[d6960c]: / Nomogram.ipynb

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{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Here are the simple examples for plotting nomogram, ROC curves, Calibration curves, and Decision curves in training and test dataset by using R language."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "# Library and data\n",
    "library(rms)\n",
    "library(pROC)\n",
    "library(rmda)\n",
    "train <-read.csv(\"E:/Experiments/YinjunDong/nomogram/EGFR-nomogram.csv\")\n",
    "test <-read.csv(\"E:/Experiments/YinjunDong/nomogram/EGFR-nomogram-test.csv\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "image/png": 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      "text/plain": [
       "plot without title"
      ]
     },
     "metadata": {
      "image/png": {
       "height": 420,
       "width": 420
      }
     },
     "output_type": "display_data"
    }
   ],
   "source": [
    "# Nomogram\n",
    "dd=datadist(train)\n",
    "options(datadist=\"dd\")\n",
    "f1 <- lrm(EGFR~ Rad\n",
    "          +Smoking\n",
    "          +Type\n",
    "          ,data = train,x = TRUE,y = TRUE)\n",
    "\n",
    "nom <- nomogram(f1, fun=plogis,fun.at=c(.001, .01, seq(.1,.9, by=.4)), lp=F, funlabel=\"EGFR Mutations\")\n",
    "plot(nom)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "Setting levels: control = 0, case = 1\n",
      "\n",
      "Setting direction: controls < cases\n",
      "\n"
     ]
    },
    {
     "data": {
      "image/png": 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WRCQ9gMiY5wZTCkXCX7k35UHBKVywxhMSQ6wo3BkBJ1uj4+qURmCHsh0RE6DIak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\nhAQIICRAwP8Bziuu5Zjx1tMAAAAASUVORK5CYII=",
      "text/plain": [
       "Plot with title \"ROC Curve\""
      ]
     },
     "metadata": {
      "image/png": {
       "height": 420,
       "width": 420
      }
     },
     "output_type": "display_data"
    }
   ],
   "source": [
    "# ROC train\n",
    "f2 <- glm(EGFR~ Rad\n",
    "          +Smoking\n",
    "          +Type\n",
    "          ,data = train,family = \"binomial\")\n",
    "\n",
    "pre <- predict(f2, type='response')\n",
    "plot.roc(train$EGFR, pre,\n",
    "         main=\"ROC Curve\", percent=TRUE,\n",
    "         print.auc=TRUE,\n",
    "         ci=TRUE, ci.type=\"bars\", \n",
    "         of=\"thresholds\",\n",
    "         thresholds=\"best\",\n",
    "         print.thres=\"best\",\n",
    "         col=\"blue\"\n",
    "         #,identity=TRUE\n",
    "         ,legacy.axes=TRUE,\n",
    "         print.auc.x=ifelse(50,50),\n",
    "         print.auc.y=ifelse(50,50)\n",
    "         )"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "Setting levels: control = 0, case = 1\n",
      "\n",
      "Setting direction: controls < cases\n",
      "\n"
     ]
    },
    {
     "data": {
