{
"cells": [
{
"cell_type": "markdown",
"id": "3f4d4eea",
"metadata": {},
"source": [
"# Extended Cohort for E-health, Environment and DNA (EXCEED)"
]
},
{
"cell_type": "code",
"execution_count": 1,
"id": "5880a534",
"metadata": {
"execution": {
"iopub.execute_input": "2025-07-28T18:43:33.377992Z",
"iopub.status.busy": "2025-07-28T18:43:33.377992Z",
"iopub.status.idle": "2025-07-28T18:43:38.024361Z",
"shell.execute_reply": "2025-07-28T18:43:38.023638Z"
},
"tags": [
"remove-input"
]
},
"outputs": [
{
"data": {
"text/markdown": [
">Last modified: 19 Sep 2025"
],
"text/plain": [
"<IPython.core.display.Markdown object>"
]
},
"metadata": {},
"output_type": "display_data"
}
],
"source": [
"\n",
"import sys\n",
"import os\n",
"sys.path.append(os.path.abspath('../../scripts/'))\n",
"from data_doc_helper import LPSSource as SS, last_modified\n",
"ss = SS(\"EXCEED\")\n",
"last_modified()\n"
]
},
{
"cell_type": "markdown",
"id": "f679b7bc",
"metadata": {},
"source": [
"## 1. Summary"
]
},
{
"cell_type": "code",
"execution_count": 2,
"id": "f82a0859",
"metadata": {
"execution": {
"iopub.execute_input": "2025-07-28T18:43:38.033385Z",
"iopub.status.busy": "2025-07-28T18:43:38.032390Z",
"iopub.status.idle": "2025-07-28T18:43:38.046773Z",
"shell.execute_reply": "2025-07-28T18:43:38.044455Z"
},
"tags": [
"remove-input"
]
},
"outputs": [
{
"data": {
"text/markdown": [
"The Extended Cohort for E-health, Environment and DNA (EXCEED) study collects information from people about genes and lifestyle to provide insight into environmental influences on a broad range of diseases and long-term health. "
],
"text/plain": [
"<IPython.core.display.Markdown object>"
]
},
"metadata": {},
"output_type": "display_data"
}
],
"source": [
"ss.summary()"
]
},
{
"cell_type": "code",
"execution_count": 3,
"id": "0b4fbbca",
"metadata": {
"execution": {
"iopub.execute_input": "2025-07-28T18:43:38.053174Z",
"iopub.status.busy": "2025-07-28T18:43:38.053174Z",
"iopub.status.idle": "2025-07-28T18:43:39.839376Z",
"shell.execute_reply": "2025-07-28T18:43:39.837846Z"
},
"tags": [
"remove-input"
]
},
"outputs": [
{
"data": {
"text/html": [
"<style type=\"text/css\">\n",
"#T_46cbe th {\n",
" text-align: left;\n",
"}\n",
"#T_46cbe_row0_col0, #T_46cbe_row0_col1, #T_46cbe_row1_col0, #T_46cbe_row1_col1, #T_46cbe_row2_col0, #T_46cbe_row2_col1, #T_46cbe_row3_col0, #T_46cbe_row3_col1, #T_46cbe_row4_col0, #T_46cbe_row4_col1, #T_46cbe_row5_col0, #T_46cbe_row5_col1, #T_46cbe_row6_col0, #T_46cbe_row6_col1, #T_46cbe_row7_col0, #T_46cbe_row7_col1, #T_46cbe_row8_col0, #T_46cbe_row8_col1, #T_46cbe_row9_col0, #T_46cbe_row9_col1, #T_46cbe_row10_col0, #T_46cbe_row10_col1, #T_46cbe_row11_col0, #T_46cbe_row11_col1, #T_46cbe_row12_col0, #T_46cbe_row12_col1 {\n",
" text-align: left;\n",
"}\n",
"</style>\n",
"<table id=\"T_46cbe\" style=\"font-size: 14px\">\n",
" <thead>\n",
" <tr>\n",
" <th id=\"T_46cbe_level0_col0\" class=\"col_heading level0 col0\" >Series Descriptor</th>\n",
" <th id=\"T_46cbe_level0_col1\" class=\"col_heading level0 col1\" >Series-specific Information</th>\n",
" </tr>\n",
" </thead>\n",
" <tbody>\n",
" <tr>\n",
