diff --git a/problem_set_3.ipynb b/problem_set_3.ipynb new file mode 100644 index 0000000..1fb0e92 --- /dev/null +++ b/problem_set_3.ipynb @@ -0,0 +1,165 @@ +{ + "cells": [ + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "# 2)" + ] + }, + { + "cell_type": "code", + "execution_count": 3, + "metadata": {}, + "outputs": [], + "source": [ + "source('./data/ps3prob2data.r')" + ] + }, + { + "cell_type": "code", + "execution_count": 11, + "metadata": {}, + "outputs": [], + "source": [ + "x = getprob2data()" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "## a) Mean and standard deviation" + ] + }, + { + "cell_type": "code", + "execution_count": 13, + "metadata": {}, + "outputs": [ + { + "data": { + "text/html": [ + "2.554528" + ], + "text/latex": [ + "2.554528" + ], + "text/markdown": [ + "2.554528" + ], + "text/plain": [ + "[1] 2.554528" + ] + }, + "metadata": {}, + "output_type": "display_data" + } + ], + "source": [ + "#mean survival in years\n", + "mean(x)" + ] + }, + { + "cell_type": "code", + "execution_count": 17, + "metadata": {}, + "outputs": [ + { + "data": { + "text/html": [ + "2.0740803501976" + ], + "text/latex": [ + "2.0740803501976" + ], + "text/markdown": [ + "2.0740803501976" + ], + "text/plain": [ + "[1] 2.07408" + ] + }, + "metadata": {}, + "output_type": "display_data" + } + ], + "source": [ + "# standard deviation in years\n", + "sqrt(var(x))" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "## b) Frequency histogram" + ] + }, + { + "cell_type": "code", + "execution_count": 23, + "metadata": {}, + "outputs": [ + { + "data": { + "image/png": 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+ "text/plain": [ + "Plot with title “Histogram of x”" + ] + }, + "metadata": { + "image/png": { + "height": 420, + "width": 420 + }, + "text/plain": { + "height": 420, + "width": 420 + } + }, + "output_type": "display_data" + } + ], + "source": [ + "hist(x, breaks=seq(0, max(x), 0.1))" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "## c) Data summary\n", + "The mean survival in the treatment arm (2.5 years) is greater than the baseline mean survival (<1 year). However, the standard deviation in the treatment arm (2.07 years) suggests a large variability in the survival in the treatment arm. The histogram reveals that patients in the treatment arm seem to segregate in two groups: responders and non-responders. The former do not benefit from the treatment at all: almost all of them are dead after 1 year of treatment. The survival of the latter is greatly improved, and most patients survive for longer than the period of the trial. Note that since the study stopped after 5 years, the true mean survival of patients in the treatment arm is certainly more than 2.5 years, and the mean survival of responders even longer.\n", + "\n", + "## d) Recommandations for further research\n", + "Comparing patient data (medical folders, genomics) between responders and non-responders may eludicate a biomarker predictive of response, and a potential intrinsic resistance mechanism in non-responders." + ] + }, + { + "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": "3.6.3" + } + }, + "nbformat": 4, + "nbformat_minor": 4 +}