Skip to content

Instantly share code, notes, and snippets.

@fonnesbeck
Created April 26, 2017 21:32
Show Gist options
  • Star 0 You must be signed in to star a gist
  • Fork 0 You must be signed in to fork a gist
  • Save fonnesbeck/fb11fa8420e23f1aacc7f8b3da10f8fe to your computer and use it in GitHub Desktop.
Save fonnesbeck/fb11fa8420e23f1aacc7f8b3da10f8fe to your computer and use it in GitHub Desktop.
Vaccine efficacy power
Display the source blob
Display the rendered blob
Raw
{
"cells": [
{
"metadata": {
"trusted": true,
"collapsed": true
},
"cell_type": "code",
"source": "from scipy.stats import norm, zscore\n\ndef sample_power_probtest(p1, p2, power=0.8, sig=0.05):\n z = norm.isf([sig/2]) \n zp = -1 * norm.isf([power]) \n d = (p1-p2)\n s =2*((p1+p2) /2)*(1-((p1+p2) /2))\n n = s * ((zp + z)**2) / (d**2)\n \n return int(round(n[0]))",
"execution_count": 1,
"outputs": []
},
{
"metadata": {
"trusted": true,
"collapsed": true
},
"cell_type": "code",
"source": "p0 = 100/1000\np20 = 80/1000\np30 = 70/1000\np40 = 60/1000\np50 = 50/1000",
"execution_count": 4,
"outputs": []
},
{
"metadata": {},
"cell_type": "markdown",
"source": "Power for detecting 20% decrease in infections"
},
{
"metadata": {
"trusted": true
},
"cell_type": "code",
"source": "sample_power_probtest(p0, p20)",
"execution_count": 5,
"outputs": [
{
"output_type": "execute_result",
"execution_count": 5,
"data": {
"text/plain": "3214"
},
"metadata": {}
}
]
},
{
"metadata": {},
"cell_type": "markdown",
"source": "Power for 30%"
},
{
"metadata": {
"trusted": true
},
"cell_type": "code",
"source": "sample_power_probtest(p0, p30)",
"execution_count": 6,
"outputs": [
{
"output_type": "execute_result",
"execution_count": 6,
"data": {
"text/plain": "1357"
},
"metadata": {}
}
]
},
{
"metadata": {},
"cell_type": "markdown",
"source": "Power for 40%"
},
{
"metadata": {
"trusted": true
},
"cell_type": "code",
"source": "sample_power_probtest(p0, p40)",
"execution_count": 7,
"outputs": [
{
"output_type": "execute_result",
"execution_count": 7,
"data": {
"text/plain": "722"
},
"metadata": {}
}
]
},
{
"metadata": {},
"cell_type": "markdown",
"source": "Power for 50%"
},
{
"metadata": {
"trusted": true
},
"cell_type": "code",
"source": "sample_power_probtest(p0, p50)",
"execution_count": 8,
"outputs": [
{
"output_type": "execute_result",
"execution_count": 8,
"data": {
"text/plain": "436"
},
"metadata": {}
}
]
}
],
"metadata": {
"kernelspec": {
"name": "python3",
"display_name": "Python 3",
"language": "python"
},
"language_info": {
"name": "python",
"version": "3.6.1",
"mimetype": "text/x-python",
"codemirror_mode": {
"name": "ipython",
"version": 3
},
"pygments_lexer": "ipython3",
"nbconvert_exporter": "python",
"file_extension": ".py"
},
"gist": {
"id": "",
"data": {
"description": "Vaccine efficacy power",
"public": true
}
}
},
"nbformat": 4,
"nbformat_minor": 2
}
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment