                condition=(
+                    (self.main_df["fasting_fbg_hrs"] < 8.0)
+                    | (self.main_df["fasting_ogtt_hrs"] < 8.0)
+                ),
+                columns=columns,
+                drop=True,
+            )
+        )
+
+        condition = (
+            (self.main_df[self.fbg_colname] < 6.1)
+            & (self.main_df[self.ogtt_colname] < 7.8)
+            & (self.main_df[self.ogtt_colname].notna())
+            & (self.main_df[self.fbg_colname].notna())
+        )
+        row_defs.add(
+            RowDefinition(
+                colname=self.colname,
+                label="FBG <6.1 mmol/l and after OGTT <7.8 mmol/l",
+                condition=condition,
+                columns=columns,
+                drop=True,
+            )
+        )
+
+        condition = (
+            (self.main_df[self.fbg_colname] < 6.1)
+            & (self.main_df[self.ogtt_colname] >= 7.8)
+            & (self.main_df[self.ogtt_colname] < 11.1)
+            & (self.main_df[self.ogtt_colname].notna())
+            & (self.main_df[self.fbg_colname].notna())
+        )
+        row_defs.add(
+            RowDefinition(
+                colname=self.colname,
+                label="FBG <6.1 mmol/l and after OGTT 7.8–11.0 mmol/l",
+                condition=condition,
+                columns=columns,
+                drop=True,
+            )
+        )
+
+        condition = (
+            (self.main_df[self.fbg_colname] >= 6.1)
+            & (self.main_df[self.fbg_colname] < 7.0)
+            & (self.main_df[self.ogtt_colname] < 7.8)
+            & (self.main_df[self.ogtt_colname].notna())
+            & (self.main_df[self.fbg_colname].notna())
+        )
+        row_defs.add(
+            RowDefinition(
+                colname=self.colname,
+                label="FBG 6.1–6.9 mmol/l and after OGTT <7.8 mmol/l",
+                condition=condition,
+                columns=columns,
+                drop=True,
+            )
+        )
+
+        condition = (
+            (self.main_df[self.fbg_colname] >= 6.1)
+            & (self.main_df[self.fbg_colname] < 7.0)
+            & (self.main_df[self.ogtt_colname] >= 7.8)
+            & (self.main_df[self.ogtt_colname] < 11.1)
+            & (self.main_df[self.ogtt_colname].notna())
+            & (self.main_df[self.fbg_colname].notna())
+        )
+        row_defs.add(
+            RowDefinition(
+                colname=self.colname,
+                label="FBG 6.1–6.9 mmol/l and after OGTT 7.8–11.0 mmol/l",
+                condition=condition,
+                columns=columns,
+                drop=True,
+            )
+        )
+
+        condition = (
+            (self.main_df[self.fbg_colname] >= 6.1)
+            & (self.main_df[self.fbg_colname] < 7.0)
+            & (self.main_df[self.ogtt_colname] >= 11.1)
+            & (self.main_df[self.ogtt_colname].notna())
+            & (self.main_df[self.fbg_colname].notna())
+        )
+        row_defs.add(
+            RowDefinition(
+                colname=self.colname,
+                label="FBG 6.1–6.9 mmol/l and after OGTT ≥11.0 mmol/l",
+                condition=condition,
+                columns=columns,
+                drop=True,
+            )
+        )
+
+        condition = (
+            (self.main_df[self.fbg_colname] >= 7.0)
+            & (self.main_df[self.ogtt_colname] < 7.8)
+            & (self.main_df[self.ogtt_colname].notna())
+            & (self.main_df[self.fbg_colname].notna())
+        )
+        row_defs.add(
+            RowDefinition(
+                colname=self.colname,
+                label="FBG ≥7.0 mmol/l and after OGTT <7.8 mmol/l",
+                condition=condition,
+                columns=columns,
+                drop=True,
+            )
+        )
+
+        condition = (
+            (self.main_df[self.fbg_colname] >= 7.0)
+            & (self.main_df[self.ogtt_colname] >= 7.8)
+            & (self.main_df[self.ogtt_colname] < 11.1)
+            & (self.main_df[self.ogtt_colname].notna())
+            & (self.main_df[self.fbg_colname].notna())
+        )
+        row_defs.add(
+            RowDefinition(
+                colname=self.colname,
+                label="FBG ≥7.0 mmol/l and after OGTT 7.8–11.0 mmol/l",
+                condition=condition,
+                columns=columns,
+                drop=True,
+            )
+        )
+
+        condition = (
+            (self.main_df[self.fbg_colname] >= 7.0)
+            & (self.main_df[self.ogtt_colname] >= 11.1)
+            & (self.main_df[self.ogtt_colname].notna())
+            & (self.main_df[self.fbg_colname].notna())
+        )
+        row_defs.add(
+            RowDefinition(
+                colname=self.colname,
+                label="FBG ≥7.0 mmol/l and after OGTT ≥11.1 mmol/l",
+                condition=condition,
+                columns=columns,
+                drop=True,
+            )
+        )
+
+        condition = (self.main_df[self.ogtt_colname].notna()) | (
+            self.main_df[self.fbg_colname].isna()
+        )
+        row_defs.add(
+            RowDefinition(
+                colname=self.colname,
+                label="FBG not measured",
+                condition=condition,
+                columns=columns,
+                drop=True,
+            )
+        )
+
+        condition = (self.main_df[self.ogtt_colname].isna()) | (
+            self.main_df[self.fbg_colname].notna()
+        )
+        row_defs.add(
+            RowDefinition(
+                colname=self.colname,
+                label="OGTT not measured",
+                condition=condition,
+                columns=columns,
+                drop=True,
+            )
+        )
+
+        condition = (self.main_df[self.ogtt_colname].isna()) | (
+            self.main_df[self.fbg_colname].isna()
+        )
+        row_defs.add(
+            RowDefinition(
+                colname=self.colname,
+                label="not measured",
+                condition=condition,
+                columns=columns,
+                drop=True,
+            )
+        )
+        return row_defs
+
+
+class FbgOgttTable(Table):
+
+    def __init__(self, main_df: pd.DataFrame = None):
+        super().__init__(colname="", main_df=main_df, title="")
+
+    def build_table_df(self) -> None:
+        df1 = FbgOgttTable1(main_df=self.main_df).table_df
+        df2 = FbgOgttTable2(main_df=self.main_df).table_df
+        self.table_df = pd.concat([df1, df2])

