[PYTHON] While studying pandas, I did a free study on when corona would end and whether lockdown was meaningful.
Corona will end.
It's been a month since the state of emergency for the coronavirus was declared. Since I was working in Europe for research, I have been suffering from this virus since the middle of March. Jobs in Europe are no longer in this turmoil, and even though I'm looking for a job in Japan, I'm having a hard time getting a reply from everyone. (Thank you for the fact that it's GW and it's natural.) It's a waste of time to spend time at home, so I did some free research to see if the corona would end, as well as studying pandas.
What to use
Our world in data corona database (CSV based)
Only this was easy and I couldn't find a good guy. Please teach if you have a good database. https://github.com/owid/covid-19-data/blob/master/public/data/owid-covid-data.csv
Wikipedia lockdown page
https://en.wikipedia.org/wiki/Curfews_and_lockdowns_related_to_the_2019%E2%80%9320_coronavirus_pandemic#cite_note-51
Jupyter and pandas
Since this area is Mr. qiita, I will omit the introduction.
Data preparation
Cook the Wikipedia page in csv first.
It's really hard.
Read csv and organize data by country
df=pd.read_csv('/home/username/COVID19/owid-covid-data.csv')
df.date = pd.to_datetime(df['date'], format='%Y-%m-%d')
countries=pd.read_csv('/home/username/COVID19/countries.csv')
countries.lockdown_begins=pd.to_datetime(countries['lockdown_begins'], format='%Y-%m-%d')
countries.lockdown_ends=pd.to_datetime(countries['lockdown_ends'], format='%Y-%m-%d')
countries=countries.dropna()
countries.index=countries.iso_code
When I enter pandas, it looks like this (I messed with the index a little)
Wiki (Lockdown start date, end (planned) date)
Raw data
Take a subset of the data by country and index the date
def country(df,country_name):
newdata=df.loc[df.iso_code==country_name]
newdata.set_index(['date'],inplace=True)
return newdata
Now let's play with the data.
Anything is fine so let's plot
So, let's make a plot of the number of confirmed infections, the date and time of death, and the cumulative total, which we often see. The 7-day moving average seems to be a good way to avoid Saturday and Sunday data. Let's calculate the 7-day moving average and the positive rate.
def rolling_average(input):
columns=input.columns
input['new_tests2']=input['total_tests'].diff()
for column in columns[2:13]:
#Is the moving average ok on this line?
input[column]=input[column].rolling(7).mean()
#From the moving average of all cases and the number of tests (number of people), the cumulative positive rate and daily positive rate are calculated.
input['positive_rate_total']=input['total_cases']/input['total_tests']
input['positive_rate_diff']=input['new_cases']/input['new_tests2']
return input
The number of newly infected people on the moving average is declining, and the number of deaths is likely to exceed the pass. That's exactly what the news says. (As of May 3)
As reported, the daily PCR positive rate seems to be around 10% for the whole country. If the data is only for Tokyo, it will be quite different.
Main subject 1 What is the effect of lockdown?
Now that you've reproduced the news on jupyter, let's look at its relationship to lockdown. I've been watching it all the time (I checked every day for the first three weeks in Europe), a free Financial Times article for now Let's plot based on the day when the moving average of the dead became 3 people with reference to. This is the reference date for the spread of coronavirus in this independent study. All plots are divided by the maximum value (the value with the maximum number of infected or dead).
The day after the state of emergency was announced (4/6), 4/7 was the day when the number of people became three, and Japan was on the dead graph of the Financial Times, which had not been on this day. It appeared and it was extremely painful. I imagined a situation in which an infection explosion would kill tens of thousands of people in Japan, and I trembled. Fortunately, however, I think it was around April 17th that I was a little relieved after passing the peak of newly infected people in less than two weeks. It was like that, right? I can't say anything about the peak of deaths, but let's have a wishful thinking that last week has passed, as the same graph in other countries is about two weeks behind. (The number of deaths seems to vary depending on the medical situation in the country.) And we will be on 5/4 of the 25th day. Cancellation of the state of emergency at the end of the month is on the far right of the graph. At first glance, the number of new confirmed infections seems to settle down. Of course, you can make this figure from various countries. That said, the content is the same as the Financial Times, so let's take a look at Britain and France, which have been indebted to us, and Australia, which is doing well in quite developed countries.