" <td id=\"T_46cbe_row0_col0\" class=\"data row0 col0\" >Citation (APA)</td>\n",
" <td id=\"T_46cbe_row0_col1\" class=\"data row0 col1\" >University of Leicester Genetic Epidemiology Group. (2021). <i>Extended Cohort for E-health, Environment and DNA (EXCEED).</i> UK Longitudinal Linkage Collaboration (UK LLC). <a href=\"https://doi.org/10.71760/ukllc-series-00007\" rel=\"noopener noreferrer\" target=\"_blank\">https://doi.org/10.71760/ukllc-series-00007</a></td>\n",
" </tr>\n",
" <tr>\n",
" <td id=\"T_46cbe_row1_col0\" class=\"data row1 col0\" >Download Citation</td>\n",
" <td id=\"T_46cbe_row1_col1\" class=\"data row1 col1\" > <a href=\"https://api.datacite.org/application/vnd.citationstyles.csl+json/10.71760/ukllc-series-00007\" rel=\"noopener noreferrer\" target=\"_blank\">Citeproc JSON</a> <a href=\"https://api.datacite.org/application/x-bibtex/10.71760/ukllc-series-00007\" rel=\"noopener noreferrer\" target=\"_blank\">BibTeX</a> <a href=\"https://api.datacite.org/application/x-research-info-systems/10.71760/ukllc-series-00007\" rel=\"noopener noreferrer\" target=\"_blank\">RIS</a></td>\n",
" </tr>\n",
" <tr>\n",
" <td id=\"T_46cbe_row2_col0\" class=\"data row2 col0\" >Owner</td>\n",
" <td id=\"T_46cbe_row2_col1\" class=\"data row2 col1\" >University of Leicester</td>\n",
" </tr>\n",
" <tr>\n",
" <td id=\"T_46cbe_row3_col0\" class=\"data row3 col0\" >Cohort</td>\n",
" <td id=\"T_46cbe_row3_col1\" class=\"data row3 col1\" >11000</td>\n",
" </tr>\n",
" <tr>\n",
" <td id=\"T_46cbe_row4_col0\" class=\"data row4 col0\" >Age at Recruitment</td>\n",
" <td id=\"T_46cbe_row4_col1\" class=\"data row4 col1\" >18+ years</td>\n",
" </tr>\n",
" <tr>\n",
" <td id=\"T_46cbe_row5_col0\" class=\"data row5 col0\" >Geographical Coverage - Nations</td>\n",
" <td id=\"T_46cbe_row5_col1\" class=\"data row5 col1\" >England</td>\n",
" </tr>\n",
" <tr>\n",
" <td id=\"T_46cbe_row6_col0\" class=\"data row6 col0\" >Geographical Coverage - Regions</td>\n",
" <td id=\"T_46cbe_row6_col1\" class=\"data row6 col1\" >Leicestershire & Rutland</td>\n",
" </tr>\n",
" <tr>\n",
" <td id=\"T_46cbe_row7_col0\" class=\"data row7 col0\" >Start Date</td>\n",
" <td id=\"T_46cbe_row7_col1\" class=\"data row7 col1\" >2013</td>\n",
" </tr>\n",
" <tr>\n",
" <td id=\"T_46cbe_row8_col0\" class=\"data row8 col0\" >Permitted Linkages</td>\n",
" <td id=\"T_46cbe_row8_col1\" class=\"data row8 col1\" >See <a href=\"https://guidebook.ukllc.ac.uk/docs/linkages/lps_linkages\" rel=\"noopener noreferrer\" target=\"_blank\">here</a></td>\n",
" </tr>\n",
" <tr>\n",
" <td id=\"T_46cbe_row9_col0\" class=\"data row9 col0\" >Inclusion in Linkages</td>\n",
" <td id=\"T_46cbe_row9_col1\" class=\"data row9 col1\" >Consent</td>\n",
" </tr>\n",
" <tr>\n",
" <td id=\"T_46cbe_row10_col0\" class=\"data row10 col0\" >Cohort Profile</td>\n",
" <td id=\"T_46cbe_row10_col1\" class=\"data row10 col1\" > <a href=\"https://doi.org/10.1093/ije/dyz073\" rel=\"noopener noreferrer\" target=\"_blank\">10.1093/ije/dyz073</a></td>\n",
" </tr>\n",
" <tr>\n",
" <td id=\"T_46cbe_row11_col0\" class=\"data row11 col0\" >LPS Homepage</td>\n",