      "image/png": 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GbDUaAByWg4CjUgmQxHwQYkg+Eo3IBkLhwFHJCMhaOQA5KpcBR0QDIUjsIOSGbC\nUeAByUg4Cj0gmQhHwQckA+Eo/ICkPxxFEJC0h6MYApLucBRFQNIcjuIISHrDUSQBSWs4iiUg\n6QxH0RQcpK/3yb3ON+EonkKDNMORMUg4iqjwIAm+jHXhKKaApCscRRWQNIWjuAKSnnAUWUDS\nEo5iC0g6wlF0AUlDOIovIMmHowgDkng4ijEgSYejKAOScDiKMyDJhqNIA5JoOIo1IEmGo2gD\nkmA4ijcgyYWjiAOSWDiKOSBJhaOoA5JQOIo7IMmEo8gDkkg4ij0gSYSj6AOSQDgizyA5dNW6\nezgizyC5dPnHLhyRf5D0j/1pOKIrkFaHI6oC0rpwRHVAWhWOqAlIa8IRtRmFdN5vVdU2Oy8b\nwjFIOKJbBiEVG3UvXTSEW5BwRF0GIWUqOV7qR/kpUdmSIZyChCO6ZxBSoi7d44tKlgzhEiQc\nUS+DkJR69cHsIRyChCPqxxppWTiiQWb3kU55/cj/fSQc0TCT099pb9ZuUywZwhVIOKKHzB5H\nyurjSMl27/dxJBzRY5zZ8Hk4oqeA9HE4oudMQip2SqWndiHeTn/jiEYyeYpQ0pxo1yzEV0g4\norGMTn8fSk2HpD7N7hmS6vdiEfYh4YhGM3pAtv4rTza5t2skHNF4Fk4RKtLUV0g4ohcZhLRR\nt4Owm9RPSDiiVxmEdFC79lGuUh8h4YheZnL6O+v0nF7PJ0wOwf34yNGMHpC9bG+P8p13kHBE\nE3Fmw8xwRFMBaV44osmANCsc0XRAmhOO6E1AmhGO6F1Aeh+O6G1AehuO6H1AeheOaEZAehOO\naE5Amg5HNCsgTYYjmheQpsIRzQxIE+GI5gak1+GIZgekl+GI5gekV+GIPghIL8IRfRKQxsMR\nfRSQRsMRfRaQxsIRfRiQRsIRfRqQnsMRfRyQnsIRfR6QHsMRLQhID+GIlgSkYTiiRQFpEI5o\nWUDqhyNaGJB64YiWBqR7OKLFAakLR7Q8IN3CEa0ISG04ojUBqQlHtCog1eGI1gWkKhzRyoB0\nxRGtD0g4IoGAhCMSCEg4IoGih4Qjkih2SDgikSKHhCOSKW5IOCKhooaEI5IqZkg4IrEihoQj\nkiteSDgiwaKFhCOSLFZIOCLRIoWEI5ItTkg4IuGihIQjki5GSDgi8SKEhCOSLz5IOCINRQcJ\nR6Sj2CDhiLQUGSQckZ7igoQj0lRUkHBEuooJEo5IWxFBwhHpKx5IOCKNRQMJR6SzWCDhiLQW\nCSQckd7igIQj0lwUkHBEuosBEo5IexFAwhHpL3xIOCIDBQ8JR2Si0CHhiIwUOCQckZnChoQj\nMlTQkHBEpgoZEo7IWAFDwhGZK1xIOCKDBQsJR2SyUCHhiIwWKCQckdnChIQjMg4Xu8MAAAhP\nSURBVFyQkHBEpgsREo7IeAFCwhGZLzxIOCILBQcJR2Sj0CDhiKwUGCQckZ3CgoQjslRQkHBE\ntgoJEo7IWgFBwhHZKxxIOCKLBQMJR2SzUCDhiKwWCCQckd3CgIQjslwQkHBEtgsBEo7IegFA\nwhHZz39IOCIH8h4SjsiFfIeEI3IizyHhiNzIb0g4IkfyGhKOyJV8hoQjciaPIeGI3MkopPN+\nq6q22XnZEH1IOCKHMgip2Kh76aIhepBwRC5lEFKmkuOlfpSfEpUtGeIOCUfkVAYhJerSPb6o\nZMkQHSQckVsZhKTUqw9mD3GDhCNyLC/XSDgi1zK7j3TK60cr95FwRM5lcvo77c3abYolQ9SQ\ncETuZfY4UlYfR0q2+xXHkXBEDubdmQ04IhdzB5Lq9+Jrvr5wRE7mDqRZQ+CI3MwvSDgiR/MK\nEo7I1XyChCNyNo8g4YjczR9IOCKH8wYSjsjlfIGEI3I6TyDhiNzOD0g4IsfzAhKOyPV8gIQj\ncj4PIOGI3M99SDgiD3IeEo7Ih1yHhCPyIsch4Yj8yG1IOCJPchoSjsiXXIaEI/ImhyHhiPzJ\nXUg4Io9yFhKOyKdchYQj8ipHIeGI/MpNSP9TRH71+bvcACQnx2Z8xhcdH0iMz/iuLcyjsRmf\n8YHE+Izv2vhAYnzGd21hHo3N+IwPJMZnfNfGBxLjM75rC/NobMZnfCAxPuO7Nj6QGJ/xXVuY\nR2MzPuMHA4komIBEJBCQiAQCEpFAQCISCEhEAgGJSCAgEQkEJCKBgEQkEJCIBAISkUBAIhII\nSEQCAYlIICARCWQZUpaoJCvMj3vYdOPaegnn9kdvZfzLTqldbm38ojeo2fEPtze89CuwCymt\nL/2/MT5uVo+bFBZfQpE0P3or45/s/vvzpBk/Nz7+5Xajid6wMq/AKqSzSi7XS6LOhse9qF1R\n/c9pZ+8lXLfNf1I74yfloMVWZZbG31Ujl/83M/7zLwdq3vC9YYVegVVImTqVfx7V3vC42+Zf\nXf1Qbb2EY3sTHivjH+s3cqESS+MrSz//g0rboXvDCr0Cq5C2qlq5X9TWzvDVD9XSS8hv/0mt\njL9Tl9tDK+O3W7UVZKPjl///aCH1hhV6BVYh9f7PZKFCpdZeQqryZkgr42/UdZ/Um7d2xt+3\nm3Z7w+NfHser/hJ6BRFDOlTrdDsvYa+OV4uQlNrWO/u2xr8eqtmG5GBhfCCJlydbWy+h3o6w\nCqmabNgZXyN07euJsv0VSDLZhFQkqbWXsKkmnq1CqvaR8mrK18r4h2rTroR8AJJMiUVI6cba\nS9jV80TNkFZ+BL33jpXxN6raPSsqyKbHbwdKxH8CDsza5RZm7fJNmlt7Cf270Fv5EfSm/62M\nr+yNP5i1y++zdqtfgVVI+/p/zad6DsdoJ5VafAl9SFZ+BM2gefVDsDJ+sxKoj2OZHr+F1BtW\n6BVEeWZD3jmyd2bD1eKZDeXeUVHtoxwtjZ+p6tS2zMaZFWGe2VBuLFel779Qtt19jWDrJXT/\nSa2Mv78PamX81Nr4t12hjfQrsAupOQvY+LC9TStbL6H7T2pn/FN6G9TO+PdBDY9/g1RIvwK7\nkIgCCUhEAgGJSCAgEQkEJCKBgEQkEJCIBAISkUBAIhIISEQCAYlIICARCQQkIoGARCQQkIgE\nAhKRQEAiEghIRAIBiUggIBEJBCQigYBkpM9vXVpkG6XSw5yFN1dD2imVDa+7W390evFNp+rK\noseN2tTXcyvaWz9uX305vQlIJvr81qVFc5vV5j6vb6oXXt2oZf8MafPiP3BeXX77rLJrVl8Z\nsbltXQUqn/PvoaeAZKAFty7dqeri5Hk6+0q6apzAq2vDp9Vy01JTfbu1ogOdWbhUZhABSX9L\nbl2q6hs2lO/wuf+BXnzhi6ePqrtd3/1Ors2Ax5kD0iAg6W/JrUv7AMrHWXct0MOmudXdtd7J\nqu+pUX6+vXBse4Pnh+dv65v7eue6ud8cqvyj94nb7W