{
 "cells": [
  {
   "cell_type": "markdown",
   "id": "3fe9124c-7364-44b4-90ba-30f2759ae143",
   "metadata": {},
   "source": [
    "# Test GDSL courses"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "efb47674-3ee0-4197-9910-f46ba73c4ad9",
   "metadata": {},
   "source": [
    "## Download"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "53b22e85-7a06-4105-87f5-219348bae97a",
   "metadata": {},
   "source": [
    "- [Web Mapping & Analysis](https://github.com/GDSL-UL/wma)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "30023233-7506-4171-abad-255f4e53a131",
   "metadata": {},
   "outputs": [],
   "source": [
    "! wget https://github.com/GDSL-UL/wma/archive/refs/heads/main.zip \\\n",
    "    && unzip main.zip \\\n",
    "    && rm main.zip"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "ba2eef6e-d179-4664-9f3f-bb9f59aa4bf7",
   "metadata": {},
   "source": [
    "- [Spatial Modelling for Data Scientists](https://github.com/GDSL-UL/san)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "c86a2322-605a-4c46-a28e-1178c329524a",
   "metadata": {},
   "outputs": [],
   "source": [
    "! wget https://github.com/GDSL-UL/san/archive/refs/heads/master.zip \\\n",
    "    && unzip master.zip \\\n",
    "    && rm master.zip"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "7028e018-f847-41f0-ac29-34862311addb",
   "metadata": {},
   "source": [
    "- [R for Population Science](https://github.com/fcorowe/r4ps)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "681e8b3c-f5bf-4a0e-809e-0bf0ab28589f",
   "metadata": {},
   "outputs": [],
   "source": [
    "! wget https://github.com/fcorowe/r4ps/archive/refs/heads/main.zip \\\n",
    "    && unzip main.zip \\\n",
    "    && rm main.zip"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "5846b86e-3416-4b60-965c-ca5258d611c1",
   "metadata": {},
   "source": [
    "## Test SMDS"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "id": "75f1ad6d-6be9-4d62-aa64-fc0970e770ae",
   "metadata": {
    "collapsed": true,
    "jupyter": {
     "outputs_hidden": true
    },
    "tags": []
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "[ 1/13] index.qmd\u001b[39m\u001b[22m\n",
      "[ 2/13] 01-overview.qmd\u001b[39m\u001b[22m\n",
      "\u001b[31m\n",
      "\n",
      "processing file: 01-overview.qmd\n",
      "                                                                                                            \n",
      "\u001b[31moutput file: 01-overview.knit.md\n",
      "\n",
      "\u001b[39m\u001b[31m\n",
      "\n",
      "processing file: 01-overview.qmd\n",
      "                                                                                                            \n",
      "\u001b[31moutput file: 01-overview.knit.md\n",
      "\n",
      "[ 3/13] 02-spatial_data.qmd\u001b[39m\u001b[22m\n",
      "\u001b[31m\n",
      "\n",
      "processing file: 02-spatial_data.qmd\n",
      "                                                                                                            \n",
      "\u001b[31moutput file: 02-spatial_data.knit.md\n",
      "\n",
      "\u001b[39m\u001b[31m\n",
      "\n",
      "processing file: 02-spatial_data.qmd\n",
      "                                                                                                            \n",
      "\u001b[31moutput file: 02-spatial_data.knit.md\n",
      "\n",
      "[ 4/13] 03-data-wrangling.qmd\u001b[39m\u001b[22m\n",
      "\u001b[31m\n",
      "\n",
      "processing file: 03-data-wrangling.qmd\n",
      "  |.                                                  |   2% (unnamed-chunk-1) \u001b[31mSystem has not been booted with systemd as init system (PID 1). Can't operate.\n",
      "Failed to connect to bus: Host is down\n",
      "                                                                                                             \n",
      "\u001b[31moutput file: 03-data-wrangling.knit.md\n",
      "\n",
      "\u001b[39m\u001b[31m\n",
      "\n",