" <td id=\"T_46cbe_row11_col1\" class=\"data row11 col1\" ><p><a href=\"https://exceed.org.uk/about/\">exceed.org.uk</a></p></td>\n",
" </tr>\n",
" <tr>\n",
" <td id=\"T_46cbe_row12_col0\" class=\"data row12 col0\" >Build a Data Request</td>\n",
" <td id=\"T_46cbe_row12_col1\" class=\"data row12 col1\" > <a href=\"https://explore.ukllc.ac.uk/\" rel=\"noopener noreferrer\" target=\"_blank\">https://explore.ukllc.ac.uk/</a></td>\n",
" </tr>\n",
" </tbody>\n",
"</table>\n"
],
"text/plain": [
"<pandas.io.formats.style.Styler at 0x194c51a97f0>"
]
},
"execution_count": 3,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"ss.info_table()"
]
},
{
"cell_type": "markdown",
"id": "9a109a99",
"metadata": {},
"source": [
"## 2. Linkage Rates"
]
},
{
"cell_type": "code",
"execution_count": 4,
"id": "12b6c59e",
"metadata": {
"execution": {
"iopub.execute_input": "2025-07-28T18:43:39.848377Z",
"iopub.status.busy": "2025-07-28T18:43:39.848377Z",
"iopub.status.idle": "2025-07-28T18:43:40.433260Z",
"shell.execute_reply": "2025-07-28T18:43:40.430377Z"
},
"tags": [
"remove-input"
]
},
"outputs": [
{
"data": {
"application/javascript": "'use strict';\n(function(root) {\n function now() {\n return new Date();\n }\n\n const force = true;\n\n if (typeof root._bokeh_onload_callbacks === \"undefined\" || force === true) {\n root._bokeh_onload_callbacks = [];\n root._bokeh_is_loading = undefined;\n }\n\nconst JS_MIME_TYPE = 'application/javascript';\n const HTML_MIME_TYPE = 'text/html';\n const EXEC_MIME_TYPE = 'application/vnd.bokehjs_exec.v0+json';\n const CLASS_NAME = 'output_bokeh rendered_html';\n\n /**\n * Render data to the DOM node\n */\n function render(props, node) {\n const script = document.createElement(\"script\");\n node.appendChild(script);\n }\n\n /**\n * Handle when an output is cleared or removed\n */\n function handleClearOutput(event, handle) {\n function drop(id) {\n const view = Bokeh.index.get_by_id(id)\n if (view != null) {\n view.model.document.clear()\n Bokeh.index.delete(view)\n }\n }\n\n const cell = handle.cell;\n\n const id = cell.output_area._bokeh_element_id;\n const server_id = cell.output_area._bokeh_server_id;\n\n // Clean up Bokeh references\n if (id != null) {\n drop(id)\n }\n\n if (server_id !== undefined) {\n // Clean up Bokeh references\n const cmd_clean = \"from bokeh.io.state import curstate; print(curstate().uuid_to_server['\" + server_id + \"'].get_sessions()[0].document.roots[0]._id)\";\n cell.notebook.kernel.execute(cmd_clean, {\n iopub: {\n output: function(msg) {\n const id = msg.content.text.trim()\n drop(id)\n }\n }\n });\n // Destroy server and session\n const cmd_destroy = \"import bokeh.io.notebook as ion; ion.destroy_server('\" + server_id + \"')\";\n cell.notebook.kernel.execute(cmd_destroy);\n }\n }\n\n /**\n * Handle when a new output is added\n */\n function handleAddOutput(event, handle) {\n const output_area = handle.output_area;\n const output = handle.output;\n\n // limit handleAddOutput to display_data with EXEC_MIME_TYPE content only\n if ((output.output_type != \"display_data\") || (!Object.prototype.hasOwnProperty.call(output.data, EXEC_MIME_TYPE))) {\n return\n }\n\n const toinsert = output_area.element.find(\".