trying to bootstrap icc estimates

preprocessed-connectomes-project · Feb 1, 2017 · 3f80354 · 3f80354
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commit 3f80354
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diff --git a/data_analysis/ABIDE_CORR_colinearity.ipynb b/data_analysis/ABIDE_CORR_colinearity.ipynb
@@ -203,6 +203,46 @@
     "                Qi1='Fraction of Artifact Voxels',\n",
     "                SNR='SNR')"
    ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 3,
+   "metadata": {
+    "collapsed": false
+   },
+   "outputs": [],
+   "source": [
+    "?install.packages"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 5,
+   "metadata": {
+    "collapsed": false
+   },
+   "outputs": [
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "Updating HTML index of packages in '.Library'\n",
+      "Making 'packages.html' ... done\n"
+     ]
+    }
+   ],
+   "source": [
+    "install.packages(\"boot\")"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "collapsed": true
+   },
+   "outputs": [],
+   "source": []
   }
  ],
  "metadata": {
@@ -218,7 +258,7 @@
    "mimetype": "text/x-r-source",
    "name": "R",
    "pygments_lexer": "r",
-   "version": "3.3.2"
+   "version": "3.3.1"
   }
  },
  "nbformat": 4,

diff --git a/data_analysis/ABIDE_measures_and_ratings.R.ipynb b/data_analysis/ABIDE_measures_and_ratings.R.ipynb
@@ -2,11 +2,58 @@
  "cells": [
   {
    "cell_type": "code",
-   "execution_count": 217,
+   "execution_count": 2,
    "metadata": {
     "collapsed": false
    },
-   "outputs": [],
+   "outputs": [
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "\n",
+      "Attaching package: ‘dplyr’\n",
+      "\n",
+      "The following object is masked from ‘package:gridExtra’:\n",
+      "\n",
+      "    combine\n",
+      "\n",
+      "The following objects are masked from ‘package:stats’:\n",
+      "\n",
+      "    filter, lag\n",
+      "\n",
+      "The following objects are masked from ‘package:base’:\n",
+      "\n",
+      "    intersect, setdiff, setequal, union\n",
+      "\n",
+      "\n",
+      "Attaching package: ‘tidyr’\n",
+      "\n",
+      "The following object is masked from ‘package:reshape2’:\n",
+      "\n",
+      "    smiths\n",
+      "\n",
+      "Loading required package: lattice\n",
+      "Loading required package: survival\n",
+      "Loading required package: Formula\n",
+      "\n",
+      "Attaching package: ‘Hmisc’\n",
+      "\n",
+      "The following objects are masked from ‘package:dplyr’:\n",
+      "\n",
+      "    combine, src, summarize\n",
+      "\n",
+      "The following object is masked from ‘package:gridExtra’:\n",
+      "\n",
+      "    combine\n",
+      "\n",
+      "The following objects are masked from ‘package:base’:\n",
+      "\n",
+      "    format.pval, round.POSIXt, trunc.POSIXt, units\n",
+      "\n"
+     ]
+    }
+   ],
    "source": [
     "# Load some needed packages\n",
     "library(grid)\n",
@@ -22,7 +69,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 218,
+   "execution_count": 3,
    "metadata": {
     "collapsed": true
    },
@@ -68,7 +115,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 231,
+   "execution_count": 4,
    "metadata": {
     "collapsed": true
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@@ -260,7 +307,7 @@
   },
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    "cell_type": "code",
-   "execution_count": 219,
+   "execution_count": 5,
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@@ -377,7 +424,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 10,
+   "execution_count": 6,
    "metadata": {
     "collapsed": false
    },
@@ -395,7 +442,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 11,
+   "execution_count": 7,
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@@ -480,7 +527,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 12,
+   "execution_count": 8,
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     "collapsed": false
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@@ -500,7 +547,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 13,
+   "execution_count": 9,
    "metadata": {
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    },
@@ -511,6 +558,52 @@
     "pheno_df$qc_func<-factor(pheno_df$qc_func, levels=c(1,2), labels=c(\"Fail\", \"OK\"))"
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": 13,
+   "metadata": {
+    "collapsed": false
+   },
+   "outputs": [
+    {
+     "data": {
+      "text/html": [
+       "<table>\n",
+       "<thead><tr><th></th><th scope=col>qc_func</th><th scope=col>qc_anat</th><th scope=col>N</th></tr></thead>\n",
+       "<tbody>\n",
+       "\t<tr><th scope=row>1</th><td>Fail</td><td>Fail</td><td>95  </td></tr>\n",
+       "\t<tr><th scope=row>2</th><td>Fail</td><td>OK  </td><td>110 </td></tr>\n",
+       "\t<tr><th scope=row>3</th><td>OK  </td><td>Fail</td><td>83  </td></tr>\n",
+       "\t<tr><th scope=row>4</th><td>OK </td><td>OK </td><td>824</td></tr>\n",
+       "</tbody>\n",
+       "</table>\n"
+      ],
+      "text/latex": [
+       "\\begin{tabular}{r|lll}\n",
+       "  & qc\\_func & qc\\_anat & N\\\\\n",
+       "\\hline\n",
+       "\t1 & Fail & Fail & 95  \\\\\n",
+       "\t2 & Fail & OK   & 110 \\\\\n",
+       "\t3 & OK   & Fail & 83  \\\\\n",
+       "\t4 & OK  & OK  & 824\\\\\n",
+       "\\end{tabular}\n"
+      ],
+      "text/plain": [
+       "  qc_func qc_anat   N\n",
+       "1    Fail    Fail  95\n",
+       "2    Fail      OK 110\n",
+       "3      OK    Fail  83\n",
+       "4      OK      OK 824"
+      ]
+     },
+     "metadata": {},
+     "output_type": "display_data"
+    }
+   ],
+   "source": [
+    "pheno_df %>% group_by(qc_func,qc_anat) %>% summarise(N=n())"
+   ]
+  },
   {
    "cell_type": "markdown",
    "metadata": {},
@@ -1210,6 +1303,26 @@
     "?gsub"
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": 1,
+   "metadata": {
+    "collapsed": false
+   },
+   "outputs": [
+    {
+     "ename": "ERROR",
+     "evalue": "Error in eval(expr, envir, enclos): object 'abide_func_df' not found\n",
+     "output_type": "error",
+     "traceback": [
+      "Error in eval(expr, envir, enclos): object 'abide_func_df' not found\nTraceback:\n"
+     ]
+    }
+   ],
+   "source": [
+    "abide_func_df$qc_func"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": null,
@@ -1233,7 +1346,7 @@
    "mimetype": "text/x-r-source",
    "name": "R",
    "pygments_lexer": "r",
-   "version": "3.3.2"
+   "version": "3.3.1"
   }
  },
  "nbformat": 4,