      "processing file: 03-data-wrangling.qmd\n",
      "  |.                                                  |   2% (unnamed-chunk-1) \u001b[31mSystem has not been booted with systemd as init system (PID 1). Can't operate.\n",
      "Failed to connect to bus: Host is down\n",
      "                                                                                                             \n",
      "\u001b[31moutput file: 03-data-wrangling.knit.md\n",
      "\n",
      "[ 5/13] 04-points.qmd\u001b[39m\u001b[22m\n",
      "\u001b[31m\n",
      "\n",
      "processing file: 04-points.qmd\n",
      "                                                                                                             \n",
      "\u001b[31moutput file: 04-points.knit.md\n",
      "\n",
      "\u001b[39m\u001b[31m\n",
      "\n",
      "processing file: 04-points.qmd\n",
      "                                                                                                             \n",
      "\u001b[31moutput file: 04-points.knit.md\n",
      "\n",
      "[ 6/13] 05-flows.qmd\u001b[39m\u001b[22m\n",
      "\u001b[31m\n",
      "\n",
      "processing file: 05-flows.qmd\n",
      "  |.                                                  |   3% (unnamed-chunk-1) \u001b[31mSystem has not been booted with systemd as init system (PID 1). Can't operate.\n",
      "\u001b[39m\u001b[31mFailed to connect to bus: Host is down\n",
      "                                                                                                             \n",
      "\u001b[31moutput file: 05-flows.knit.md\n",
      "\n",
      "\u001b[39m\u001b[31m\n",
      "\n",
      "processing file: 05-flows.qmd\n",
      "  |.                                                  |   3% (unnamed-chunk-1) \u001b[31mSystem has not been booted with systemd as init system (PID 1). Can't operate.\n",
      "Failed to connect to bus: Host is down\n",
      "                                                                                                             \n",
      "\u001b[31moutput file: 05-flows.knit.md\n",
      "\n",
      "[ 7/13] 06-spatial-econometrics.qmd\u001b[39m\u001b[22m\n",
      "\u001b[31m\n",
      "\n",
      "processing file: 06-spatial-econometrics.qmd\n",
      "                                                                                                             \n",
      "\u001b[31moutput file: 06-spatial-econometrics.knit.md\n",
      "\n",
      "\u001b[39m\u001b[31m\n",
      "\n",
      "processing file: 06-spatial-econometrics.qmd\n",
      "                                                                                                             \n",
      "\u001b[31moutput file: 06-spatial-econometrics.knit.md\n",
      "\n",
      "[ 8/13] 07-multilevel-01.qmd\u001b[39m\u001b[22m\n",
      "\u001b[31m\n",
      "\n",
      "processing file: 07-multilevel-01.qmd\n",
      "  |.                                                  |   3% (unnamed-chunk-1) \u001b[31mSystem has not been booted with systemd as init system (PID 1). Can't operate.\n",
      "Failed to connect to bus: Host is down\n",
      "                                                                                                             \n",
      "\u001b[31moutput file: 07-multilevel-01.knit.md\n",
      "\n",
      "\u001b[39m\u001b[31m\n",
      "\n",
      "processing file: 07-multilevel-01.qmd\n",
      "  |.                                                  |   3% (unnamed-chunk-1) \u001b[31mSystem has not been booted with systemd as init system (PID 1). Can't operate.\n",
      "Failed to connect to bus: Host is down\n",
      "                                                                                                             \n",
      "\u001b[31moutput file: 07-multilevel-01.knit.md\n",
      "\n",
      "[ 9/13] 08-multilevel-02.qmd\u001b[39m\u001b[22m\n",
      "\u001b[31m\n",
      "\n",
      "processing file: 08-multilevel-02.qmd\n",
