ACCLAB · sangyu · Jul 29, 2026 · Jul 24, 2026 · Jul 24, 2026
diff --git a/dabest/_api.py b/dabest/_api.py
@@ -1,4 +1,6 @@
-"""Loading data and relevant groups"""
+"""Loading data and relevant groups
+
+Docs: https://acclab.github.io/DABEST-python/API/load.html.md"""
 
 # AUTOGENERATED! DO NOT EDIT! File to edit: ../nbs/API/load.ipynb.
 

diff --git a/dabest/_bootstrap_tools.py b/dabest/_bootstrap_tools.py
@@ -1,3 +1,5 @@
+"""Docs: https://acclab.github.io/DABEST-python/API/bootstrap.html.md"""
+
 # AUTOGENERATED! DO NOT EDIT! File to edit: ../nbs/API/bootstrap.ipynb.
 
 # %% auto #0

diff --git a/dabest/_dabest_object.py b/dabest/_dabest_object.py
@@ -1,4 +1,6 @@
-"""Main class for estimating statistics and generating plots."""
+"""Main class for estimating statistics and generating plots.
+
+Docs: https://acclab.github.io/DABEST-python/API/dabest_object.html.md"""
 
 # AUTOGENERATED! DO NOT EDIT! File to edit: ../nbs/API/dabest_object.ipynb.
 

diff --git a/dabest/_delta_objects.py b/dabest/_delta_objects.py
@@ -1,4 +1,6 @@
-"""Auxiliary delta classes for estimating statistics and generating plots."""
+"""Auxiliary delta classes for estimating statistics and generating plots.
+
+Docs: https://acclab.github.io/DABEST-python/API/delta_objects.html.md"""
 
 # AUTOGENERATED! DO NOT EDIT! File to edit: ../nbs/API/delta_objects.ipynb.
 

diff --git a/dabest/_effsize_objects.py b/dabest/_effsize_objects.py
@@ -1,4 +1,6 @@
-"""The auxiliary classes involved in the computations of bootstrapped effect sizes."""
+"""The auxiliary classes involved in the computations of bootstrapped effect sizes.
+
+Docs: https://acclab.github.io/DABEST-python/API/effsize_objects.html.md"""
 
 # AUTOGENERATED! DO NOT EDIT! File to edit: ../nbs/API/effsize_objects.ipynb.
 
@@ -1304,7 +1306,7 @@ def plot(
         group_summaries : ['mean_sd', 'median_quartiles', 'None'], default "mean_sd".
             Plots the summary statistics for each group. If 'mean_sd', then
             the mean and standard deviation of each group is plotted as a
-            notched line beside each group. If 'median_quantiles', then the
+            notched line beside each group. For proportion and Sankey plots, this error is the binomial standard error (BSE), sqrt(p(1-p)/n), not the SD. If 'median_quantiles', then the
             median and 25th and 75th percentiles of each group is plotted
             instead. If 'None', the summaries are not shown.
         fig_size : tuple, default None

diff --git a/dabest/_stats_tools/confint_1group.py b/dabest/_stats_tools/confint_1group.py
@@ -1,4 +1,6 @@
-"""A range of functions to compute bootstraps for a single sample."""
+"""A range of functions to compute bootstraps for a single sample.
+
+Docs: https://acclab.github.io/DABEST-python/API/confint_1group.html.md"""
 
 # AUTOGENERATED! DO NOT EDIT! File to edit: ../../nbs/API/confint_1group.ipynb.
 

diff --git a/dabest/_stats_tools/confint_2group_diff.py b/dabest/_stats_tools/confint_2group_diff.py
@@ -1,4 +1,6 @@
-"""A range of functions to compute bootstraps for the mean difference"""
+"""A range of functions to compute bootstraps for the mean difference
+
+Docs: https://acclab.github.io/DABEST-python/API/confint_2group_diff.html.md"""
 
