Drop .ipynb_checkpoints

.gitignore

@@ -0,0 +1 @@
+.ipynb_checkpoints

vocalisations/scripts/.ipynb_checkpoints/figures-checkpoint.ipynb

@@ -1,714 +0,0 @@
-{
- "cells": [
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "%matplotlib inline"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "import IPython.display as ipd\n",
-    "import sys\n",
-    "import io\n",
-    "import numpy as np\n",
-    "import pandas as pd\n",
-    "import matplotlib as mpl\n",
-    "import matplotlib.pyplot as plt\n",
-    "import scipy.stats as sps"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "Global information\n",
-    "==="
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "mpl.rcParams[\"font.family\"] = \"TeX Gyre Pagella\"\n",
-    "mpl.rcParams[\"font.size\"] = 8\n",
-    "rst_column_width = 3.3\n",
-    "rst_total_width = 7"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "deaf_pups = {\"b3\", \"b5\", \"b8\"}\n",
-    "hearing_pups = {\"b2\", \"b4\", \"b7\"}\n",
-    "all_pups = deaf_pups.union(hearing_pups)"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "group_colors = dict(hearing=\"#7bb992\", deaf=\"#5f0f00\")\n",
-    "bat_colors = {**{bat: group_colors[\"deaf\"] for bat in deaf_pups},\n",
-    "              **{bat: group_colors[\"hearing\"] for bat in hearing_pups}}\n",
-    "bat_markers = dict(zip(sorted(all_pups), [\"P\", \"o\", \"*\", \"s\", \"X\", \"D\"]))"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "Load data for juveniles\n",
-    "==="
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "pup_sessions = pd.read_csv(\"../pup_sessions.csv\", index_col=0, parse_dates=[\"start_time\"],\n",
-    "                           dtype=dict(before_deafening=np.bool))\n",
-    "pup_calls = pd.read_csv(\"../pup_calls.csv\", index_col=[0, 1], parse_dates=[\"start_time\"], na_values=[\"--\"],\n",
-    "                        dtype=dict(calling_bat_deaf=np.bool, calling_bat_mother=np.bool, before_deafening=np.bool))\n",
-    "\n",
-    "# filter out mother vocalisations\n",
-    "pup_calls = pup_calls[~pup_calls[\"calling_bat_mother\"]].reset_index()"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "bat_birthdates = pd.DataFrame([(\"b2\", \"2017/01/26\"),\n",
-    "                               (\"b4\", \"2017/01/30\"),\n",
-    "                               (\"b7\", \"2017/02/08\"),\n",
-    "                               (\"b3\", \"2017/01/29\"),\n",
-    "                               (\"b5\", \"2017/02/02\"),\n",
-    "                               (\"b8\", \"2017/02/08\")], columns=[\"bat\", \"birthdate\"])\n",
-    "bat_birthdates[\"birthdate\"] = pd.to_datetime(bat_birthdates[\"birthdate\"])\n",
-    "bat_birthdates.set_index(\"bat\", inplace=True)"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "# determine ages (in full days) of the calling bats\n",
-    "\n",
-    "birth_dates = bat_birthdates.loc[pup_calls[\"calling_bat\"]][\"birthdate\"].reset_index(drop=True)\n",
-    "ages = pup_calls[\"start_time\"] - birth_dates\n",
-    "pup_calls[\"calling_bat_age_in_days\"] = ages.dt.days\n",
-    "pup_calls[\"calling_bat_age_in_weeks\"] = ages.dt.days // 7\n",
-    "pup_calls[\"call_rms\"] = pup_calls[\"call_rms\"] + 55"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "Load data for adults\n",
-    "==="
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "def single_value(values):\n",
-    "    value_set = set(values)\n",
-    "    if len(value_set) != 1:\n",
-    "        raise ValueError(\"non-unity set\")\n",
-    "    return next(iter(value_set))"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "adult_calls = pd.read_csv(\"../adult_calls.csv\",\n",
-    "                          parse_dates=[\"start_time\"],\n",
