Tool for FreeBSD which extracts, curve-fits a logistic function and transposes JHU-CSSE's Covid-19 data by country

rigoletto@

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my uncle in Sao Paulo swears by the Albert Einstein hospital, which is clearly very good and private.
The two best private hospitals in Brazil are Albert Einstein and Sírio-Libanês, hard to know which one is better (and more luxurious), and a large part (likely the majority) of the doctors in those hospitals, specially the most specialized ones, are also the ones you will meet in the top public ones.

The public ones is where they make their name and the private ones is where they make their wealth. :)
 

PMc

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That is why I like this place. Someone solves a problem he has, makes that public, and the sure-as-heck to come probing (otherwise known as bickering) of the methods is both civil and on a level most people out there won't get. Great.

W.r.t. Russia, my grapevine sings about them stamping almost all deaths of this bug as pneumonia. That may be technically correct.
Well, it is correct. What we happen to have is a flu and a mass hysteria.

There were kinds of flu in the past which were highly contagious, and a flu could always lead to pneumonia, and that could always be fatal, specifically for the old and the weak. There is nothing out of the ordinary.

One lesson learned from this is to check and heavily control the use of antibiotics in livestock management. The areas with high rates of people dying correlates with high-density animal farming. MRSA is a high cause factor here.
This is not surprizing, but there is a lot more to it. We are used to have vaccination against flu, which lots of people get.
The effect is that the physis does never learn how to go thru a severe infection and survive, which leads to generally less stamina in that regard - because, just like everything in the physis (brain, muscles, etc.), this also has to be trained. And worse, at work we are not expected to be ill for a week or two and go thru it, we are expected to have the modern medicine just switch the illness off. That is against nature.
Furthermore, we have a high population of elderly people, many of these being still alive only because of the features of that modern medicine, and being trained to be dependent on these. Otoh, it was always the task of nature to weed out the old, weak and permanently ill, and that is true for as long as life exists. Over all, the regimen of "modern science" is against nature in almost all regards, and sooner or later that must backfire.
 

Crivens

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PMc well, what we have is a flu that doubles the normal amount of dead people in a city per time. That is not normal.

And we can be really really happy this is something from the tribe of flu and not from f.e. measels. Then the world would be really deep in the popy. Without a depth gauge.
 

rigoletto@

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One lesson learned from this is to check and heavily control the use of antibiotics in livestock management. The areas with high rates of people dying correlates with high-density animal farming. MRSA is a high cause factor here.

There was a article about the concern of the USA with its military personal, specially abroad, because of the high use of prophylactic antibiotics used by the military to treat anything...
 

ralphbsz

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Hospitals in Dresden and now hospitals in Nordrhein Westfalen were opened for and received already the first patients from northern Italy in order to help out with their capacities. Per Google Maps, Bergamo to Dresden is 951 km and a 10 h drive. Of course this can be done in Brazil and elsewhere as well.
The first two patients from Italy went to Leipzig last night (saw it in the German newspaper). They were transported in an Italian airforce transport plane, a C130, in isolation intensive care litters, directly from Bergamo to Leipzig. There are impressive pictures in some newspapers ("Die Zeit" hat an article I read). The patients were so critical that they had to be re-stabilized after transport. I haven't had time today to read newspapers; right now is the first time I have 15 minutes of free time today, and it is nearly 11 at night!

I do not have much experience with hospitals neither in Brazil nor in Germany. My son was born in a private hospital in São Bernardo do Campo and my daughter was born in the pseudo public IAMSP hospital in São Paulo.
Small world! I was born in Campinas, but that was nearly 60 years ago. Unfortunately, I have had too much experience with hospitals in Brasil; that happens whenyou have elderly parents.

I believe that dedication of the medical staff is as least if not more important than the technical resources.
Exactly. And this is one of the reasons the SUS (the public health system in Brasil) is so good: Well trained and highly caring and dedicated staff.

Regarding your question what countries I'm interested in: Obviously the US. I just haven't had time to download and run your code, been super busy. But I will immediately add a word of warning: It is silly to speak about "the US", because that is an average over vastly different regions. The pandemic first hit in California (right here, in the bay area), and then in New York a few days later. In the meantime, it has grown much larger in New York. But looking at "the US" as a whole ends up averaging totally disparate regions. Bay Area and New York are similarly rich, and similarly well networked internationally, but the Bay Area has much more connection to Asia, in particular China, while New York has much more connection to Europe. The US is also very big, the distance from Seattle to Miami is about like Madrid to Moscow, not just in kilometers, but also in cultural and economic difference. And the US has subregions that are economically and geograpically very distinct; Kentucky and Montana are neither like Boston, or Chicago, or San Francisco. Taking infection statistics and averaging then over all of the US really makes a mess of the data.
 

unitrunker

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I've been using this for reference - but working with the data directly has its own appeal.

https://www.worldometers.info/coronavirus/

Caution: above does have ads in the sidebar.

Looking at the John Hopkins data - the USA data is under "daily reports".

I'm comparing the numbers above to what the State of Texas reports.

https://txdshs.maps.arcgis.com/apps/opsdashboard/index.html#/ed483ecd702b4298ab01e8b9cafc8b83

If that link does not work ... go to the main page and click on the "COVID-19 Dashboard" link.

https://dshs.texas.gov/coronavirus/

The numbers aren't exact 1:1 but seem to agree.
 
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obsigna

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I've been using this for reference - but working with the data directly has its own appeal.

https://www.worldometers.info/coronavirus/

Caution: above does have ads in the sidebar.