7ow4CkvyW3Ls3UrttUq3d+2qtTb+8X\nqk5v+1APkJ6eL7+p3oC8r/7O6tAsodm0u6+QqtWn+fsJhBCQjPT5jeJKDpvs3H5Nszt1rO9H\nU7730+qNf6we7qp9qG4Lrf5j+Hwzc6d21XJ23W5U1tzWvJ1syPtTHhfzN9kJIiAZacEdF0/V\nPTOS5t5+zR186g3C5l539cNze4+hIaTh883ym1vk3b2kzR7Y9VRPf2/VqZsHbyYf6OOAZKRl\nty497+tZvcF3dffRuH/nENLw+eajQ7VRd75PbAxGvZSGunlwSzci9T9+akZ6f+vS7j4zgy4P\nN0xeCKm9OV4++I5b5Qqpmwd//BzNjZ+akd7funQIqedrbD02+JIZkOrphM1m5HubicP7EoC0\nMH5qRvr01qXbZlrttq9zvrYzBtv7/Fr6Yh8pHdlHKrWkl94hq9s+UjPUpQ+JfaRlAclIn57Z\ncFbqUJ3Dk1agbrN29VRd+bDc5dnWh3mL5j6sQ0jD528nPGxU0jv1IbsPWx/J6m3anZm1WxSQ\njPTxrUuzdl8orb+5PjRUbwQ2Z+gl+XV4vKj/x+D5cpSk+r7T4LS+3rxDtULqnXRXrik5jrQk\nIBnp81uXXnZJCejYfvNWbdrTGQ4ljfZYbYltm1+fIA2eP28aSIUanIy0uQFuT604ddPfnNmw\nLCC5n8Tu/2l4Uuvp1VneueIXKRYFJPeTgJSq4a82pS/WhZz9vTAgud96SM87Y7ka/UUnfh9p\naUByv/WQkueTzE+7sS/csWG3MCARCQQkIoGARCQQkIgEAhKRQEAiEghIRAIBiUggIBEJBCQi\ngYBEJBCQiAQCEpFAQCISCEhEAv0fO8OlOS1aSO0AAAAASUVORK5CYII=",
      "text/plain": [
       "Plot with title \"ROC Curve\""
      ]
     },
     "metadata": {
      "image/png": {
       "height": 420,
       "width": 420
      }
     },
     "output_type": "display_data"
    }
   ],
   "source": [
    "# ROC test\n",
    "pre1 <- predict(f2,newdata = test)\n",
    "plot.roc(test$EGFR, pre1,\n",
    "         main=\"ROC Curve\", percent=TRUE,\n",
    "         print.auc=TRUE,\n",
    "         ci=TRUE, ci.type=\"bars\",\n",
    "         of=\"thresholds\",\n",
    "         thresholds=\"best\",\n",
    "         print.thres=\"best\",\n",
    "         col=\"blue\",legacy.axes=TRUE,\n",
    "         print.auc.x=ifelse(50,50),\n",
    "         print.auc.y=ifelse(50,50)\n",
    "         )"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "Setting levels: control = 0, case = 1\n",
      "\n",
      "Setting direction: controls < cases\n",
      "\n"
     ]
    },
    {
     "data": {
      "text/html": [
       "<style>\n",
       ".list-inline {list-style: none; margin:0; padding: 0}\n",
       ".list-inline>li {display: inline-block}\n",
       ".list-inline>li:not(:last-child)::after {content: \"\\00b7\"; padding: 0 .5ex}\n",
       "</style>\n",
       "<ol class=list-inline><li>0.820159806082131</li><li>0.890810810810811</li><li>0.961461815539491</li></ol>\n"
      ],
      "text/latex": [
       "\\begin{enumerate*}\n",
       "\\item 0.820159806082131\n",
       "\\item 0.890810810810811\n",
       "\\item 0.961461815539491\n",
       "\\end{enumerate*}\n"
      ],
      "text/markdown": [
       "1. 0.820159806082131\n",
       "2. 0.890810810810811\n",
       "3. 0.961461815539491\n",
       "\n",
       "\n"
      ],
      "text/plain": [
       "95% CI: 0.8202-0.9615 (DeLong)"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "singular information matrix in lrm.fit (rank= 3 ).  Offending variable(s):\n",
      "Type \n",
      "\n",
      "Divergence or singularity in 1 samples\n",
      "\n",
      "n=87   Mean absolute error=0.012   Mean squared error=0.00019\n",
      "0.9 Quantile of absolute error=0.02\n",
      "\n"
     ]
    },
    {
     "data": {
      "image/png": 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3Q/yN1GFLApe75sLru/73WPXcHFThTg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",
      "text/plain": [