-    "                          na_values=[\"--\"],\n",
-    "                          dtype=dict(calling_bat_deaf=np.bool, session_id=np.int),\n",
-    "                          index_col=[\"session_id\", \"call_id\"])\n",
-    "adult_calls[\"recording_day\"] = adult_calls[\"start_time\"].dt.date\n",
-    "adult_calls[\"call_rms\"] -= adult_calls[\"call_rms\"].min()\n",
-    "adult_calls[\"group\"] = np.where(adult_calls[\"calling_bat_deaf\"], \"deaf\", \"hearing\")\n",
-    "\n",
-    "adult_sessions = pd.read_csv(\"../adult_sessions.csv\",\n",
-    "                             parse_dates=[\"start_time\"],\n",
-    "                             dtype=dict(group=\"category\"),\n",
-    "                             index_col=0)\n",
-    "\n",
-    "adult_recording_days = adult_sessions[[\"group\"]].groupby(adult_sessions[\"start_time\"].dt.date).agg(single_value)\n",
-    "adult_recording_days.index.name = \"recording_day\""
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "Data to be dropped\n",
-    "==="
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "Possible echolocation calls (3 ms or shorter)\n",
-    "---"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "pup_calls = pup_calls[pup_calls[\"call_duration\"] > 3e-3]\n",
-    "adult_calls = adult_calls[adult_calls[\"call_duration\"] > 3e-3]"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "Sessions shorter than 20 minutes\n",
-    "---"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "session_gaps = pup_sessions.sort_values(\"start_time\")[\"start_time\"].diff()\n",
-    "new_index = session_gaps.index.insert(0, -1)\n",
-    "new_index = new_index[:-1]\n",
-    "session_gaps.index = new_index\n",
-    "session_gaps.drop(-1, inplace=True)"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "ids_to_drop = session_gaps[session_gaps < pd.Timedelta(20, \"m\")].index"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "pup_calls = pup_calls[~pup_calls[\"session_id\"].isin(ids_to_drop)]\n",
-    "pup_sessions = pup_sessions.drop(ids_to_drop)"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "Last two recordings with mother for pups that have more than others\n",
-    "---"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "sorted_pup_mother_sessions = pup_sessions[pup_sessions[\"animal2\"].str.startswith(\"m\")].sort_values(\"start_time\")\n",
-    "session_counts_with_mothers = sorted_pup_mother_sessions[\"animal1\"].value_counts()\n",
-    "num_sessions_to_drop = session_counts_with_mothers - session_counts_with_mothers.min()\n",
-    "\n",
-    "ids_to_drop = set()\n",
-    "for bat, drop_count in num_sessions_to_drop.iteritems():\n",
-    "    if drop_count == 0:\n",
-    "        continue\n",
-    "    this_bat_sessions = sorted_pup_mother_sessions[sorted_pup_mother_sessions[\"animal1\"] == bat]\n",
-    "    ids_to_drop = ids_to_drop.union(this_bat_sessions.tail(drop_count).index)\n",
-    "\n",
-    "pup_calls = pup_calls[~pup_calls[\"session_id\"].isin(ids_to_drop)]\n",
-    "pup_sessions = pup_sessions.drop(index=ids_to_drop)"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "Compute activity statistics (separately for pups before and after deafening)\n",
-    "==="
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "calls_per_pup_and_session = pup_calls.reset_index().groupby([\"calling_bat\", \"session_id\"])[[\"calling_bat\"]].count() / (20*6) # per 10 seconds\n",
-    "calls_per_pup_and_session.columns = [\"calls_per_10s\"]\n",
-    "calls_per_pup_and_session.reset_index(inplace=True)\n",
-    "\n",
-    "session_dates = pup_sessions.loc[calls_per_pup_and_session[\"session_id\"]][\"start_time\"]\n",
