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calculate and add coverage info, change format #30

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Jun 23, 2020
Merged

calculate and add coverage info, change format #30

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176 changes: 123 additions & 53 deletions functions/Untitled.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,7 @@
"cells": [
{
"cell_type": "code",
"execution_count": 2,
"execution_count": 1,
"metadata": {},
"outputs": [
{
Expand Down Expand Up @@ -414,7 +414,7 @@
},
{
"cell_type": "code",
"execution_count": 3,
"execution_count": 2,
"metadata": {},
"outputs": [
{
Expand Down Expand Up @@ -445,7 +445,7 @@
},
{
"cell_type": "code",
"execution_count": 4,
"execution_count": 3,
"metadata": {
"scrolled": true
},
Expand All @@ -463,7 +463,7 @@
},
{
"cell_type": "code",
"execution_count": 5,
"execution_count": 4,
"metadata": {},
"outputs": [
{
Expand All @@ -480,7 +480,7 @@
},
{
"cell_type": "code",
"execution_count": 6,
"execution_count": 5,
"metadata": {},
"outputs": [
{
Expand Down Expand Up @@ -928,7 +928,7 @@
},
{
"cell_type": "code",
"execution_count": 7,
"execution_count": 6,
"metadata": {},
"outputs": [
{
Expand Down Expand Up @@ -1183,7 +1183,7 @@
"[3142 rows x 9 columns]"
]
},
"execution_count": 7,
"execution_count": 6,
"metadata": {},
"output_type": "execute_result"
}
Expand All @@ -1194,7 +1194,7 @@
},
{
"cell_type": "code",
"execution_count": 8,
"execution_count": 7,
"metadata": {},
"outputs": [],
"source": [
Expand All @@ -1214,12 +1214,12 @@
"date2 = []\n",
"k = 0\n",
"while True:\n",
" d = datetime.today() - timedelta(days=i)\n",
" date2.append(d+timedelta(days=7))\n",
" d = (datetime.today() - timedelta(days=i)).date()\n",
" i += 1\n",
" if cached_dir is not None:\n",
" cached_fname = oj(cached_dir, f'preds_{d.month}_{d.day}_cached.pkl')\n",
" if os.path.exists(cached_fname):\n",
" date2.append(d+timedelta(days=7))\n",
" add_predictions_7day(pd.read_pickle(cached_fname),df_tab)\n",
" else:\n",
" k += 1\n",
Expand All @@ -1229,7 +1229,7 @@
},
{
"cell_type": "code",
"execution_count": 25,
"execution_count": 65,
"metadata": {
"scrolled": true
},
Expand All @@ -1240,7 +1240,7 @@
"'test.html'"
]
},
"execution_count": 25,
"execution_count": 65,
"metadata": {},
"output_type": "execute_result"
}
Expand All @@ -1249,17 +1249,36 @@
"row = df_tab.iloc[0]\n",
"state,county,FIPS = row['State'],row['County']+\" County\",row['countyFIPS']\n",
"newdates = date1\n",
"fig = make_subplots(rows=1, cols=2, specs=[[{\"secondary_y\": True},{\"secondary_y\": True}]],subplot_titles=(\"Time series with 7 day prediction\",\"Time series with historical prediction\"))\n",
"fig = make_subplots(rows=1, cols=2, specs=[[{\"secondary_y\": True},{\"secondary_y\": True}]],\n",
" subplot_titles=(\"Time series with 7 day prediction\",\n",
" \"Time series with historical prediction(7 day)\"))\n",
"traces = []\n",
"keys_curves=['deaths','cases']\n",
"credstr ='rgb(179,0,10)'\n",
"cbluestr = 'rgb(42,100,244)'\n",
"fill_strings = ['rgba(179,0,10,0.4)','rgba(42,100,244,0.4)']\n",
"color_strings = [credstr, cbluestr]\n",
"\n",
"\n",
"red = '179,74,71'\n",
"blue = '83,137,190'\n",
"credstr ='rgb(' + red + ')'\n",
"cbluestr = 'rgb(' + blue + ')'\n",
"fill_strings = ['rgba(' + red + ',0.4)','rgba(' + blue + ',0.4)']\n",
"color_strings=[credstr,cbluestr]\n",
"\n",
"def make_traces(fig, row, pre, date1, date2, r, c, show_lengend,keys_curves=['deaths','cases']):\n",
"def cal_coverage(row,date1,date2,keys = ['deaths', 'cases']):\n",
" def cal(key, key_inv):\n",
" dic_real = {}\n",
" dic_pre = {}\n",
" for i in range(len(date1)):\n",
" dic_real[date1[i]] = row[key][i]\n",
" for i in range(len(date2)):\n",
" dic_pre[date2[i]] = row[key_inv][i]\n",
" hit = miss = 0\n",
" for d in dic_pre.keys():\n",
" if d in dic_real:\n",