       "Plot with title \"Calibration Curve\""
      ]
     },
     "metadata": {
      "image/png": {
       "height": 420,
       "width": 420
      }
     },
     "output_type": "display_data"
    }
   ],
   "source": [
    "# Calibration Curve train\n",
    "rocplot1 <- roc(train$EGFR, pre)\n",
    "ci.auc(rocplot1)\n",
    "cal <- calibrate(f1,  method = \"boot\", B = 1000)\n",
    "plot(cal, xlab = \"Nomogram Predicted Mutation\", ylab = \"Actual Mutation\",main = \"Calibration Curve\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "Setting levels: control = 0, case = 1\n",
      "\n",
      "Setting direction: controls < cases\n",
      "\n"
     ]
    },
    {
     "data": {
      "text/html": [
       "<style>\n",
       ".list-inline {list-style: none; margin:0; padding: 0}\n",
       ".list-inline>li {display: inline-block}\n",
       ".list-inline>li:not(:last-child)::after {content: \"\\00b7\"; padding: 0 .5ex}\n",
       "</style>\n",
       "<ol class=list-inline><li>0.664403069452139</li><li>0.797570850202429</li><li>0.930738630952719</li></ol>\n"
      ],
      "text/latex": [
       "\\begin{enumerate*}\n",
       "\\item 0.664403069452139\n",
       "\\item 0.797570850202429\n",
       "\\item 0.930738630952719\n",
       "\\end{enumerate*}\n"
      ],
      "text/markdown": [
       "1. 0.664403069452139\n",
       "2. 0.797570850202429\n",
       "3. 0.930738630952719\n",
       "\n",
       "\n"
      ],
      "text/plain": [
       "95% CI: 0.6644-0.9307 (DeLong)"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\n",
      "n=45   Mean absolute error=0.029   Mean squared error=0.00123\n",
      "0.9 Quantile of absolute error=0.058\n",
      "\n"
     ]
    },
    {
     "data": {
      "image/png": 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Fdy/NGT3eDY6LU7TAoYze73k5nFE1HD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\nQmCC",
      "text/plain": [
       "Plot with title \"Calibration Curve\""
      ]
     },
     "metadata": {
      "image/png": {
       "height": 420,
       "width": 420
      }
     },
     "output_type": "display_data"
    }
   ],
   "source": [
    "# Calibration Curve test\n",
    "rocplot2 <- roc(test$EGFR,pre1)\n",
    "ci.auc(rocplot2)\n",
    "f3 <- lrm(test$EGFR ~ pre1,x = TRUE,y = TRUE)\n",
    "cal2 <- calibrate(f3,  method = \"boot\", B = 1000)\n",
    "plot(cal2, xlab = \"Nomogram Predicted Mutation\", ylab = \"Actual Mutation\",main = \"Calibration Curve\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "Calculating net benefit curves for case-control data. All calculations are done conditional on the outcome prevalence provided.\n",
      "\n",
      "Calculating net benefit curves for case-control data. All calculations are done conditional on the outcome prevalence provided.\n",
      "\n",
      "Note:  The data provided is used to both fit a prediction model and to estimate the respective decision curve. This may cause bias in decision curve estimates leading to over-confidence in model performance. \n",
      "\n",
      "Calculating net benefit curves for case-control data. All calculations are done conditional on the outcome prevalence provided.\n",
      "\n",