-    "birth_dates = bat_birthdates.loc[calls_per_pup_and_session[\"calling_bat\"]][\"birthdate\"]\n",
-    "calls_per_pup_and_session[\"calling_bat_age_in_days\"] = \\\n",
-    "    (session_dates.reset_index(drop=True) - birth_dates.reset_index(drop=True)).dt.days\n",
-    "calls_per_pup_and_session[\"calling_bat_age_in_weeks\"] = \\\n",
-    "    calls_per_pup_and_session[\"calling_bat_age_in_days\"] // 7\n",
-    "calls_per_pup_and_session = pd.merge(calls_per_pup_and_session, pup_sessions[[\"before_deafening\"]],\n",
-    "                                     left_on=\"session_id\", right_index=True,)"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "dfs = []\n",
-    "\n",
-    "for before_deafening in [False, True]:\n",
-    "    mask = pup_calls[\"before_deafening\"]\n",
-    "    if not before_deafening:\n",
-    "        mask = ~mask\n",
-    "    gr = pup_calls[mask].groupby([\"calling_bat\", \"calling_bat_age_in_weeks\"])\n",
-    "    gr = gr[[\"call_duration\", \"mean_aperiodicity\", \"f0_mean\", \"call_rms\"]]\n",
-    "    params_per_pup_and_week = gr.median()\n",
-    "    params_per_pup_and_week[\"calls_this_week\"] = gr.size()\n",
-    "    \n",
-    "    mask = calls_per_pup_and_session[\"before_deafening\"]\n",
-    "    if not before_deafening:\n",
-    "        mask = ~mask\n",
-    "    gr = calls_per_pup_and_session[mask].groupby([\"calling_bat\", \"calling_bat_age_in_weeks\"])\n",
-    "    params_per_pup_and_week[\"calls_per_10s\"] = gr[\"calls_per_10s\"].mean()\n",
-    "    params_per_pup_and_week.reset_index(inplace=True)\n",
-    "    params_per_pup_and_week[\"before_deafening\"] = before_deafening\n",
-    "    \n",
-    "    dfs.append(params_per_pup_and_week)\n",
-    "    \n",
-    "params_per_pup_and_week = pd.concat(dfs)"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "gr = adult_calls.groupby([\"group\", \"session_id\"], observed=True)\n",
-    "calls_per_adult_group_and_session = gr.size().to_frame(name=\"calls_per_10s\").reset_index()"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "Quantities of extracted data\n",
-    "==="
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "print(\"Total calls by pups: {}\\nCalls by deaf pups: {} ({:.1f} %)\\nCalls by hearing pups: {} ({:.1f} %)\".format(\n",
-    "        len(pup_calls),\n",
-    "        np.sum(pup_calls[\"calling_bat_deaf\"]),\n",
-    "        np.sum(pup_calls[\"calling_bat_deaf\"]) / len(pup_calls) * 100,\n",
-    "        np.sum(~pup_calls[\"calling_bat_deaf\"]),\n",
-    "        np.sum(~pup_calls[\"calling_bat_deaf\"] / len(pup_calls) * 100)))"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "print(\"Total calls by adults: {}\\nCalls by deaf adults: {} ({:.1f} %)\\nCalls by hearing adults: {} ({:.1f} %)\".format(\n",
-    "        len(adult_calls),\n",
-    "        np.sum(adult_calls[\"calling_bat_deaf\"]),\n",
-    "        np.sum(adult_calls[\"calling_bat_deaf\"]) / len(adult_calls) * 100,\n",
-    "        np.sum(~adult_calls[\"calling_bat_deaf\"]),\n",
-    "        np.sum(~adult_calls[\"calling_bat_deaf\"] / len(adult_calls) * 100)))"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "Main figure\n",
-    "==="
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "def plot_trajectories(ax, values, parameter, scale):\n",
-    "    line_artists = {}\n",
-    "    for bat, df in values.groupby(\"calling_bat\"):\n",
-    "        bat_color, bat_marker = bat_colors[bat], bat_markers[bat]\n",
-    "        line_artist, = ax.plot(df[\"calling_bat_age_in_weeks\"] + 1, df[parameter] * scale,\n",
-    "                               c=bat_color, linewidth=0.8)\n",
-    "        ax.plot(df[\"calling_bat_age_in_weeks\"] + 1, df[parameter] * scale,\n",