      "  |...                                                |   6% (unnamed-chunk-1) \u001b[31mSystem has not been booted with systemd as init system (PID 1). Can't operate.\n",
      "Failed to connect to bus: Host is down\n",
      "                                                                                                             \n",
      "\u001b[31moutput file: 08-multilevel-02.knit.md\n",
      "\n",
      "\u001b[39m\u001b[31m\n",
      "\n",
      "processing file: 08-multilevel-02.qmd\n",
      "  |...                                                |   6% (unnamed-chunk-1) \u001b[31mSystem has not been booted with systemd as init system (PID 1). Can't operate.\n",
      "Failed to connect to bus: Host is down\n",
      "                                                                                                             \n",
      "\u001b[31moutput file: 08-multilevel-02.knit.md\n",
      "\n",
      "[10/13] 09-gwr.qmd\u001b[39m\u001b[22m\n",
      "\u001b[31m\n",
      "\n",
      "processing file: 09-gwr.qmd\n",
      "  |...                                                |   5% (unnamed-chunk-1) \u001b[31mSystem has not been booted with systemd as init system (PID 1). Can't operate.\n",
      "Failed to connect to bus: Host is down\n",
      "                                                                                                             \n",
      "\u001b[31moutput file: 09-gwr.knit.md\n",
      "\n",
      "\u001b[39m\u001b[31m\n",
      "\n",
      "processing file: 09-gwr.qmd\n",
      "  |...                                                |   5% (unnamed-chunk-1) \u001b[31mSystem has not been booted with systemd as init system (PID 1). Can't operate.\n",
      "Failed to connect to bus: Host is down\n",
      "                                                                                                             \n",
      "\u001b[31moutput file: 09-gwr.knit.md\n",
      "\n",
      "[11/13] 10-st_analysis.qmd\u001b[39m\u001b[22m\n",
      "\u001b[31m\n",
      "\n",
      "processing file: 10-st_analysis.qmd\n",
      "  |..                                                 |   3% (unnamed-chunk-1) \u001b[31mSystem has not been booted with systemd as init system (PID 1). Can't operate.\n",
      "Failed to connect to bus: Host is down\n",
      "                                                                                                             \n",
      "\u001b[31moutput file: 10-st_analysis.knit.md\n",
      "\n",
      "\u001b[39m\u001b[31m\n",
      "\n",
      "processing file: 10-st_analysis.qmd\n",
      "  |..                                                 |   3% (unnamed-chunk-1) \u001b[31mSystem has not been booted with systemd as init system (PID 1). Can't operate.\n",
      "Failed to connect to bus: Host is down\n",
      "                                                                                                             \n",
      "\u001b[31moutput file: 10-st_analysis.knit.md\n",
      "\n",
      "[12/13] 11-datasets.qmd\u001b[39m\u001b[22m\n",
      "\u001b[31m\n",
      "\n",
      "processing file: 11-datasets.qmd\n",
      "                                                                                                            \n",
      "\u001b[31moutput file: 11-datasets.knit.md\n",
      "\n",
      "\u001b[39m\u001b[31m\n",
      "\n",
      "processing file: 11-datasets.qmd\n",
      "                                                                                                            \n",
      "\u001b[31moutput file: 11-datasets.knit.md\n",
      "\n",
      "[13/13] references.qmd\u001b[39m\u001b[22m\n",
      "\n",
      "\u001b[1mpandoc \u001b[22m\n",
      "  to: latex\n",
      "  output-file: index.tex\n",
      "  standalone: true\n",
      "  toc: true\n",
      "  number-sections: true\n",
      "  top-level-division: chapter\n",
      "  pdf-engine: xelatex\n",
      "  variables:\n",
      "    graphics: true\n",
      "    tables: true\n",
      "  default-image-extension: pdf\n",
