Data on Jean-Etienne's blog

COVID-19 cases in Maryland congregate living facilities

Sun, 15 Nov 2020 14:31:07 +0000

Five months ago, I was wondering why Maryland remove COVID-19 cases from its count in congregate living facilities (nursing homes, prisons, …). I still don’t have any answer but I found a technical solution :-)

The Python script (in src/ in the MD-coronavirus repo on Github) just fills in the latest data for days where data is missing. On a side note, it also fix some basic issues like a reporting date in year “0200” (instead of “2020”). You can play with the fixed data file here.

COVID-19 cases in Wallonia schools

Mon, 26 Oct 2020 23:25:29 +0000

In Wallonia (Southern part of Belgium), universities are already back to only giving online classes, schools will be closed two additional days after the Autumn holidays (so November 2-11), and secondary schools (12-18 years-old children) will be virtual for the 3 days before the Autumn holidays (so October 28-30). The reason? The exploding number of COVID-19 cases in schools.

In Wallonia, education is in the hands of the French-speaking Community (along with Brussels) but its statistics department doesn’t seem to provide public data on COVID-19. For that, we have to look at ONE (roughly: " Office for births and infancy") that communicate weekly numbers of cases and quarantines in children in schools via press releases (forcing us to parse PDFs but it’s better than no data).

COVID-19 clusters in Belgium

Mon, 19 Oct 2020 22:15:08 +0000

Recently (I’m writing this on October 20), the (new) Belgian government decided to apply more stringent prophylaxis measures to contain COVID-19. One of the controversial measure is to close bars and restaurants for a month.

Unfortunately, in a way, at approximately the same time, AVIQ released its latest poll on COVID-19 clusters in Wallonia ( AVIQ is the Walloon agency for well-being, health, handicap and family). I wrote it was unfortunate because I read and heard several people who criticized the closing of bars and restaurants by citing this poll. But this poll cannot answer in favor or against this closure; it doesn’t look at that …

A third of Maryland counties tested more than 25% of residents

Tue, 11 Aug 2020 15:25:11 +0000

Sometimes, you think that you found something interesting but the Maryland Department of Health is already presenting it on its COVID-19 dashboard :-D

For instance, I calculated the percentage of residents of the different counties ever tested (regardless of the test result). I found out that a third of Maryland counties (8/24) tested at least once more than 25% of their residents. Indeed, as of yesterday (August 10), here are the counties in that category:

COVID-19 hospitalization by age in Maryland

Sun, 09 Aug 2020 17:37:08 +0000

Since mid-July 2020 in Maryland, we understood that the 20-59 yr age group was problematic, especially the 20-29 yr age group that is racing to overtake all age groups in terms of number of COVID-19 cases (relative to their population, see top chart below).

In terms of COVID-19 hospitalizations, we also saw a small rebound (see chart below; it seems that it subsides since beginning of August).

But what we didn’t know (for this small peak as well as since the beginning) was what is the age of these hospitalized populations. Did these hospitalizations impacted more the older adults? The younger ones? Or the children? The Maryland Department of Health COVID-19 dashboard doesn’t report that information (nor in the API).

What does release from home isolation mean in Maryland?

Wed, 05 Aug 2020 11:05:10 +0000

Since the beginning of this pandemic, one metric intrigued many of us in Maryland: the cumulative number of people released from isolation. Initially (before the data release via API, when there was only the MDH dashboard), it was even thought to be the number of hospital patients released from isolation. It’s not: the API page mentions:

Total Number Released from Isolation data layer is a collection of the statewide cumulative total of individuals who tested positive for COVID-19 that have been reported each day by each local health department via the ESSENCE system as having been released from home isolation. As “recovery” can mean different things as people experience COVID-19 disease to varying degrees of severity, MDH reports on individuals released from isolation. “Released from isolation” refers to those who have met criteria and are well enough to be released from home isolation. Some of these individuals may have been hospitalized at some point.