-    "                c=bat_color, marker=bat_marker, markersize=5, clip_on=False,\n",
-    "                markerfacecolor=\"none\", linestyle=\"\")\n",
-    "        line_artists[bat] = line_artist\n",
-    "    return line_artists"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "def plot_histograms(ax, values, parameter, scale, y_range):\n",
-    "    data = {}\n",
-    "\n",
-    "    if \"group\" in values:\n",
-    "        for group, hearing in [(\"deaf\", False), (\"hearing\", True)]:\n",
-    "            data[hearing] = (values.loc[values[\"group\"] == group, parameter] * scale).values\n",
-    "    else:\n",
-    "        for hearing, df in values.groupby(values[\"calling_bat\"].isin(hearing_pups)):\n",
-    "            data[hearing] = (df[parameter] * scale).values\n",
-    "\n",
-    "    ax.hist([data[True], data[False]], density=True,\n",
-    "            range=y_range, bins=15,\n",
-    "            color=[group_colors[\"hearing\"], group_colors[\"deaf\"]],\n",
-    "            orientation=\"horizontal\", rwidth=0.85)"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "def plot_boxplots(ax, values, parameter, scale, test_significance=False):\n",
-    "    data = []\n",
-    "    for group in [\"deaf\", \"hearing\"]:\n",
-    "        data.append(scale * values.loc[values[\"group\"] == group, parameter].dropna().values)\n",
-    "\n",
-    "    artists = boxplot_ax.boxplot(data, vert=True, manage_ticks=False, showfliers=False, widths=0.75,\n",
-    "                                 patch_artist=True,\n",
-    "                                 boxprops=dict(linewidth=0.5),\n",
-    "                                 whiskerprops=dict(linewidth=0.5),\n",
-    "                                 medianprops=dict(linewidth=1, color=\"bisque\"),\n",
-    "                                 capprops=dict(linewidth=0.5))\n",
-    "\n",
-    "    artists[\"boxes\"][0].set_facecolor(group_colors[\"deaf\"])\n",
-    "    artists[\"boxes\"][1].set_facecolor(group_colors[\"hearing\"])\n",
-    "    \n",
-    "    if test_significance:\n",
-    "        p = sps.mannwhitneyu(data[0], data[1], alternative=\"two-sided\").pvalue\n",
-    "        if p < 0.05:\n",
-    "            ax.annotate(\"*\", (0.8, 0.8), xycoords=\"axes fraction\")"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "call_parameters = [(\"calls_per_10s\", 1, \"Vocal activity\\n[calls/10 s]\", (0, 100), 20),\n",
-    "                   (\"call_rms\", 1, \"Amplitude\\n[dB]\", (0, 54), 12),\n",
-    "                   (\"call_duration\", 1e3, \"Duration\\n[ms]\", (0, 80), 20),\n",
-    "                   (\"f0_mean\", 1e-3, \"Fundamental\\nfrequency [kHz]\", (0, 40), 10),\n",
-    "                   (\"mean_aperiodicity\", 1, \"Aperiodicity\\n[1]\", (0, 1), 0.25)]\n",
-    "\n",
-    "fig_width = rst_total_width\n",
-    "fig_height = 0.7 * fig_width\n",
-    "left_margin, right_margin = 0.75, 0.1\n",
-    "bottom_margin, top_margin = 0.45, 0.45\n",
-    "spacing = 0.2\n",
-    "boxplot_extra_spacing = 0.1\n",
-    "\n",
-    "row_height = (fig_height - bottom_margin - top_margin - (len(call_parameters) - 1) * spacing) / len(call_parameters)\n",
-    "trajectory_width = 3.2\n",
-    "boxplot_width = 0.2\n",
-    "histogram_width = (fig_width - left_margin - right_margin - trajectory_width - boxplot_width - 4 * spacing - boxplot_extra_spacing) / 3\n",
-    "\n",
-    "fig = plt.figure(figsize=(fig_width, fig_height))\n",
-    "\n",
-    "roman_numerals = [\"I\", \"II\", \"III\", \"IV\", \"V\"]\n",
-    "\n",
-    "for i, (parameter, scale, y_label, y_range, y_tick_interval) in enumerate(reversed(call_parameters)):\n",
-    "    early_ax = \\\n",