In the UK, eight days after the moving average of three deaths had passed, the number of infected and dead people continued to increase for the next two weeks. It's very painful for me to be taken care of. At this stage, of course, there is no chance of unlocking the lockdown. By the way, the rightmost line is today. sad.
France was late in the lockdown, but by imposing a strict ban on going out and fines for unnecessary going out, it forced a significant restriction on the movement of people. The effect is very good now, and in terms of numbers, about 1,000 people are still confirmed to be infected every day, but the number of newly infected people is decreasing to 20% in the worst case, and the number of deaths is decreasing. At that time, I was confused by the strict prohibition of going out, but now I am getting a very high effect. The rightmost line is today's date.
Australia is not very familiar with the situation (did it not lock down?), But it seems that it stopped operating international flights from a very early stage. (That day is used instead of the lockdown start date.) As you can see, the effect is extremely high in Australia, where measures were taken before the deaths occurred, and the peak number of infected people ended before the death toll reached three. .. That means that at the time of the three dead, it has been cleared up. The line on the right is 5/3 days. In this case, if you go out carefully and avoid the clusters (three dense), you will be able to return to your original life by the end of this year.
how was it? It's a simple graph, but I feel that you can see the importance of lockdown and border protection.
Main subject 2 Disgusting graph
Apparently, the speed of lockdown and border measures was the key to corona measures. Calling this a cool name, Lockdown Delta, I tried various plots of the number of deaths and infections in the top 50 countries with the highest cumulative number of infections, and there were only two interesting figures. The first one is here. It's a very disgusting graph. After all, the vertical axis is the people we lost.
(I say lockdown efficiency, but there is a difference between the day when I just locked down and the cumulative total of 3 dead. It's a lockdown delta. Lol) The lockdown delta locked down faster as it went to the left and slower as it went to the right. Indicates that. The moving average peak death toll is taken vertically. As you can see, there is a clear correlation without machine learning or drawing a line. Japan has a lockdown delta of -1, so I think it's a pretty good one among other countries. The cluster from the end of February, the effect of avoiding three stakes may have come out. There is some debate about issuing a state of emergency a week earlier, but it can't be helped. Next, issue a state of emergency quickly. nice to meet you. </ ul> </ b> France, Spain, the United Kingdom, the United States, etc., where the lockdown delta has been delayed by more than 5 days, seems to have had very severe results. I think China was often able to lock down at this speed without any information. However, Russia and Brazil seem to be struggling even though the lockdown period is about the same as Japan.
When will the main subject end?
This is the relationship between the lockdown delta and the lockdown period at the place where the corona seems to have converged and where the lockdown was released.
Where the lockdown delta is small, the peak infection is fast and the infection starts to decrease immediately, and the number of deaths is small, resulting in a short time to release the lockdown. Fortunately, Japan's state of emergency was lockdown Δ = -1, so the lockdown period is about 65 days. I made everything in one day, so I didn't have time to draw a straight line, but I feel like I can unlock the lockdown at the beginning of June. On the contrary, those who are willing to move now are still sweet and may call for the next wave. Let's continue to visit May with Sutehom, Bisefu, Bikaind </ b> </ ul>
Europe has many countries with positive lockdown deltas, so it will take some time. If you pull the last graph in a straight line, I feel that it will take twice as much. It's hard, but I support you. By the way, in Australia, which I introduced earlier, the lockdown period is short because the lockdown was quick. Is there anything you care about? That's right, Norway. What's happening? Let's take a look.
The Norwegian lockdown was one step ahead of Europe on March 12th. The moving average reached three on April 3rd, which means that we had locked down more than 20 days ago. The lockdown ends on April 13th, which is only about 10 days after the moving average reaches three people. It's a fairly quick lockdown release, if not a complete return to your normal routine. The average daily moving average is eight, and a cumulative total of 200 people have been killed, but it is probably the best in Europe, where people are moving actively.
At the end
how was it? It may seem uncertain in times of turbulence, but unless your country becomes a singular point, it seems that you can predict the future a little with simple data organization. This is my first free study, but if anyone finds it interesting, I will continue to post it frequently. I'll publish the source if you wish, but don't expect it as I'm not a very good programmer. If you have a chance to meet again, see you somewhere.