 # AUTOGENERATED! DO NOT EDIT! File to edit: ../../nbs/API/confint_2group_diff.ipynb.
 

diff --git a/dabest/_stats_tools/effsize.py b/dabest/_stats_tools/effsize.py
@@ -1,4 +1,6 @@
-"""A range of functions to compute various effect sizes."""
+"""A range of functions to compute various effect sizes.
+
+Docs: https://acclab.github.io/DABEST-python/API/effsize.html.md"""
 
 # AUTOGENERATED! DO NOT EDIT! File to edit: ../../nbs/API/effsize.ipynb.
 

diff --git a/dabest/_stats_tools/precompile.py b/dabest/_stats_tools/precompile.py
@@ -1,4 +1,6 @@
-"""A tool to pre-compile Numba functions for speeding up DABEST bootstrapping"""
+"""A tool to pre-compile Numba functions for speeding up DABEST bootstrapping
+
+Docs: https://acclab.github.io/DABEST-python/API/precompile.html.md"""
 
 # AUTOGENERATED! DO NOT EDIT! File to edit: ../../nbs/API/precompile.ipynb.
 

diff --git a/dabest/forest_plot.py b/dabest/forest_plot.py
@@ -1,4 +1,6 @@
-"""Creating forest plots from contrast objects."""
+"""Creating forest plots from contrast objects.
+
+Docs: https://acclab.github.io/DABEST-python/API/forest_plot.html.md"""
 
 # AUTOGENERATED! DO NOT EDIT! File to edit: ../nbs/API/forest_plot.ipynb.
 

diff --git a/dabest/misc_tools.py b/dabest/misc_tools.py
@@ -1,4 +1,6 @@
-"""Convenience functions that don't directly deal with plotting or bootstrap computations are placed here."""
+"""Convenience functions that don't directly deal with plotting or bootstrap computations are placed here.
+
+Docs: https://acclab.github.io/DABEST-python/API/misc_tools.html.md"""
 
 # AUTOGENERATED! DO NOT EDIT! File to edit: ../nbs/API/misc_tools.ipynb.
 

diff --git a/dabest/multi.py b/dabest/multi.py
@@ -1,3 +1,5 @@
+"""Docs: https://acclab.github.io/DABEST-python/API/multi.html.md"""
+
 # AUTOGENERATED! DO NOT EDIT! File to edit: ../nbs/API/multi.ipynb.
 
 # %% auto #0

diff --git a/dabest/plot_tools.py b/dabest/plot_tools.py
@@ -1,4 +1,6 @@
-"""A set of convenience functions used for producing plots in `dabest`."""
+"""A set of convenience functions used for producing plots in `dabest`.
+
+Docs: https://acclab.github.io/DABEST-python/API/plot_tools.html.md"""
 
 # AUTOGENERATED! DO NOT EDIT! File to edit: ../nbs/API/plot_tools.ipynb.
 
@@ -70,7 +72,7 @@ def error_bar(
     data: pd.DataFrame,  # This DataFrame should be in 'long' format.
     x: str,  # x column to be plotted.
     y: str,  # y column to be plotted.
-    type: str = "mean_sd",  # Choose from ['mean_sd', 'median_quartiles']. Plots the summary statistics for each group. If 'mean_sd', then the mean and standard deviation of each group is plotted as a gapped line. If 'median_quantiles', then the median and 25th and 75th percentiles of each group is plotted instead.
+    type: str = "mean_sd",  # Choose from ['mean_sd', 'median_quartiles']. Plots the summary statistics for each group. If 'mean_sd', then the mean and standard deviation of each group is plotted as a gapped line. For proportion and Sankey plots, the error shown is the binomial standard error (BSE), sqrt(p(1-p)/n), rather than the SD. If 'median_quantiles', then the median and 25th and 75th percentiles of each group is plotted instead.
     offset: float = 0.2,  # Give a single float (that will be used as the x-offset of all gapped lines), or an iterable containing the list of x-offsets.
     ax=None,  # If a matplotlib Axes object is specified, the gapped lines will be plotted in order on this axes. If None, the current axes (plt.gca()) is used.
     line_color="black",  # The color of the gapped lines.
@@ -85,11 +87,10 @@ def error_bar(
 ):
     """
     Function to plot the standard deviations as vertical errorbars.
+    For proportion and Sankey plots, the vertical bars instead show the
+    BSE of the proportion.
     The mean is a gap defined by negative space.
 