Looking at the John Hopkins data - the USA data is under "daily reports".

I'm comparing the numbers above to what the State of Texas reports.

https://txdshs.maps.arcgis.com/apps/opsdashboard/index.html#/ed483ecd702b4298ab01e8b9cafc8b83

If that link does not work ... go to the main page and click on the "COVID-19 Dashboard" link.

https://dshs.texas.gov/coronavirus/

The numbers aren't exact 1:1 but seem to agree.
This thread is about analysis of time series and not about the competition on who is able to report the latest and greatest numbers. For analysis of time series, consistency of the data set is the most important factor. Differences of the numbers between data sources can be mostly attributed to different reporting periods, and this must be consistent along the series.

CSSE@JHU provides the whole Covid-19 data set for download. They even do maintain the data set by correcting numbers from previous days if erratas arrive. Can we download somewhere any sort of maintained Covid-19 time series from Worldometer's site? Or from anywhere else?
 

unitrunker

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Can we download somewhere any sort of maintained Covid-19 time series from Worldometer's site? Or from anywhere else?
Unknown. If I find such a source, I'll post here. How I got here was compiling my own time series from local reported daily numbers which quickly became a pain.

It's a little odd that the JH data does include USA numbers but omits the data in their time series. Not a big deal to generate the series from the daily files.

As stated above, working directly with the data has its own appeal.
 

PMc

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PMc well, what we have is a flu that doubles the normal amount of dead people in a city per time. That is not normal.
Okay. But then, who defines "normal"?
I prefer a different approach: there was a way people used to live, right from the beginning (say minus 100k years, or maybe a million) until about 100 years ago, and it did not change so very much during this long time. That way of living has proven to work, because otherwise we wouldn't be here.
And there is an other way how people live, that was established during the last 100 years. If you care to look, that way is very different - and it has not yet proven to work.
In the old way, it was normal to grow your own food, and to work mostly outside. It was also normal to get 10 children, where six of them would die before the age of 4.
I don't say the old way was better, I only say, the changes aren't yet verified to be ok (that takes a couple of generations).

In my youth I was told that good food and working mostly outside (or doing things like walking barefoot in the snow) strengthens the resistability against catching a cold and such. Few people nowadays do such things; they rather prefer to believe in antibiotics and medicine.
There are many such little changes, and all together they may explain the death toll.
 

unitrunker

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Can we download somewhere any sort of maintained Covid-19 time series from Worldometer's site? Or from anywhere else?
Summary of alternatives.


None look as good as the JH dataset. Turns out the Texas link above derives from the JH dataset.
 
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obsigna

obsigna

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Summary of alternatives.


None look as good as the JH dataset. Turns out the Texas link above derives from the JH dataset.
OK, I will stay with the CSSE@JHU Covid-19 time series. I am back at the drawing board of modelling now. A group at the Humboldt University in Berlin set up modified SIR differential equations in order to explain why almost all the curves are not exponential ad infinitum: http://rocs.hu-berlin.de/corona/docs/forecast/model/
I know why, because according to Einstein only two things are infinite, the universe and human stupidity, and he continued, that he is even not sure about the former. Anyway, I will build an ODE integrator into my tool, so it can do curve fitting of a set of ordinary differential equations against said CSSE series. Don't tell me that it is not possible to use an ODE solver together with the LM algorithm, I did this in the past several times with success.
 

ralphbsz

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I prefer a different approach: there was a way people used to live, right from the beginning (say minus 100k years, or maybe a million) until about 100 years ago, and it did not change so very much during this long time. That way of living has proven to work, because otherwise we wouldn't be here.
It worked barely. Humanity was nearly wiped out several times by infectious diseases, such as the bubonic plague. At times, whole parts humanity (geographic, cultural or ethnic groups) were fully wiped out; if you look at the history of for example the pacific island nations or Greenland, quite a few were settled multiple times, because the previous settlers had become extinct. Not to mention wars; the 30 year war was way more brutal than anything in recent memory.

Compared to that, the last 100 years were not particularly worse. Except from an ethical point of views.

In the old way, it was normal to grow your own food, and to work mostly outside.
That has not been the norm since about roman times in the west, so this is old news.
 

Crivens

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PMc you may be partly right, but almost exactly 100 years ago the spanish flu was out and about. And it killed more people than WW1 did. So the lifestyle does not really serve as an argument. We have factors in both ways. I for one do not know enough of these factors to have a conclusion. But I know whom to ask...
 

PMc

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PMc you may be partly right, but almost exactly 100 years ago the spanish flu was out and about. And it killed more people than WW1 did.
I am most times only partial right - that's human nature. But this is basically what I am saying: such things have happened before - there is nothing out of the ordinary. And yes, it kills people. That is also normal, it fact there is only one thing we know for certain: that we will die.
I travelled quite a bit thru Africa and Asia, and one thing that impressed me very much, is, that death is much more conscious there, as something that is normal and can always happen. Consequentially, life is also more vivid and colourful there, because that relates, and you can't have one without the other. And I for my part enjoyed that freedom much, not being protected 24-hours by buerocrats, but actually being allowed to take care for myself. Only that way I learned that actually Nature -or God, which equates- takes care for me, and I found many things that way, even water in the desert.
In contrast, our super-protected and super-insured, super-sterile western life makes us being full of fear and neurosis that something bad might happen to that life which we most of the time don't really live. But probably, now, we can make a great step forward and reduce ourselves further to mere online-creatures, cage-kept roboters existing only for work and consume.
 
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