      "  \n",
      "\u001b[1mmetadata\u001b[22m\n",
      "  crossref:\n",
      "    chapters: true\n",
      "  documentclass: scrreprt\n",
      "  papersize: letter\n",
      "  classoption:\n",
      "    - DIV=11\n",
      "    - numbers=noendperiod\n",
      "  header-includes:\n",
      "    - '\\KOMAoption{captions}{tableheading}'\n",
      "  block-headings: true\n",
      "  bibliography:\n",
      "    - references.bib\n",
      "  editor: visual\n",
      "  title: Spatial Modelling for Data Scientists\n",
      "  author: 'Francisco Rowe, Dani Arribas-Bel'\n",
      "  date: '2023-04-05T00:00:00+00:00'\n",
      "  \n",
      "\u001b[1mrunning xelatex - 1\u001b[22m\n",
      "  This is XeTeX, Version 3.141592653-2.6-0.999993 (TeX Live 2022/dev/Debian) (preloaded format=xelatex)\n",
      "   restricted \\write18 enabled.\n",
      "  entering extended mode\n",
      "  \n",
      "\u001b[1mrunning xelatex - 2\u001b[22m\n",
      "  This is XeTeX, Version 3.141592653-2.6-0.999993 (TeX Live 2022/dev/Debian) (preloaded format=xelatex)\n",
      "   restricted \\write18 enabled.\n",
      "  entering extended mode\n",
      "  \n",
      "\u001b[1mrunning xelatex - 3\u001b[22m\n",
      "  This is XeTeX, Version 3.141592653-2.6-0.999993 (TeX Live 2022/dev/Debian) (preloaded format=xelatex)\n",
      "   restricted \\write18 enabled.\n",
      "  entering extended mode\n",
      "  \n",
      "\n",
      "Output created: docs/index.html\n",
      "\n"
     ]
    }
   ],
   "source": [
    "! cd san-master \\\n",
    "    && quarto render"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "32588fdc-6f06-4c30-a6a2-69669eb9d2d3",
   "metadata": {},
   "source": [
    "## Test WMA"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "c8ae6719-8c87-4461-9725-70cac3603452",
   "metadata": {
    "tags": []
   },
   "outputs": [],
   "source": [
    "! cd wma-main \\\n",
    "    && quarto render"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "31d820af-ec00-4acd-9e56-eb070be9da76",
   "metadata": {},
   "source": [
    "## Test R4PS"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "id": "825c7d15-2cc1-4fd1-914d-7a2759da3e2c",
   "metadata": {
    "collapsed": true,
    "jupyter": {
     "outputs_hidden": true
    },
    "tags": []
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "[ 1/13] index.qmd\u001b[39m\u001b[22m\n",
      "[ 2/13] intro.qmd\u001b[39m\u001b[22m\n",
      "[ 3/13] intro-population-science.qmd\u001b[39m\u001b[22m\n",
      "[ 4/13] geodemographics.qmd\u001b[39m\u001b[22m\n",
      "\u001b[31m\n",
      "\n",
      "processing file: geodemographics.qmd\n",
      "                                                                                                             \n",
      "\u001b[31moutput file: geodemographics.knit.md\n",
      "\n",
      "\u001b[39m\u001b[31m\n",
      "\n",
      "processing file: geodemographics.qmd\n",
      "                                                                                                             \n",
      "\u001b[31moutput file: geodemographics.knit.md\n",
      "\n",
      "[ 5/13] sequence-analysis.qmd\u001b[39m\u001b[22m\n",
      "\u001b[31m\n",
      "\n",
      "processing file: sequence-analysis.qmd\n",
      "  |...                                                |   6% (unnamed-chunk-2) \u001b[31mSystem has not been booted with systemd as init system (PID 1). Can't operate.\n",
      "Failed to connect to bus: Host is down\n",
      "                                                                                                             \n",
      "\u001b[31moutput file: sequence-analysis.knit.md\n",
      "\n",
      "\u001b[39m\u001b[31m\n",
      "\n",
      "processing file: sequence-analysis.qmd\n",
      "  |...                                                |   6% (unnamed-chunk-2) \u001b[31mSystem has not been booted with systemd as init system (PID 1). Can't operate.\n",
      "Failed to connect to bus: Host is down\n",