\" + CLASS_NAME.split(' ')[0]);\n\n if (output.metadata[EXEC_MIME_TYPE][\"id\"] !== undefined) {\n toinsert[toinsert.length - 1].firstChild.textContent = output.data[JS_MIME_TYPE];\n // store reference to embed id on output_area\n output_area._bokeh_element_id = output.metadata[EXEC_MIME_TYPE][\"id\"];\n }\n if (output.metadata[EXEC_MIME_TYPE][\"server_id\"] !== undefined) {\n const bk_div = document.createElement(\"div\");\n bk_div.innerHTML = output.data[HTML_MIME_TYPE];\n const script_attrs = bk_div.children[0].attributes;\n for (let i = 0; i < script_attrs.length; i++) {\n toinsert[toinsert.length - 1].firstChild.setAttribute(script_attrs[i].name, script_attrs[i].value);\n toinsert[toinsert.length - 1].firstChild.textContent = bk_div.children[0].textContent\n }\n // store reference to server id on output_area\n output_area._bokeh_server_id = output.metadata[EXEC_MIME_TYPE][\"server_id\"];\n }\n }\n\n function register_renderer(events, OutputArea) {\n\n function append_mime(data, metadata, element) {\n // create a DOM node to render to\n const toinsert = this.create_output_subarea(\n metadata,\n CLASS_NAME,\n EXEC_MIME_TYPE\n );\n this.keyboard_manager.register_events(toinsert);\n // Render to node\n const props = {data: data, metadata: metadata[EXEC_MIME_TYPE]};\n render(props, toinsert[toinsert.length - 1]);\n element.append(toinsert);\n return toinsert\n }\n\n /* Handle when an output is cleared or removed */\n events.on('clear_output.CodeCell', handleClearOutput);\n events.on('delete.Cell', handleClearOutput);\n\n /* Handle when a new output is added */\n events.on('output_added.OutputArea', handleAddOutput);\n\n /**\n * Register the mime type and append_mime function with output_area\n */\n OutputArea.prototype.register_mime_type(EXEC_MIME_TYPE, append_mime, {\n /* Is output safe? */\n safe: true,\n /* Index of renderer in `output_area.display_order` */\n index: 0\n });\n }\n\n // register the mime type if in Jupyter Notebook environment and previously unregistered\n if (root.Jupyter !== undefined) {\n const events = require('base/js/events');\n const OutputArea = require('notebook/js/outputarea').OutputArea;\n\n if (OutputArea.prototype.mime_types().indexOf(EXEC_MIME_TYPE) == -1) {\n register_renderer(events, OutputArea);\n }\n }\n if (typeof (root._bokeh_timeout) === \"undefined\" || force === true) {\n root._bokeh_timeout = Date.now() + 5000;\n root._bokeh_failed_load = false;\n }\n\n const NB_LOAD_WARNING = {'data': {'text/html':\n \"<div style='background-color: #fdd'>\\n\"+\n \"<p>\\n\"+\n \"BokehJS does not appear to have successfully loaded. If loading BokehJS from CDN, this \\n\"+\n \"may be due to a slow or bad network connection. Possible fixes:\\n\"+\n \"</p>\\n\"+\n \"<ul>\\n\"+\n \"<li>re-rerun `output_notebook()` to attempt to load from CDN again, or</li>\\n\"+\n \"<li>use INLINE resources instead, as so:</li>\\n\"+\n \"</ul>\\n\"+\n \"<code>\\n\"+\n \"from bokeh.resources import INLINE\\n\"+\n \"output_notebook(resources=INLINE)\\n\"+\n \"</code>\\n\"+\n \"</div>\"}};\n\n function display_loaded(error = null) {\n const el = document.getElementById(null);\n if (el != null) {\n const html = (() => {\n if (typeof root.Bokeh === \"undefined\") {\n if (error == null) {\n return \"BokehJS is loading ...