-    "        fig.add_axes([left_margin / fig_width,\n",
-    "                      (bottom_margin + i * (row_height + spacing)) / fig_height,\n",
-    "                      histogram_width / fig_width,\n",
-    "                      row_height / fig_height])\n",
-    "    late_ax = \\\n",
-    "        fig.add_axes([(left_margin + histogram_width + spacing) / fig_width,\n",
-    "                      (bottom_margin + i * (row_height + spacing)) / fig_height,\n",
-    "                      histogram_width / fig_width,\n",
-    "                      row_height / fig_height])\n",
-    "    adult_ax = \\\n",
-    "        fig.add_axes([(left_margin + 2 * (histogram_width + spacing)) / fig_width,\n",
-    "                      (bottom_margin + i * (row_height + spacing)) / fig_height,\n",
-    "                      histogram_width / fig_width,\n",
-    "                      row_height / fig_height])\n",
-    "    trajectory_ax = \\\n",
-    "        fig.add_axes([(left_margin + 3 * (histogram_width + spacing)) / fig_width,\n",
-    "                      (bottom_margin + i * (row_height + spacing)) / fig_height,\n",
-    "                      trajectory_width / fig_width,\n",
-    "                      row_height / fig_height])\n",
-    "    boxplot_ax = \\\n",
-    "        fig.add_axes([(left_margin + 3 * histogram_width + trajectory_width + 4 * spacing + boxplot_extra_spacing) / fig_width,\n",
-    "                      (bottom_margin + i * (row_height + spacing)) / fig_height,\n",
-    "                      boxplot_width / fig_width,\n",
-    "                      row_height / fig_height])\n",
-    "    overall_ax = \\\n",
-    "        fig.add_axes([left_margin / fig_width,\n",
-    "                      (bottom_margin + i * (row_height + spacing)) / fig_height,\n",
-    "                      (fig_width - left_margin - right_margin) / fig_width,\n",
-    "                      row_height / fig_height], frameon=False)\n",
-    "    overall_ax.set_xticks([])\n",
-    "    overall_ax.set_yticks([])\n",
-    "    \n",
-    "    if parameter == \"calls_per_10s\":\n",
-    "        df = calls_per_pup_and_session\n",
-    "    else:\n",
-    "        df = pup_calls\n",
-    "    plot_histograms(early_ax,\n",
-    "                    df.query(\"before_deafening\"),\n",
-    "                    parameter, scale, y_range)\n",
-    "    plot_histograms(late_ax,\n",
-    "                    df.query(\"not before_deafening\"),\n",
-    "                    parameter, scale, y_range)\n",
-    "    \n",
-    "    if parameter == \"calls_per_10s\":\n",
-    "        df = calls_per_adult_group_and_session\n",
-    "    else:\n",
-    "        df = adult_calls\n",
-    "    plot_histograms(adult_ax, df,\n",
-    "                    parameter, scale, y_range if parameter != \"calls_per_10s\" else (0, 400))\n",
-    "    \n",
-    "    plot_trajectories(trajectory_ax,\n",
-    "                      params_per_pup_and_week.query(\"not before_deafening and calling_bat_age_in_weeks <= 24\"),\n",
-    "                      parameter, scale)\n",
-    "    \n",
-    "    trajectory_ax.xaxis.set_major_locator(mpl.ticker.MultipleLocator(4))\n",
-    "    trajectory_ax.set_xlim(2, 25)\n",
-    "    trajectory_ax.spines[\"left\"].set_position((\"outward\", 3))\n",
-    "\n",
-    "    plot_boxplots(boxplot_ax, df, parameter, scale, test_significance=True)\n",
-    "    boxplot_ax.set_xlim(0.25, 2.75)\n",
-    "    \n",
-    "    if i == 0:\n",
-    "        trajectory_ax.set_xlabel(\"Week of age\")\n",
-    "        trajectory_ax.xaxis.set_major_formatter(mpl.ticker.FuncFormatter(lambda x, pos: \"{}th\".format(int(x))))\n",