      "Note:  The data provided is used to both fit a prediction model and to estimate the respective decision curve. This may cause bias in decision curve estimates leading to over-confidence in model performance. \n",
      "\n",
      "Warning message:\n",
      "\"glm.fit: fitted probabilities numerically 0 or 1 occurred\"\n",
      "Warning message:\n",
      "\"glm.fit: fitted probabilities numerically 0 or 1 occurred\"\n",
      "Warning message:\n",
      "\"glm.fit: fitted probabilities numerically 0 or 1 occurred\"\n",
      "Warning message:\n",
      "\"glm.fit: fitted probabilities numerically 0 or 1 occurred\"\n",
      "Note: When multiple decision curves are plotted, decision curves for 'All' are calculated using the prevalence from the first DecisionCurve object in the list provided.\n",
      "\n"
     ]
    },
    {
     "data": {
      "image/png": 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wtFWmeSdvm19+20y49IQkzl++iStMu/TCR5k7TLj0hCCIq0yiTt8mvv22mXH5GE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\n11kXzf0/AAAAAElFTkSuQmCC",
      "text/plain": [
       "plot without title"
      ]
     },
     "metadata": {
      "image/png": {
       "height": 420,
       "width": 420
      }
     },
     "output_type": "display_data"
    }
   ],
   "source": [
    "# Decision Curve train\n",
    "Rad<- decision_curve(EGFR~ \n",
    "                          Rad, data = train, family = binomial(link ='logit'),\n",
    "                          thresholds= seq(0,1, by = 0.01),\n",
    "                          confidence.intervals =0.95,study.design = 'case-control',\n",
    "                          population.prevalence = 0.3)\n",
    "\n",
    "Clinical<- decision_curve(EGFR~ \n",
    "                         Smoking+Type, data = train, family = binomial(link ='logit'),\n",
    "                         thresholds= seq(0,1, by = 0.01),\n",
    "                         confidence.intervals =0.95,study.design = 'case-control',\n",
    "                         population.prevalence = 0.3)\n",
    "\n",
    "clinical_Rad<- decision_curve(EGFR~ Rad\n",
    "                         +Smoking+Type, data = train,\n",
    "                         family = binomial(link ='logit'), thresholds = seq(0,1, by = 0.01),\n",
    "                         confidence.intervals= 0.95,study.design = 'case-control',\n",
    "                         population.prevalence= 0.3)\n",
    "\n",
    "List<- list(Clinical,Rad,clinical_Rad)\n",
    "plot_decision_curve(List,curve.names= c('Clinical','Rad-Score','Nomogram'),\n",
    "                    cost.benefit.axis =FALSE,col = c('green','red','blue'),\n",
    "                    confidence.intervals =FALSE,standardize = FALSE,\n",
    "                    #legend.position = \"none\"\n",
    "                    legend.position = \"bottomleft\"\n",
    "                    )"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "Calculating net benefit curves for case-control data. All calculations are done conditional on the outcome prevalence provided.\n",
      "\n",
      "Calculating net benefit curves for case-control data. All calculations are done conditional on the outcome prevalence provided.\n",
      "\n",