      "                                                                                                             \n",
      "\u001b[31moutput file: sequence-analysis.knit.md\n",
      "\n",
      "[ 6/13] network.qmd\u001b[39m\u001b[22m\n",
      "\u001b[31m\n",
      "\n",
      "processing file: network.qmd\n",
      "  |................                                   |  32% (unnamed-chunk-16)as_data_frame              package:igraph              R Documentation\n",
      "\n",
      "Creating igraph graphs from data frames or vice-versa\n",
      "\n",
      "Description:\n",
      "\n",
      "     This function creates an igraph graph from one or two data frames\n",
      "     containing the (symbolic) edge list and edge/vertex attributes.\n",
      "\n",
      "Usage:\n",
      "\n",
      "     as_data_frame(x, what = c(\"edges\", \"vertices\", \"both\"))\n",
      "     \n",
      "     graph_from_data_frame(d, directed = TRUE, vertices = NULL)\n",
      "     \n",
      "     from_data_frame(...)\n",
      "     \n",
      "Arguments:\n",
      "\n",
      "       x: An igraph object.\n",
      "\n",
      "    what: Character constant, whether to return info about vertices,\n",
      "          edges, or both. The default is 'edges'.\n",
      "\n",
      "       d: A data frame containing a symbolic edge list in the first two\n",
      "          columns. Additional columns are considered as edge\n",
      "          attributes.  Since version 0.7 this argument is coerced to a\n",
      "          data frame with 'as.data.frame'.\n",
      "\n",
      "directed: Logical scalar, whether or not to create a directed graph.\n",
      "\n",
      "vertices: A data frame with vertex metadata, or 'NULL'. See details\n",
      "          below. Since version 0.7 this argument is coerced to a data\n",
      "          frame with 'as.data.frame', if not 'NULL'.\n",
      "\n",
      "     ...: Passed to 'graph_from_data_frame()'.\n",
      "\n",
      "Details:\n",
      "\n",
      "     'graph_from_data_frame()' creates igraph graphs from one or two\n",
      "     data frames. It has two modes of operation, depending whether the\n",
      "     'vertices' argument is 'NULL' or not.\n",
      "\n",
      "     If 'vertices' is 'NULL', then the first two columns of 'd' are\n",
      "     used as a symbolic edge list and additional columns as edge\n",
      "     attributes. The names of the attributes are taken from the names\n",
      "     of the columns.\n",
      "\n",
      "     If 'vertices' is not 'NULL', then it must be a data frame giving\n",
      "     vertex metadata. The first column of 'vertices' is assumed to\n",
      "     contain symbolic vertex names, this will be added to the graphs as\n",
      "     the ''name'' vertex attribute. Other columns will be added as\n",
      "     additional vertex attributes. If 'vertices' is not 'NULL' then the\n",
      "     symbolic edge list given in 'd' is checked to contain only vertex\n",
      "     names listed in 'vertices'.\n",
      "\n",
      "     Typically, the data frames are exported from some spreadsheet\n",
      "     software like Excel and are imported into R via 'read.table()',\n",
      "     'read.delim()' or 'read.csv()'.\n",
      "\n",
      "     All edges in the data frame are included in the graph, which may\n",
      "     include multiple parallel edges and loops.\n",
      "\n",
      "     'as_data_frame()' converts the igraph graph into one or more data\n",
      "     frames, depending on the 'what' argument.\n",
      "\n",
      "     If the 'what' argument is 'edges' (the default), then the edges of\n",
      "     the graph and also the edge attributes are returned. The edges\n",
      "     will be in the first two columns, named 'from' and 'to'. (This\n",
      "     also denotes edge direction for directed graphs.)  For named\n",
      "     graphs, the vertex names will be included in these columns, for\n",