-    "        #trajectory_ax.xaxis.set_label_coords(0.5, -0.4)\n",
-    "    else:\n",
-    "        for ax in [early_ax, late_ax, trajectory_ax]:\n",
-    "            ax.set_xticklabels([])\n",
-    "            \n",
-    "    if i == len(call_parameters) - 1:\n",
-    "        early_ax.set_title(\"a)\\n\\n< 2 weeks\", fontsize=8)\n",
-    "        late_ax.set_title(\"b)\\n\\n2–25 weeks\", fontsize=8)\n",
-    "        adult_ax.set_title(\"c)\\n\\n2 years\", fontsize=8)\n",
-    "        boxplot_ax.set_title(\"e)\\n\\n2 years\", fontsize=8)\n",
-    "        trajectory_ax.set_title(\"d)\\nDevelopment trajectory of median parameter values\\nat 2–25 weeks of age\", fontsize=8)\n",
-    "        early_ax.annotate(\"hearing\",\n",
-    "                         xy=(0, 1), xycoords=\"axes fraction\",\n",
-    "                         xytext=(5, -10), textcoords=\"offset points\",\n",
-    "                         verticalalignment=\"top\", horizontalalignment=\"left\",\n",
-    "                         color=group_colors[\"hearing\"])\n",
-    "        early_ax.annotate(\"deafened\",\n",
-    "                         xy=(0, 1), xycoords=\"axes fraction\",\n",
-    "                         xytext=(5, 0), textcoords=\"offset points\",\n",
-    "                         verticalalignment=\"top\", horizontalalignment=\"left\",\n",
-    "                         color=group_colors[\"deaf\"])\n",
-    "            \n",
-    "    for ax in [early_ax, late_ax, adult_ax, trajectory_ax, boxplot_ax]:\n",
-    "        if ax is adult_ax and parameter == \"calls_per_10s\":\n",
-    "            ax.set_ylim(0, 400)\n",
-    "            ax.yaxis.set_major_locator(mpl.ticker.MultipleLocator(100))\n",
-    "        else:\n",
-    "            ax.set_ylim(y_range[0], y_range[1])\n",
-    "            ax.yaxis.set_major_locator(mpl.ticker.MultipleLocator(y_tick_interval))\n",
-    "\n",
-    "        for spine in [\"right\", \"top\"]:\n",
-    "            ax.spines[spine].set_visible(False)\n",
-    "        ax.spines[\"bottom\"].set_position((\"outward\", 3))\n",
-    "            \n",
-    "    for ax in [late_ax, adult_ax, trajectory_ax, boxplot_ax]:\n",
-    "        if (ax is not adult_ax or parameter != \"calls_per_10s\") \\\n",
-    "                and (ax is not trajectory_ax or parameter != \"calls_per_10s\"):\n",
-    "            ax.set_yticklabels([])\n",
-    "        \n",
-    "    for ax in [early_ax, late_ax, adult_ax, boxplot_ax]:\n",
-    "        ax.set_xticks([])\n",
-    "        ax.spines[\"bottom\"].set_visible(False)\n",
-    "        \n",
-    "    early_ax.set_ylabel(y_label)\n",
-    "    early_ax.yaxis.set_label_coords(-0.32 / histogram_width, 0.5)\n",
-    "    \n",
-    "    overall_ax.set_ylabel(roman_numerals[-i - 1],\n",
-    "                          rotation=\"0\",\n",
-    "                          verticalalignment=\"center\",\n",
-    "                         labelpad=49)\n",
-    "    \n",
-    "fig.savefig(\"../parameters.pdf\")"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "Parameter table\n",
-    "==="
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "per_session_parameters = [(\"call_rms\", 1, \"Amplitude [dB]\"),\n",
-    "                          (\"call_duration\", 1e3, \"Duration [ms]\"),\n",
-    "                          (\"f0_min\", 1e-3, \"Minimum fundamental frequency [kHz]\"),\n",
-    "                          (\"f0_mean\", 1e-3, \"Mean fundamental frequency [kHz]\"),\n",
-    "                          (\"f0_max\", 1e-3, \"Maximum fundamental frequency [kHz]\"),\n",
-    "                          (\"f0_start\", 1e-3, \"Fundamental frequency at call onset [kHz]\"),\n",