\";\n } else {\n return \"BokehJS failed to load.\";\n }\n } else {\n const prefix = `BokehJS ${root.Bokeh.version}`;\n if (error == null) {\n return `${prefix} successfully loaded.`;\n } else {\n return `${prefix} <b>encountered errors</b> while loading and may not function as expected.`;\n }\n }\n })();\n el.innerHTML = html;\n\n if (error != null) {\n const wrapper = document.createElement(\"div\");\n wrapper.style.overflow = \"auto\";\n wrapper.style.height = \"5em\";\n wrapper.style.resize = \"vertical\";\n const content = document.createElement(\"div\");\n content.style.fontFamily = \"monospace\";\n content.style.whiteSpace = \"pre-wrap\";\n content.style.backgroundColor = \"rgb(255, 221, 221)\";\n content.textContent = error.stack ?? error.toString();\n wrapper.append(content);\n el.append(wrapper);\n }\n } else if (Date.now() < root._bokeh_timeout) {\n setTimeout(() => display_loaded(error), 100);\n }\n }\n\n function run_callbacks() {\n try {\n root._bokeh_onload_callbacks.forEach(function(callback) {\n if (callback != null)\n callback();\n });\n } finally {\n delete root._bokeh_onload_callbacks\n }\n console.debug(\"Bokeh: all callbacks have finished\");\n }\n\n function load_libs(css_urls, js_urls, callback) {\n if (css_urls == null) css_urls = [];\n if (js_urls == null) js_urls = [];\n\n root._bokeh_onload_callbacks.push(callback);\n if (root._bokeh_is_loading > 0) {\n console.debug(\"Bokeh: BokehJS is being loaded, scheduling callback at\", now());\n return null;\n }\n if (js_urls == null || js_urls.length === 0) {\n run_callbacks();\n return null;\n }\n console.debug(\"Bokeh: BokehJS not loaded, scheduling load and callback at\", now());\n root._bokeh_is_loading = css_urls.length + js_urls.length;\n\n function on_load() {\n root._bokeh_is_loading--;\n if (root._bokeh_is_loading === 0) {\n console.debug(\"Bokeh: all BokehJS libraries/stylesheets loaded\");\n run_callbacks()\n }\n }\n\n function on_error(url) {\n console.error(\"failed to load \" + url);\n }\n\n for (let i = 0; i < css_urls.length; i++) {\n const url = css_urls[i];\n const element = document.createElement(\"link\");\n element.onload = on_load;\n element.onerror = on_error.bind(null, url);\n element.rel = \"stylesheet\";\n element.type = \"text/css\";\n element.href = url;\n console.debug(\"Bokeh: injecting link tag for BokehJS stylesheet: \", url);\n document.body.appendChild(element);\n }\n\n for (let i = 0; i < js_urls.length; i++) {\n const url = js_urls[i];\n const element = document.createElement('script');\n element.onload = on_load;\n element.onerror = on_error.bind(null, url);\n element.async = false;\n element.src = url;\n console.debug(\"Bokeh: injecting script tag for BokehJS library: \", url);\n document.head.appendChild(element);\n }\n };\n\n function inject_raw_css(css) {\n const element = document.createElement(\"style\");\n element.appendChild(document.createTextNode(css));\n document.body.appendChild(element);\n }\n\n const js_urls = [\"https://cdn.bokeh.org/bokeh/release/bokeh-3.7.2.