      "     other graphs, the numeric vertex ids. The edge attributes will be\n",
      "     in the other columns. It is not a good idea to have an edge\n",
      "     attribute named 'from' or 'to', because then the column named in\n",
      "     the data frame will not be unique. The edges are listed in the\n",
      "     order of their numeric ids.\n",
      "\n",
      "     If the 'what' argument is 'vertices', then vertex attributes are\n",
      "     returned. Vertices are listed in the order of their numeric vertex\n",
      "     ids.\n",
      "\n",
      "     If the 'what' argument is 'both', then both vertex and edge data\n",
      "     is returned, in a list with named entries 'vertices' and 'edges'.\n",
      "\n",
      "Value:\n",
      "\n",
      "     An igraph graph object for 'graph_from_data_frame()', and either a\n",
      "     data frame or a list of two data frames named 'edges' and\n",
      "     'vertices' for 'as.data.frame'.\n",
      "\n",
      "Note:\n",
      "\n",
      "     For 'graph_from_data_frame()' 'NA' elements in the first two\n",
      "     columns 'd' are replaced by the string \"NA\" before creating the\n",
      "     graph. This means that all 'NA's will correspond to a single\n",
      "     vertex.\n",
      "\n",
      "     'NA' elements in the first column of 'vertices' are also replaced\n",
      "     by the string \"NA\", but the rest of 'vertices' is not touched. In\n",
      "     other words, vertex names (=the first column) cannot be 'NA', but\n",
      "     other vertex attributes can.\n",
      "\n",
      "Author(s):\n",
      "\n",
      "     Gabor Csardi <mailto:csardi.gabor@gmail.com>\n",
      "\n",
      "See Also:\n",
      "\n",
      "     'graph_from_literal()' for another way to create graphs,\n",
      "     'read.table()' to read in tables from files.\n",
      "\n",
      "     Other conversion: 'as.directed()', 'as.matrix.igraph()',\n",
      "     'as_adj_list()', 'as_adjacency_matrix()', 'as_edgelist()',\n",
      "     'as_graphnel()', 'as_incidence_matrix()', 'as_long_data_frame()',\n",
      "     'graph_from_adj_list()', 'graph_from_graphnel()'\n",
      "\n",
      "Examples:\n",
      "\n",
      "     ## A simple example with a couple of actors\n",
      "     ## The typical case is that these tables are read in from files....\n",
      "     actors <- data.frame(\n",
      "       name = c(\n",
      "         \"Alice\", \"Bob\", \"Cecil\", \"David\",\n",
      "         \"Esmeralda\"\n",
      "       ),\n",
      "       age = c(48, 33, 45, 34, 21),\n",
      "       gender = c(\"F\", \"M\", \"F\", \"M\", \"F\")\n",
      "     )\n",
      "     relations <- data.frame(\n",
      "       from = c(\n",
      "         \"Bob\", \"Cecil\", \"Cecil\", \"David\",\n",
      "         \"David\", \"Esmeralda\"\n",
      "       ),\n",
      "       to = c(\"Alice\", \"Bob\", \"Alice\", \"Alice\", \"Bob\", \"Alice\"),\n",
      "       same.dept = c(FALSE, FALSE, TRUE, FALSE, FALSE, TRUE),\n",
      "       friendship = c(4, 5, 5, 2, 1, 1), advice = c(4, 5, 5, 4, 2, 3)\n",
      "     )\n",
      "     g <- graph_from_data_frame(relations, directed = TRUE, vertices = actors)\n",
      "     print(g, e = TRUE, v = TRUE)\n",
      "     \n",
      "     ## The opposite operation\n",
      "     as_data_frame(g, what = \"vertices\")\n",
      "     as_data_frame(g, what = \"edges\")\n",
      "     \n",
      "\n",
      "                                                                                                             \n",
      "\u001b[31moutput file: network.knit.md\n",
      "\n",
      "\u001b[39m\u001b[31m\n",
      "\n",
      "processing file: network.qmd\n",
      "  |................                                   |  32% (unnamed-chunk-16)as_data_frame              package:igraph              R Documentation\n",
      "\n",
      "Creating igraph graphs from data frames or vice-versa\n",
      "\n",
      "Description:\n",
      "\n",
