Demographics_Data_Processing.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "import pandas as pd"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "path = ### PUT PATH TO DATA HERE ###"

   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "We need to merge enroll date and diagnosis to create the Parkinson's disease and healthy control cohorts."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "ds = pd.read_csv(path + 'Randomization_table.csv',index_col=0)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "ds.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "patdemo = pd.read_csv(path + 'Screening___Demographics.csv')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "patdemo.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "df = ds[['PATNO', 'ENROLLDT', 'BIRTHDT', 'GENDER']].merge(patdemo[['PATNO', 'APPRDX']], how='outer', on='PATNO')"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Merge with PD features to include predominantly affected side information"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "dis_feat = pd.read_csv(path + 'PD_Features.csv')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "df = df.merge(dis_feat[['PATNO', 'DOMSIDE']], how='outer', on='PATNO')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "df[~df.ENROLLDT.isnull()].groupby('APPRDX').PATNO.count()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "df.to_csv('demographics.csv')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
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