" if dic_real[d] >= round(dic_pre[d][0],0) and dic_real[d] <= round(dic_pre[d][1],0):\n",
" hit += 1\n",
" else:\n",
" miss += 1\n",
" return (hit/(hit+miss))\n",
" return [cal(key, 'pred_7day_' + key +'_interval') for key in keys]\n",
"def make_traces(fig, row, pre, date1, date2, r, c, width,show_lengend,keys_curves=['deaths','cases']):\n",
" for j, key_curve in enumerate(keys_curves):\n",
" curve = row[key_curve]\n",
" traces = []\n",
Expand All @@ -1268,7 +1287,7 @@
" showlegend=show_lengend,\n",
" visible=True, #key == key0,# False, #key == key0,\n",
" name=key_curve,\n",
" line=dict(color=color_strings[j], width=4)) )\n",
" line=dict(color=color_strings[j], width=width)) )\n",
" low = np.hstack((curve[-1],[x[0] for x in row[pre+key_curve+'_interval']]))\n",
" up = np.hstack((curve[-1],[x[1] for x in row[pre+key_curve+'_interval']]))\n",
" if pre == 'pred_7day_':\n",
Expand All @@ -1279,20 +1298,20 @@
" showlegend= False,\n",
" x = date2,\n",
" y = up,\n",
" marker = dict(size=0),\n",
" line=dict(dash ='solid',color=fill_strings[j], width=0)))\n",
" traces.append(go.Scatter(x= date2,\n",
" y=row[pre+key_curve],\n",
" name = key_curve +' prediction',\n",
" showlegend= show_lengend,\n",
" visible=True,\n",
" mode = 'lines',\n",
" line=dict(dash ='dash',color=color_strings[j], width=4),\n",
" line=dict(dash ='dash',color=color_strings[j], width=width),\n",
" fillcolor = fill_strings[j],\n",
" fill ='tonexty'))\n",
" traces.append(go.Scatter(\n",
" name = 'Lower Bound',\n",
" visible = True,\n",
" showlegend= False,\n",
" marker = dict(size=0),\n",
" x = date2,\n",
" y = low,\n",
" fill ='tonexty',\n",
Expand All @@ -1301,61 +1320,112 @@
" for trace in traces:\n",
" fig.add_trace(trace, secondary_y=key_curve==\"deaths\", row=r,col=c)\n",
" return fig\n",
"fig = make_traces(fig, row,'pred_7day_',date1,date2,1,2,False)\n",
"fig = make_traces(fig, row,'pred_7day_',date1,date2,1,2,3,False)\n",
"newdates = [date1[-1] + timedelta(days =i) for i in range(0,8)]\n",
"fig = make_traces(fig, row,'pred_',date1,newdates,1,1,True) \n",
"fig = make_traces(fig, row,'pred_',date1,newdates,1,1,4,True) \n",
"for i in fig['layout']['annotations']:\n",
" i['font'] = dict(size=15,color='white') \n",
"\n",
"deaths_cov,cases_cov = cal_coverage(row,date1,date2)\n",
"# Update the margins to add a title and see graph x-labels.\n",
"fig.layout.margin.update({'t':150, 'b':120})\n",
" \n",
"fig.layout.update(\n",
" title ={'text':state+' '+county+ '<br>' + 'FIPS:'+row['countyFIPS'], 'y':0.92,\n",
" 'x':0.03, \n",
" 'yanchor': 'top'},\n",
" width=1200,\n",
" height=700,\n",
" font=dict(\n",
" size=12))\n",
"fig.update_layout(legend=dict(x=0.9, y=1.3))\n",
" title = dict(text = county+', '+state+ '<br>' + 'FIPS:'+row['countyFIPS'], \n",
" y = 0.92,\n",
" x = 0.03, \n",
" yanchor = 'top'),\n",
" width=1200,height=700,\n",
" font=dict(size=12),\n",
" legend=dict(x=0.5, y=1.2),\n",
" legend_orientation=\"h\"\n",
" )\n",
"fig.add_annotation(dict(font=dict(color=\"white\",size=11),\n",
" x=0.8,\n",
" y=0.9,\n",
" showarrow=False,\n",
" text='Cases Prediction coverage: '+str(round(cases_cov, 2))+'<br>'\n",
" ' Deaths Prediction coverage: '+str(round(deaths_cov, 2)),\n",
" textangle=0,\n",
" xref=\"paper\",\n",
" yref=\"paper\"\n",
" ))\n",
"fig.add_annotation(dict(font=dict(color=\"white\",size=12),\n",
" x=0.9,\n",
" y=1.3,\n",
" showarrow=False,\n",
" text='Modebar '+u'\\u2191',\n",
" textangle=0,\n",
" xref=\"paper\",\n",
" yref=\"paper\"\n",
" ))\n",
"## Set plot1 axes properties\n",
"y1 = max([x[1] for x in row['pred_cases_interval']])\n",
"y2 = max([x[1] for x in row['pred_deaths_interval']])\n",
"fig.update_xaxes(title_text=\"Date\",range=[datetime(2020, 3, 25), newdates[-1]],domain = [0,0.41],row=1, col=1)\n",
"fig.update_yaxes(title_text=\"Cases\", color='rgb(42,130,244)',rangemode = 'tozero',\n",
