aipecs.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "id": "c19a848d",
   "metadata": {},
   "source": [
    "Below I tabulate the expected number of detected cancers under a range of values for the number of women prospectively consented to have their Mirai score evaluated, `total_consented`; the number of women selected for intensive surveillance, `total_intensive_surveilled`; the cancer incidence in the general UCM breast cancer screening population, `real_cancer_incidence`; and the true positive rate, `tpr` of Mirai. Conservative ranges for Mirai's true positive rate are taken from Yala et. al. [1] table 2 and figure 3.\n",
    "\n",
    "[1] [https://pubmed.ncbi.nlm.nih.gov/33504648/](https://pubmed.ncbi.nlm.nih.gov/33504648/)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "id": "4a865fe5",
   "metadata": {},
   "outputs": [],
   "source": [
    "import tabulate"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "id": "4d96372d",
   "metadata": {},
   "outputs": [],
   "source": [
    "total_consented_options = [\n",
    "    1000,\n",
    "    5000,\n",
    "    10000,\n",
    "]  # number of women we consent to prospectively run Mirai on\n",
    "real_cancer_incidences = [5 / 1000.0, 10 / 1000.0, 15 / 1000.0]\n",
    "tprs = [0.2, 0.3, 0.4, 0.5]  # true positive rates"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "id": "211ec56b",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\n",
      "\n",
      "\n",
      "*****************************************total consented 1000*****************************************\n",
      "     cancer       real    detected cancers    detected cancers    detected cancers    detected cancers\n",
      "  incidence    cancers             tpr=0.2             tpr=0.3             tpr=0.4             tpr=0.5\n",
      "-----------  ---------  ------------------  ------------------  ------------------  ------------------\n",
      "      0.005          5                   1                   1                   2                   2\n",
      "      0.01          10                   2                   3                   4                   5\n",
      "      0.015         15                   3                   4                   6                   7\n",
      "\n",
      "\n",
      "\n",
      "*****************************************total consented 5000*****************************************\n",
      "     cancer       real    detected cancers    detected cancers    detected cancers    detected cancers\n",
      "  incidence    cancers             tpr=0.2             tpr=0.3             tpr=0.4             tpr=0.5\n",
      "-----------  ---------  ------------------  ------------------  ------------------  ------------------\n",
      "      0.005         25                   5                   7                  10                  12\n",
      "      0.01          50                  10                  15                  20                  25\n",
      "      0.015         75                  15                  22                  30                  37\n",
      "\n",
      "\n",
      "\n",
      "*****************************************total consented 10000*****************************************\n",
      "     cancer       real    detected cancers    detected cancers    detected cancers    detected cancers\n",
      "  incidence    cancers             tpr=0.2             tpr=0.3             tpr=0.4             tpr=0.5\n",
      "-----------  ---------  ------------------  ------------------  ------------------  ------------------\n",
      "      0.005         50                  10                  15                  20                  25\n",
      "      0.01         100                  20                  30                  40                  50\n",
      "      0.015        150                  30                  45                  60                  75\n"
     ]
    }
   ],
   "source": [
    "for total_consented in total_consented_options:\n",
    "    print(\n",
    "        \"\\n\\n\\n\"\n",
    "        + \"*\" * 41\n",
    "        + \"total consented {}\".format(total_consented)\n",
    "        + \"*\" * 41\n",
    "    )\n",
    "    table = []\n",
    "    for real_cancer_incidence in real_cancer_incidences:\n",
    "        real_cancers = real_cancer_incidence * total_consented\n",
    "        row = [\"{:>03f}\".format(real_cancer_incidence), real_cancers]\n",
    "        for tpr in tprs:\n",
    "            row += [int(tpr * real_cancers)]\n",
    "        table += [row]\n",
    "    print(\n",
    "        tabulate.tabulate(\n",
    "            table,\n",
    "            [\"cancer\\nincidence\", \"real\\ncancers\"]\n",
    "            + [\"detected cancers\\ntpr={:0.1f}\".format(tpr) for tpr in tprs],\n",
    "        )\n",
    "    )"
   ]
  }
 ],
 "metadata": {
  "gist": {
   "data": {
    "description": "stats.ipynb",
    "public": true
   },
   "id": ""
  },
  "kernelspec": {
   "display_name": "Python [conda env:maicara] *",
   "language": "python",
   "name": "conda-env-maicara-py"
  },
  "language_info": {
   "codemirror_mode": {
    "name": "ipython",
    "version": 3
   },
   "file_extension": ".py",
   "mimetype": "text/x-python",
   "name": "python",
   "nbconvert_exporter": "python",
   "pygments_lexer": "ipython3",
   "version": "3.9.5"
  }
 },
 "nbformat": 4,
 "nbformat_minor": 5
}