      "     This function creates an igraph graph from one or two data frames\n",
      "     containing the (symbolic) edge list and edge/vertex attributes.\n",
      "\n",
      "Usage:\n",
      "\n",
      "     as_data_frame(x, what = c(\"edges\", \"vertices\", \"both\"))\n",
      "     \n",
      "     graph_from_data_frame(d, directed = TRUE, vertices = NULL)\n",
      "     \n",
      "     from_data_frame(...)\n",
      "     \n",
      "Arguments:\n",
      "\n",
      "       x: An igraph object.\n",
      "\n",
      "    what: Character constant, whether to return info about vertices,\n",
      "          edges, or both. The default is 'edges'.\n",
      "\n",
      "       d: A data frame containing a symbolic edge list in the first two\n",
      "          columns. Additional columns are considered as edge\n",
      "          attributes.  Since version 0.7 this argument is coerced to a\n",
      "          data frame with 'as.data.frame'.\n",
      "\n",
      "directed: Logical scalar, whether or not to create a directed graph.\n",
      "\n",
      "vertices: A data frame with vertex metadata, or 'NULL'. See details\n",
      "          below. Since version 0.7 this argument is coerced to a data\n",
      "          frame with 'as.data.frame', if not 'NULL'.\n",
      "\n",
      "     ...: Passed to 'graph_from_data_frame()'.\n",
      "\n",
      "Details:\n",
      "\n",
      "     'graph_from_data_frame()' creates igraph graphs from one or two\n",
      "     data frames. It has two modes of operation, depending whether the\n",
      "     'vertices' argument is 'NULL' or not.\n",
      "\n",
      "     If 'vertices' is 'NULL', then the first two columns of 'd' are\n",
      "     used as a symbolic edge list and additional columns as edge\n",
      "     attributes. The names of the attributes are taken from the names\n",
      "     of the columns.\n",
      "\n",
      "     If 'vertices' is not 'NULL', then it must be a data frame giving\n",
      "     vertex metadata. The first column of 'vertices' is assumed to\n",
      "     contain symbolic vertex names, this will be added to the graphs as\n",
      "     the ''name'' vertex attribute. Other columns will be added as\n",
      "     additional vertex attributes. If 'vertices' is not 'NULL' then the\n",
      "     symbolic edge list given in 'd' is checked to contain only vertex\n",
      "     names listed in 'vertices'.\n",
      "\n",
      "     Typically, the data frames are exported from some spreadsheet\n",
      "     software like Excel and are imported into R via 'read.table()',\n",
      "     'read.delim()' or 'read.csv()'.\n",
      "\n",
      "     All edges in the data frame are included in the graph, which may\n",
      "     include multiple parallel edges and loops.\n",
      "\n",
      "     'as_data_frame()' converts the igraph graph into one or more data\n",
      "     frames, depending on the 'what' argument.\n",
      "\n",
      "     If the 'what' argument is 'edges' (the default), then the edges of\n",
      "     the graph and also the edge attributes are returned. The edges\n",
      "     will be in the first two columns, named 'from' and 'to'. (This\n",
      "     also denotes edge direction for directed graphs.)  For named\n",
      "     graphs, the vertex names will be included in these columns, for\n",
      "     other graphs, the numeric vertex ids. The edge attributes will be\n",
      "     in the other columns. It is not a good idea to have an edge\n",
      "     attribute named 'from' or 'to', because then the column named in\n",
      "     the data frame will not be unique. The edges are listed in the\n",
      "     order of their numeric ids.\n",
      "\n",
      "     If the 'what' argument is 'vertices', then vertex attributes are\n",
      "     returned. Vertices are listed in the order of their numeric vertex\n",
      "     ids.\n",
      "\n",
      "     If the 'what' argument is 'both', then both vertex and edge data\n",