edc_analytics/custom_tables/gender.py

@@ -0,0 +1,12 @@
+import pandas as pd
+
+from ..table import Table
+
+
+class GenderTable(Table):
+    def __init__(self, main_df: pd.DataFrame = None):
+        super().__init__(
+            colname="gender",
+            main_df=main_df,
+            title="Gender",
+        )

edc_analytics/custom_tables/hba1c.py

@@ -0,0 +1,87 @@
+import pandas as pd
+from edc_constants.constants import FEMALE, MALE
+
+from ..constants import MEAN_95CI, N_ONLY, N_WITH_COL_PROP, N_WITH_ROW_PROP
+from ..row import RowDefinition, RowDefinitions
+from ..table import Table
+
+
+class HbA1cTable(Table):
+    def __init__(self, main_df: pd.DataFrame = None):
+        super().__init__(
+            colname="hba1c_value",
+            main_df=main_df,
+            title="HbA1C (%) categories",
+        )
+
+    @property
+    def row_definitions(self) -> RowDefinitions:
+        df_tmp = self.main_df.copy()
+        row_defs = RowDefinitions(reverse_rows=False)
+        row0 = RowDefinition(
+            title=self.title,
+            label=self.default_sublabel,
+            condition=(df_tmp["gender"].notna()),
+            columns={FEMALE: (N_ONLY, 2), MALE: (N_ONLY, 2), "All": (N_ONLY, 2)},
+            drop=False,
+        )
+        row_defs.add(row0)
+
+        columns = {
+            FEMALE: (MEAN_95CI, 2),
+            MALE: (MEAN_95CI, 2),
+            "All": (MEAN_95CI, 2),
+        }
+        row_mean = RowDefinition(
+            colname=self.colname,
+            label="Mean (95% CI)",
+            condition=(self.main_df[self.colname].notna()),
+            columns=columns,
+            drop=False,
+        )
+
+        columns = {
+            FEMALE: (N_WITH_COL_PROP, 2),
+            MALE: (N_WITH_COL_PROP, 2),
+            "All": (N_WITH_ROW_PROP, 2),
+        }
+        row_defs.add(
+            RowDefinition(
+                colname=self.colname,
+                label="<6.0",
+                condition=(self.main_df[self.colname] < 6.0),
+                columns=columns,
+                drop=False,
+            )
+        )
+        row_defs.add(
+            RowDefinition(
+                colname=self.colname,
+                label="≥6.0 and ≤6.4",
+                condition=(
+                    (self.main_df[self.colname] >= 6.0) & (self.main_df[self.colname] <= 6.4)
+                ),
+                columns=columns,
+                drop=False,
+            )
+        )
+        row_defs.add(
+            RowDefinition(
+                colname=self.colname,
+                label=">6.4",
+                condition=(self.main_df[self.colname] > 6.4),
+                columns=columns,
+                drop=False,
+            )
+        )
+        row_defs.add(
+            RowDefinition(
+                colname=self.colname,
+                label="not measured",
+                condition=(self.main_df[self.colname].isna()),
+                columns=columns,
+                drop=False,
+            )
+        )
+        row_defs.add(row_mean)
+        return row_defs