-    "                          (\"f0_end\", 1e-3, \"Fundamental frequency at end of call [kHz]\"),\n",
-    "                          (\"f_min\", 1e-3, \"Minimum frequency [kHz]\"),\n",
-    "                          (\"f_max\", 1e-3, \"Maximum frequency [kHz]\"),\n",
-    "                          (\"bandwidth\", 1e-3, \"Bandwidth [kHz]\"),\n",
-    "                          (\"spectral_centroid\", 1e-3, \"Spectral centroid frequency [kHz]\"),\n",
-    "                          (\"mean_aperiodicity\", 1, \"Aperiodicity [1]\")]"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "adult_calls.loc[:, \"bandwidth\"] = adult_calls[\"f_max\"] - adult_calls[\"f_min\"]\n",
-    "def q25(series):\n",
-    "    return series.quantile(0.25)\n",
-    "def q75(series):\n",
-    "    return series.quantile(0.75)\n",
-    "\n",
-    "adult_groups = adult_calls[[p[0] for p in per_session_parameters] + [\"group\"]].groupby(\"group\")\n",
-    "adult_summary = adult_groups.agg([q25, \"median\", q75])"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "per_session_parameters.insert(0, (\"calls_per_10s\", 1, \"Vocal activity [calls/10 s]\"))\n",
-    "adult_activity_summary = calls_per_adult_group_and_session.groupby(\"group\")[[\"calls_per_10s\"]].agg([q25, \"median\", q75])\n",
-    "adult_summary = pd.concat([adult_activity_summary, adult_summary], axis=1)"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "fout = io.StringIO()\n",
-    "print(\"<!DOCTYPE html><body><table>\", file=fout)\n",
-    "print(\"<tr><th></th><th colspan='3'>Hearing (N={})</th><th colspan='3'>Deaf (N={})</th></tr>\".format(*adult_calls[\"group\"].value_counts().loc[[\"hearing\", \"deaf\"]]), file=fout)\n",
-    "print(\"<tr><th></th>{}<th>p &lt; 0.05 (Mann–Whitney)</th></tr>\".format(\"<th>Q25</th><th>Q50</th><th>Q75</th>\" * 2), file=fout)\n",
-    "\n",
-    "for parameter_name, scale, parameter_description in per_session_parameters:\n",
-    "    print(\"<tr><th>{}</th>\".format(parameter_description), file=fout, end=\"\")\n",
-    "    test_data = []\n",
-    "    for group in [\"hearing\", \"deaf\"]:\n",
-    "        for statistic in [\"q25\", \"median\", \"q75\"]:\n",
-    "            print(\"<td>{:.2f}</td>\".format(adult_summary.loc[group, (parameter_name, statistic)] * scale), file=fout, end=\"\")\n",
-    "        if parameter_name != \"calls_per_10s\":\n",
-    "            test_data.append(adult_calls.loc[adult_calls[\"group\"] == group, parameter_name].values)\n",
-    "    if not test_data:\n",
-    "        print(\"<td>(see plot)</td>\", file=fout)\n",
-    "    else:\n",
-    "        p = sps.mannwhitneyu(test_data[0], test_data[1], alternative=\"two-sided\").pvalue\n",
-    "        if p < 0.05:\n",
-    "            print(\"<td>*</td>\".format(p), file=fout)\n",
-    "        else:\n",
-    "            print(\"<td>{:.2f}</td>\".format(p), file=fout)\n",
-    "    print(\"</tr>\", file=fout)\n",
-    "print(\"</table></body>\", file=fout)\n",
-    "\n",
-    "parameters_table = fout.getvalue()"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "ipd.display(ipd.HTML(parameters_table))\n",
-    "with open(\"../parameters_table.html\", \"wt\") as fout:\n",
-    "    print(parameters_table, file=fout, end=\"\")"
-   ]
-  }
- ],
- "metadata": {
-  "kernelspec": {
-   "display_name": "Python 3",
-   "language": "python",
-   "name": "python3"
-  },
-  "language_info": {
-   "codemirror_mode": {
-    "name": "ipython",
-    "version": 3
-   },
-   "file_extension": ".py",
-   "mimetype": "text/x-python",
-   "name": "python",
-   "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython3",
-   "version": "3.8.5"
-  }
- },
- "nbformat": 4,
- "nbformat_minor": 4
-}