      "     is returned, in a list with named entries 'vertices' and 'edges'.\n",
      "\n",
      "Value:\n",
      "\n",
      "     An igraph graph object for 'graph_from_data_frame()', and either a\n",
      "     data frame or a list of two data frames named 'edges' and\n",
      "     'vertices' for 'as.data.frame'.\n",
      "\n",
      "Note:\n",
      "\n",
      "     For 'graph_from_data_frame()' 'NA' elements in the first two\n",
      "     columns 'd' are replaced by the string \"NA\" before creating the\n",
      "     graph. This means that all 'NA's will correspond to a single\n",
      "     vertex.\n",
      "\n",
      "     'NA' elements in the first column of 'vertices' are also replaced\n",
      "     by the string \"NA\", but the rest of 'vertices' is not touched. In\n",
      "     other words, vertex names (=the first column) cannot be 'NA', but\n",
      "     other vertex attributes can.\n",
      "\n",
      "Author(s):\n",
      "\n",
      "     Gabor Csardi <mailto:csardi.gabor@gmail.com>\n",
      "\n",
      "See Also:\n",
      "\n",
      "     'graph_from_literal()' for another way to create graphs,\n",
      "     'read.table()' to read in tables from files.\n",
      "\n",
      "     Other conversion: 'as.directed()', 'as.matrix.igraph()',\n",
      "     'as_adj_list()', 'as_adjacency_matrix()', 'as_edgelist()',\n",
      "     'as_graphnel()', 'as_incidence_matrix()', 'as_long_data_frame()',\n",
      "     'graph_from_adj_list()', 'graph_from_graphnel()'\n",
      "\n",
      "Examples:\n",
      "\n",
      "     ## A simple example with a couple of actors\n",
      "     ## The typical case is that these tables are read in from files....\n",
      "     actors <- data.frame(\n",
      "       name = c(\n",
      "         \"Alice\", \"Bob\", \"Cecil\", \"David\",\n",
      "         \"Esmeralda\"\n",
      "       ),\n",
      "       age = c(48, 33, 45, 34, 21),\n",
      "       gender = c(\"F\", \"M\", \"F\", \"M\", \"F\")\n",
      "     )\n",
      "     relations <- data.frame(\n",
      "       from = c(\n",
      "         \"Bob\", \"Cecil\", \"Cecil\", \"David\",\n",
      "         \"David\", \"Esmeralda\"\n",
      "       ),\n",
      "       to = c(\"Alice\", \"Bob\", \"Alice\", \"Alice\", \"Bob\", \"Alice\"),\n",
      "       same.dept = c(FALSE, FALSE, TRUE, FALSE, FALSE, TRUE),\n",
      "       friendship = c(4, 5, 5, 2, 1, 1), advice = c(4, 5, 5, 4, 2, 3)\n",
      "     )\n",
      "     g <- graph_from_data_frame(relations, directed = TRUE, vertices = actors)\n",
      "     print(g, e = TRUE, v = TRUE)\n",
      "     \n",
      "     ## The opposite operation\n",
      "     as_data_frame(g, what = \"vertices\")\n",
      "     as_data_frame(g, what = \"edges\")\n",
      "     \n",
      "\n",
      "                                                                                                             \n",
      "\u001b[31moutput file: network.knit.md\n",
      "\n",
      "[ 7/13] sentiment-analysis.qmd\u001b[39m\u001b[22m\n",
      "\u001b[31m\n",
      "\n",
      "processing file: sentiment-analysis.qmd\n",
      "  |...                                                |   6% (unnamed-chunk-2) \u001b[31mSystem has not been booted with systemd as init system (PID 1). Can't operate.\n",
      "Failed to connect to bus: Host is down\n",
      "  |...........................                        |  54% (unnamed-chunk-19)\u001b[31mQuitting from lines 291-292 (sentiment-analysis.qmd) \n",
      "Error: The textdata package is required to download the NRC word-emotion association lexicon.\n",
      "Install the textdata package to access this dataset.\n",
      "                                                                                                             \n",
      "\u001b[31mExecution halted\n",
      "\u001b[39m"
     ]
    }
   ],
   "source": [
    "! cd r4ps-main \\\n",
    "    && quarto render"
   ]
  }
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