-    This function combines the functionality of gapped_lines(),
-    proportional_error_bar(), and sankey_error_bar().
-
     """
 
     if gap_width_percent < 0 or gap_width_percent > 100:

diff --git a/dabest/plotter.py b/dabest/plotter.py
@@ -1,4 +1,6 @@
-"""Creating estimation plots."""
+"""Creating estimation plots.
+
+Docs: https://acclab.github.io/DABEST-python/API/plotter.html.md"""
 
 # AUTOGENERATED! DO NOT EDIT! File to edit: ../nbs/API/plotter.ipynb.
 

diff --git a/nbs/02-about.ipynb b/nbs/02-about.ipynb
@@ -32,7 +32,7 @@
     "\n",
     "- Statistics supervision by Hyungwon Choi\n",
     "\n",
-    "- Alpha testers from the Claridge-Chang lab: [Sangyu Xu](https://github.com/sangyu), [Xianyuan Zhang](https://github.com/XYZfar), [Farhan Mohammad](https://github.com/farhan8igib), Jurga Mituzaitė, Stanislav Ott, Tayfun Tumkaya, Jonathan Anns, Nicole Lee and Yishan Mai.\n",
+    "- Alpha testers from the Claridge-Chang lab: [Sangyu Xu](https://github.com/sangyu), [Xianyuan Zhang](https://github.com/XYZfar), [Farhan Mohammad](https://github.com/farhan8igib), Jurga Mituzaitė, Stanislav Ott, [Tayfun Tumkaya](https://github.com/ttumkaya), [Jonathan Anns](https://github.com/JAnns98), [Nicole Lee](https://github.com/mnicolee) and [Yishan Mai](https://github.com/maiyishan).\n",
     "\n",
     "- DizietAsahi ([DizietAsahi](https://github.com/DizietAsahi)) with [PR #86](https://github.com/ACCLAB/DABEST-python/pull/86):  Fix bugs in slopegraph and reference line keyword parsing.\n",
     "\n",

diff --git a/nbs/API/effsize_objects.ipynb b/nbs/API/effsize_objects.ipynb
@@ -1515,7 +1515,7 @@
     "        group_summaries : ['mean_sd', 'median_quartiles', 'None'], default \"mean_sd\".\n",
     "            Plots the summary statistics for each group. If 'mean_sd', then\n",
     "            the mean and standard deviation of each group is plotted as a\n",
-    "            notched line beside each group. If 'median_quantiles', then the\n",
+    "            notched line beside each group. For proportion and Sankey plots, this error is the binomial standard error (BSE), sqrt(p(1-p)/n), not the SD. If 'median_quantiles', then the\n",
     "            median and 25th and 75th percentiles of each group is plotted\n",
     "            instead. If 'None', the summaries are not shown.\n",
     "        fig_size : tuple, default None\n",