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-gl-3.7.2.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-widgets-3.7.2.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-tables-3.7.2.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-mathjax-3.7.2.min.js\"];\n const css_urls = [];\n\n const inline_js = [ function(Bokeh) {\n Bokeh.set_log_level(\"info\");\n },\nfunction(Bokeh) {\n }\n ];\n\n function run_inline_js() {\n if (root.Bokeh !== undefined || force === true) {\n try {\n for (let i = 0; i < inline_js.length; i++) {\n inline_js[i].call(root, root.Bokeh);\n }\n\n } catch (error) {throw error;\n }} else if (Date.now() < root._bokeh_timeout) {\n setTimeout(run_inline_js, 100);\n } else if (!root._bokeh_failed_load) {\n console.log(\"Bokeh: BokehJS failed to load within specified timeout.\");\n root._bokeh_failed_load = true;\n } else if (force !== true) {\n const cell = $(document.getElementById(null)).parents('.cell').data().cell;\n cell.output_area.append_execute_result(NB_LOAD_WARNING)\n }\n }\n\n if (root._bokeh_is_loading === 0) {\n console.debug(\"Bokeh: BokehJS loaded, going straight to plotting\");\n run_inline_js();\n } else {\n load_libs(css_urls, js_urls, function() {\n console.debug(\"Bokeh: BokehJS plotting callback run at\", now());\n run_inline_js();\n });\n }\n}(window));",
"application/vnd.bokehjs_load.v0+json": ""
},
"metadata": {},
"output_type": "display_data"
},
{
"data": {
"text/html": [
"\n",
" <div id=\"e8085401-5b5e-4e04-8956-bf88d8787814\" data-root-id=\"p1001\" style=\"display: contents;\"></div>\n"
]
},
"metadata": {},
"output_type": "display_data"
},
{
"data": {
"application/javascript": "(function(root) {\n function embed_document(root) {\n const docs_json = {\"a07060fc-9176-4d4f-8b91-b56f40e51327\":{\"version\":\"3.7.2\",\"title\":\"Bokeh Application\",\"roots\":[{\"type\":\"object\",\"name\":\"Figure\",\"id\":\"p1001\",\"attributes\":{\"height\":400,\"x_range\":{\"type\":\"object\",\"name\":\"FactorRange\",\"id\":\"p1011\",\"attributes\":{\"factors\":[\"NHS England\",\"NHS Wales\"]}},\"y_range\":{\"type\":\"object\",\"name\":\"DataRange1d\",\"id\":\"p1003\",\"attributes\":{\"start\":0,\"end\":100}},\"x_scale\":{\"type\":\"object\",\"name\":\"CategoricalScale\",\"id\":\"p1012\"},\"y_scale\":{\"type\":\"object\",\"name\":\"LinearScale\",\"id\":\"p1013\"},\"title\":{\"type\":\"object\",\"name\":\"Title\",\"id\":\"p1004\",\"attributes\":{\"text\":\"Linkage rates (%) of EXCEED participants to linked Datasets for Freeze 13\"}},\"renderers\":[{\"type\":\"object\",\"name\":\"GlyphRenderer\",\"id\":\"p1046\",\"attributes\":{\"data_source\":{\"type\":\"object\",\"name\":\"ColumnDataSource\",\"id\":\"p1037\",\"attributes\":{\"selected\":{\"type\":\"object\",\"name\":\"Selection\",\"id\":\"p1038\",\"attributes\":{\"indices\":[],\"line_indices\":[]}},\"selection_policy\":{\"type\":\"object\",\"name\":\"UnionRenderers\",\"id\":\"p1039\"},\"data\":{\"type\":\"map\",\"entries\":[[\"link_series\",[\"NHS