      "Note:  The data provided is used to both fit a prediction model and to estimate the respective decision curve. This may cause bias in decision curve estimates leading to over-confidence in model performance. \n",
      "\n",
      "Calculating net benefit curves for case-control data. All calculations are done conditional on the outcome prevalence provided.\n",
      "\n",
      "Note:  The data provided is used to both fit a prediction model and to estimate the respective decision curve. This may cause bias in decision curve estimates leading to over-confidence in model performance. \n",
      "\n",
      "Note: When multiple decision curves are plotted, decision curves for 'All' are calculated using the prevalence from the first DecisionCurve object in the list provided.\n",
      "\n"
     ]
    },
    {
     "data": {
      "image/png": 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m3AEEkQRDIjXwnpJmlUJBmTZu/iCU8k2W+CSB6YEWmVSWMFKWRSMf7x1Nz/xheI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\nMj9MkYqRiztH7apPizezi6+DDQtMUlWRYs8PVKQs7Z1Hqj8t30z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      "text/plain": [
       "plot without title"
      ]
     },
     "metadata": {
      "image/png": {
       "height": 420,
       "width": 420
      }
     },
     "output_type": "display_data"
    }
   ],
   "source": [
    "# Decision Curve test\n",
    "Rad1<- decision_curve(EGFR~ \n",
    "                     Rad, data = test, family = binomial(link ='logit'),\n",
    "                     thresholds= seq(0,1, by = 0.01),\n",
    "                     confidence.intervals =0.95,study.design = 'case-control',\n",
    "                     population.prevalence = 0.3)\n",
    "\n",
    "Clinical1<- decision_curve(EGFR~ \n",
    "                          Smoking+Type, data = test, family = binomial(link ='logit'),\n",
    "                          thresholds= seq(0,1, by = 0.01),\n",
    "                          confidence.intervals =0.95,study.design = 'case-control',\n",
    "                          population.prevalence = 0.3)\n",
    "\n",
    "clinical_Rad1<- decision_curve(EGFR~ Rad\n",
    "                              +Smoking+Type, data = test,\n",
    "                              family = binomial(link ='logit'), thresholds = seq(0,1, by = 0.01),\n",
    "                              confidence.intervals= 0.95,study.design = 'case-control',\n",
    "                              population.prevalence= 0.3)\n",
    "\n",
    "List1<- list(Clinical1, Rad1, clinical_Rad1)\n",
    "plot_decision_curve(List1,curve.names= c('Clinical','Rad-Score','Nomogram'),\n",
    "                    cost.benefit.axis =FALSE,col = c('green','red','blue'),\n",
    "                    confidence.intervals =FALSE,standardize = FALSE,\n",
    "                    legend.position = \"bottomleft\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
 ],
 "metadata": {
  "kernelspec": {
   "display_name": "R",
   "language": "R",
   "name": "ir"
  },
  "language_info": {
   "codemirror_mode": "r",
   "file_extension": ".r",
   "mimetype": "text/x-r-source",
   "name": "R",
   "pygments_lexer": "r",
   "version": "4.0.2"
  }
 },
 "nbformat": 4,
 "nbformat_minor": 2
}