" dtick = y1/5,range=[0,y1], domain=[0,0.95],row=1, col=1) \n",
"fig.update_yaxes(title_text=\"Deaths\",rangemode = 'tozero',color='rgb(255,50,50)',\n",
" dtick = y2*1.3/5, range=[0,y2*1.3], secondary_y=True, row=1,col=1)\n",
"fig.update_xaxes(title_text=\"Date\",range=[datetime(2020, 3, 24), newdates[-1]],domain = [0,0.41],row=1, col=1)\n",
"fig.update_yaxes(title_text=\"Cases\", color=cbluestr,rangemode = 'tozero',\n",
" dtick = (y1-y11)/5,range=[y11,y1], domain=[0,0.95],row=1, col=1) \n",
"fig.update_yaxes(title_text=\"Deaths\",showgrid=False,rangemode = 'tozero',color=credstr,\n",
" dtick = (y2*1.3-y22)/5, range=[y22,y2*1.3], secondary_y=True, row=1,col=1)\n",
" ## Set plot2 axes properties\n",
"y1 = max([x[1] for x in row['pred_7day_cases_interval'][7:]])\n",
"y11 = min([x[0] for x in row['pred_7day_cases_interval'][7:]])\n",
"y2 = max([x[1] for x in row['pred_7day_deaths_interval'][7:]])\n",
"y22 = min([x[0] for x in row['pred_7day_deaths_interval'][7:]])\n",
"fig.update_xaxes(title_text=\"Date\",range=[date2[-1], date2[7]],domain = [0.59,1], row=1, col=2)\n",
"fig.update_yaxes(title_text=\"Cases\", color='rgb(42,130,244)',rangemode = 'tozero',\n",
" dtick = (y1-y11)/5,range=[y11,y1],domain=[0,0.95], row=1, col=2)\n",
"fig.update_yaxes(title_text=\"Deaths\",showgrid=False,rangemode = 'tozero',color='rgb(255,50,50)',\n",
" dtick = (y2*1.5-y22)/5, range=[y22,y2*1.5], secondary_y=True, row=1,col=2)\n",
"fig.update_yaxes(title_text=\"Cases\", color=cbluestr,rangemode = 'tozero',\n",
" dtick = (y1-y11)/5,range=[y11,y1], domain=[0,0.95],row=1, col=2) \n",
"fig.update_yaxes(title_text=\"Deaths\",rangemode = 'tozero',color=credstr,\n",
" dtick = (y2-y22)*1.3/5, showgrid=False,range=[y22,y2*1.3], secondary_y=True, row=1,col=2)\n",
"fig.layout.template = 'plotly_dark'\n",
"plotly.offline.plot(fig, filename='test.html', auto_open=True)"
]
},
{
"cell_type": "code",
"execution_count": 30,
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"print(len(date2))\n",
"len(row['pred_7day_cases_interval'])"
]
},
{
"cell_type": "code",
"execution_count": 18,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"2020-06-20 21:39:59.601047\n"
"ename": "ValueError",
"evalue": "Unknown format code 'd' for object of type 'float'",
"output_type": "error",
"traceback": [
"\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
"\u001b[0;31mValueError\u001b[0m Traceback (most recent call last)",
"\u001b[0;32m<ipython-input-18-f18988ccf924>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m\u001b[0m\n\u001b[0;32m----> 1\u001b[0;31m \u001b[0;34mf'{10.324335:03d}'\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m",
"\u001b[0;31mValueError\u001b[0m: Unknown format code 'd' for object of type 'float'"
]
}
],
"source": [
"print(date2[7])"
"f'{10.324335:03d}'"
]
},
{
"cell_type": "code",
"execution_count": 27,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"'↑'"
]
},
"execution_count": 27,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"u'\\u2191'"
]
},
{
Expand Down
10 changes: 5 additions & 5 deletions functions/test.html
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4 changes: 2 additions & 2 deletions functions/update_search.py
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Original file line number Diff line number Diff line change
Expand Up @@ -46,12 +46,12 @@ def add_predictions_7day(data,df):
date2 = []
k = 0
while True:
d = datetime.today() - timedelta(days=i)
date2.append(d+timedelta(days=7))
d = (datetime.today() - timedelta(days=i)).date()
i += 1
if cached_dir is not None:
cached_fname = oj(cached_dir, f'preds_{d.month}_{d.day}_cached.pkl')
if os.path.exists(cached_fname):
date2.append(d+timedelta(days=7))
add_predictions_7day(pd.read_pickle(cached_fname),df_tab)
else:
k += 1
Expand Down
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