England\",\"NHS Wales\"]],[\"link_pct\",[85.27667984189723,0]],[\"n_perm\",[11132,11132]],[\"n_sent\",[11149,0]],[\"n_linked\",[9493,0]]]}}},\"view\":{\"type\":\"object\",\"name\":\"CDSView\",\"id\":\"p1047\",\"attributes\":{\"filter\":{\"type\":\"object\",\"name\":\"AllIndices\",\"id\":\"p1048\"}}},\"glyph\":{\"type\":\"object\",\"name\":\"VBar\",\"id\":\"p1043\",\"attributes\":{\"x\":{\"type\":\"field\",\"field\":\"link_series\"},\"width\":{\"type\":\"value\",\"value\":0.8},\"top\":{\"type\":\"field\",\"field\":\"link_pct\"},\"line_color\":{\"type\":\"value\",\"value\":\"#1f77b4\"},\"fill_color\":{\"type\":\"value\",\"value\":\"#1f77b4\"}}},\"nonselection_glyph\":{\"type\":\"object\",\"name\":\"VBar\",\"id\":\"p1044\",\"attributes\":{\"x\":{\"type\":\"field\",\"field\":\"link_series\"},\"width\":{\"type\":\"value\",\"value\":0.8},\"top\":{\"type\":\"field\",\"field\":\"link_pct\"},\"line_color\":{\"type\":\"value\",\"value\":\"#1f77b4\"},\"line_alpha\":{\"type\":\"value\",\"value\":0.1},\"fill_color\":{\"type\":\"value\",\"value\":\"#1f77b4\"},\"fill_alpha\":{\"type\":\"value\",\"value\":0.1},\"hatch_alpha\":{\"type\":\"value\",\"value\":0.1}}},\"muted_glyph\":{\"type\":\"object\",\"name\":\"VBar\",\"id\":\"p1045\",\"attributes\":{\"x\":{\"type\":\"field\",\"field\":\"link_series\"},\"width\":{\"type\":\"value\",\"value\":0.8},\"top\":{\"type\":\"field\",\"field\":\"link_pct\"},\"line_color\":{\"type\":\"value\",\"value\":\"#1f77b4\"},\"line_alpha\":{\"type\":\"value\",\"value\":0.2},\"fill_color\":{\"type\":\"value\",\"value\":\"#1f77b4\"},\"fill_alpha\":{\"type\":\"value\",\"value\":0.2},\"hatch_alpha\":{\"type\":\"value\",\"value\":0.2}}}}}],\"toolbar\":{\"type\":\"object\",\"name\":\"Toolbar\",\"id\":\"p1010\",\"attributes\":{\"tools\":[{\"type\":\"object\",\"name\":\"PanTool\",\"id\":\"p1024\"},{\"type\":\"object\",\"name\":\"WheelZoomTool\",\"id\":\"p1025\",\"attributes\":{\"renderers\":\"auto\"}},{\"type\":\"object\",\"name\":\"BoxZoomTool\",\"id\":\"p1026\",\"attributes\":{\"dimensions\":\"both\",\"overlay\":{\"type\":\"object\",\"name\":\"BoxAnnotation\",\"id\":\"p1027\",\"attributes\":{\"syncable\":false,\"line_color\":\"black\",\"line_alpha\":1.0,\"line_width\":2,\"line_dash\":[4,4],\"fill_color\":\"lightgrey\",\"fill_alpha\":0.5,\"level\":\"overlay\",\"visible\":false,\"left\":{\"type\":\"number\",\"value\":\"nan\"},\"right\":{\"type\":\"number\",\"value\":\"nan\"},\"top\":{\"type\":\"number\",\"value\":\"nan\"},\"bottom\":{\"type\":\"number\",\"value\":\"nan\"},\"left_units\":\"canvas\",\"right_units\":\"canvas\",\"top_units\":\"canvas\",\"bottom_units\":\"canvas\",\"handles\":{\"type\":\"object\",\"name\":\"BoxInteractionHandles\",\"id\":\"p1033\",\"attributes\":{\"all\":{\"type\":\"object\",\"name\":\"AreaVisuals\",\"id\":\"p1032\",\"attributes\":{\"fill_color\":\"white\",\"hover_fill_color\":\"lightgray\"}}}}}}}},{\"type\":\"object\",\"name\":\"SaveTool\",\"id\":\"p1034\"},{\"type\":\"object\",\"name\":\"ResetTool\",\"id\":\"p1035\"},{\"type\":\"object\",\"name\":\"HelpTool\",\"id\":\"p1036\"},{\"type\":\"object\",\"name\":\"HoverTool\",\"id\":\"p1049\",\"attributes\":{\"renderers\":\"auto\",\"tooltips\":[[\"Linked