diff --git a/nbs/API/plot_tools.ipynb b/nbs/API/plot_tools.ipynb
@@ -121,7 +121,7 @@
     "    data: pd.DataFrame,  # This DataFrame should be in 'long' format.\n",
     "    x: str,  # x column to be plotted.\n",
     "    y: str,  # y column to be plotted.\n",
-    "    type: str = \"mean_sd\",  # Choose from ['mean_sd', 'median_quartiles']. Plots the summary statistics for each group. If 'mean_sd', then the mean and standard deviation of each group is plotted as a gapped line. If 'median_quantiles', then the median and 25th and 75th percentiles of each group is plotted instead.\n",
+    "    type: str = \"mean_sd\",  # Choose from ['mean_sd', 'median_quartiles']. Plots the summary statistics for each group. If 'mean_sd', then the mean and standard deviation of each group is plotted as a gapped line. For proportion and Sankey plots, the error shown is the binomial standard error (BSE), sqrt(p(1-p)/n), rather than the SD. If 'median_quantiles', then the median and 25th and 75th percentiles of each group is plotted instead.\n",
     "    offset: float = 0.2,  # Give a single float (that will be used as the x-offset of all gapped lines), or an iterable containing the list of x-offsets.\n",
     "    ax=None,  # If a matplotlib Axes object is specified, the gapped lines will be plotted in order on this axes. If None, the current axes (plt.gca()) is used.\n",
     "    line_color=\"black\",  # The color of the gapped lines.\n",
@@ -136,11 +136,10 @@
     "):\n",
     "    \"\"\"\n",
     "    Function to plot the standard deviations as vertical errorbars.\n",
+    "    For proportion and Sankey plots, the vertical bars instead show the\n",
+    "    BSE of the proportion.\n",
     "    The mean is a gap defined by negative space.\n",
     "\n",
-    "    This function combines the functionality of gapped_lines(),\n",
-    "    proportional_error_bar(), and sankey_error_bar().\n",
-    "\n",
     "    \"\"\"\n",
     "\n",
     "    if gap_width_percent < 0 or gap_width_percent > 100:\n",

diff --git a/nbs/tutorials/04-proportion_plot.ipynb b/nbs/tutorials/04-proportion_plot.ipynb
@@ -646,7 +646,7 @@
    "id": "243a1a0b",
    "metadata": {},
    "source": [
-    "Instead of a Gardner-Altman plot, you can generate a **Cumming estimation plot** by setting ``float_contrast=False`` in the ``.plot()`` method. This will plot the bootstrap effect sizes below the raw data."
+    "Instead of a Gardner-Altman plot, you can generate a **Cumming estimation plot** by setting ``float_contrast=False`` in the ``.plot()`` method. This will plot the bootstrap effect sizes below the raw data. The gapped lines show the mean (gap) and the binomial standard error (BSE) of each group."
    ]
   },
   {
@@ -1098,7 +1098,7 @@
    "id": "17832542",
    "metadata": {},
    "source": [
-    "The Sankey plots for paired proportions also supports the ``float_contrast`` parameter, which can be set to ``False`` to produce a **Cumming estimation plot**.\n"
+    "The Sankey plots for paired proportions also supports the ``float_contrast`` parameter, which can be set to ``False`` to produce a **Cumming estimation plot**. The gapped lines show the mean and the BSE of each group.\n"
    ]
   },
   {
@@ -1687,7 +1687,7 @@
     }
    ],
    "source": [
-    "two_groups_unpaired.mean_diff.plot(barplot_kwargs={\"alpha\":0.5, \"edgecolor\":\"red\", \"linewidth\":2, 'errorbar': ('sd', 0.1)});"
+    "two_groups_unpaired.mean_diff.plot(barplot_kwargs={\"alpha\":0.5, \"edgecolor\":\"red\", \"linewidth\":2});"
    ]
   },
   {

diff --git a/nbs/tutorials/08-plot_aesthetics.ipynb b/nbs/tutorials/08-plot_aesthetics.ipynb
@@ -1299,7 +1299,7 @@
    "source": [
     "The type of group summary can be specified via `group_summaries` in the `.plot()` method and must be one of these: `'median_quartiles'`, `'mean_sd'`, `None`.\n",
     "\n",
-    "By default, the group summary is set to `'mean_sd'`."
+    "By default, the group summary is set to `'mean_sd'`. For proportion and Sankey plots, the `'mean_sd'` gapped line shows the BSE, not the standard deviation."
    ]
   },
   {