Participants\",\"@n_linked\"],[\"Participants sent to UK LLC\",\"@n_sent\"],[\"Participants with linkage permission\",\"@n_perm\"]]}}]}},\"left\":[{\"type\":\"object\",\"name\":\"LinearAxis\",\"id\":\"p1019\",\"attributes\":{\"ticker\":{\"type\":\"object\",\"name\":\"BasicTicker\",\"id\":\"p1020\",\"attributes\":{\"mantissas\":[1,2,5]}},\"formatter\":{\"type\":\"object\",\"name\":\"BasicTickFormatter\",\"id\":\"p1021\"},\"major_label_policy\":{\"type\":\"object\",\"name\":\"AllLabels\",\"id\":\"p1022\"}}}],\"below\":[{\"type\":\"object\",\"name\":\"CategoricalAxis\",\"id\":\"p1014\",\"attributes\":{\"ticker\":{\"type\":\"object\",\"name\":\"CategoricalTicker\",\"id\":\"p1015\"},\"formatter\":{\"type\":\"object\",\"name\":\"CategoricalTickFormatter\",\"id\":\"p1016\"},\"major_label_orientation\":0.7853981633974483,\"major_label_policy\":{\"type\":\"object\",\"name\":\"AllLabels\",\"id\":\"p1017\"}}}],\"center\":[{\"type\":\"object\",\"name\":\"Grid\",\"id\":\"p1018\",\"attributes\":{\"axis\":{\"id\":\"p1014\"}}},{\"type\":\"object\",\"name\":\"Grid\",\"id\":\"p1023\",\"attributes\":{\"dimension\":1,\"axis\":{\"id\":\"p1019\"}}}]}}]}};\n const render_items = [{\"docid\":\"a07060fc-9176-4d4f-8b91-b56f40e51327\",\"roots\":{\"p1001\":\"e8085401-5b5e-4e04-8956-bf88d8787814\"},\"root_ids\":[\"p1001\"]}];\n void root.Bokeh.embed.embed_items_notebook(docs_json, render_items);\n }\n if (root.Bokeh !== undefined) {\n embed_document(root);\n } else {\n let attempts = 0;\n const timer = setInterval(function(root) {\n if (root.Bokeh !== undefined) {\n clearInterval(timer);\n embed_document(root);\n } else {\n attempts++;\n if (attempts > 100) {\n clearInterval(timer);\n console.log(\"Bokeh: ERROR: Unable to run BokehJS code because BokehJS library is missing\");\n }\n }\n }, 10, root)\n }\n})(window);",
"application/vnd.bokehjs_exec.v0+json": ""
},
"metadata": {
"application/vnd.bokehjs_exec.v0+json": {
"id": "p1001"
}
},
"output_type": "display_data"
}
],
"source": [
"ss.linkages_plot()"
]
},
{
"cell_type": "markdown",
"id": "febc9211",
"metadata": {},
"source": [
"## 3. Documentation"
]
},
{
"cell_type": "code",
"execution_count": 5,
"id": "7b5a0007",
"metadata": {
"execution": {
"iopub.execute_input": "2025-07-28T18:43:40.444357Z",
"iopub.status.busy": "2025-07-28T18:43:40.444357Z",
"iopub.status.idle": "2025-07-28T18:43:40.462719Z",
"shell.execute_reply": "2025-07-28T18:43:40.460701Z"
},
"tags": [
"remove-input"
]
},
"outputs": [
{
"data": {
"text/markdown": [
"We are currently building a documentation storage system which will host useful documents related to datasets and data owners. We will surface these documents on Guidebook."
],
"text/plain": [
"<IPython.core.display.Markdown object>"
]
},
"metadata": {},
"output_type": "display_data"
}
],
"source": [
"ss.documentation()"
]
}
],
"metadata": {
"kernelspec": {
"display_name": "jupbook",
"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": "3.13.2"
}
},
"nbformat": 4,
"nbformat_minor": 5
}