A first insight on COVID-19 contact tracing in Maryland

Mon, 03 Aug 2020 21:47:09 +0000

I may have missed when the data was first released but I discovered the Maryland Department of Health (MDH) is publishing some data about COVID-19 contact tracing (in Maryland). This data is not on the main COVID-19 dashboard but on the contact tracing page (and in the datasets that can be downloaded). Here is a first insight of what happened so far …

Note: if you just look for where to get tested in Maryland, the official information is here.

What is the COVID-19 positivity rate in Maryland?

Mon, 27 Jul 2020 03:32:50 +0000

Every day, Governor Hogan and members of his team are communicating news on the COVID-19 situation in Maryland via Twitter (and other media): @GovLarryHogan, @riccimike, @katadhall, … (and of course: @MDHealthDept too!). A number of data enthusiasts are also parsing the MD Department of Health data: @TylerFogarty7, @MikeBReporter, @JauquetW, @PrayagGordy, … and of course: @jepoirrier) … And this is only on Twitter!

But also every day, there is one thing that constantly changes: how everyone is calculating the COVID-19 positivity rate. Today (July 26), for instance, the different daily positivity rates announced are: 3.77% ( Hogan), 4.47% ( Hogan again in the same tweet, Hall, Ricci, MD Health Department, Fogarty) and ~6% (for me, the exact number behind the ~ is 6.14%). This doesn’t show the 7-days (or n-days) averages and other measures. And this is only on Twitter.

Gender of COVID-19 cases and deaths in Maryland

Wed, 15 Jul 2020 02:37:12 +0000

After my previous posts about age of COVID-19 cases and deaths in Maryland, it was logical that I write about the gender of these cases and deaths. Rest assured: this time, it will be much shorter ;-)

Indeed, in a nutshell, in Maryland (like in the rest of the world), women are more impacted than men by the disease. But men are dying of the disease a little bit more than women.

Note: this post was updated on July 15, 2020, to fix an error in my code!

Age of COVID-19 deaths in Maryland

Fri, 10 Jul 2020 03:51:31 +0000

After my previous post on the age of COVID-19 cases in Maryland, it was logical that I write about the age of COVID-19 deaths in Maryland. So far, media and State Departments of Health all agreed that the older someone is, the more risk this person has to die from coronavirus.

So far, this is unfortunately also true in Maryland. In the graph below, we clearly see that people 50-59 years old have more than 250 deaths, people 60-69 have more than 500 deaths, people 70-79 have more than 750 deaths and people 80+ have nearly … 1,5000 deaths! The graph at the bottom also clearly shows that people in age categories 60 and above provide most of the new daily deaths due to COVID-19 (even if we came back down from a peak at about 40 deaths in 80+ at the end of April).

Age of COVID-19 cases in Maryland

Thu, 09 Jul 2020 13:02:00 +0000

We recently heard in the US media that, if COVID-19 affected more the older population, beginning of 2020, the younger population was now more affected, especially young adults (various reasons were mentioned: the various academic breaks, being more active or “forced” to work, the sentiment of invincibility …). I wanted to see if one could see a similar trend in Maryland.

If you look at the section of the Maryland population by age (graph below), as of today (July 9, 2020), you see that cumulatively, people 30-39 have the majority of cases, followed by people aged 40-49, 50-59 and 20-29 years old. There are relatively few cases above 70 years old and fewer cases below 20 years old.

Why would Maryland remove COVID-19 data from nursing homes?

Fri, 26 Jun 2020 03:16:33 +0000

Since the beginning of the COVID-19 pandemic, we suspected and saw that nursing homes and other facilities where people are grouped together (prisons, …) could be at higher risk of transmission. The focus on nursing homes was because deaths seem to disproportionately affect the older population that also resides there. And nursing homes are also home for frail people with comorbidities.

In its dashboard, the Maryland Department of Health quickly started to build a dedicated page with numbers from different “congregate facility settings”. As I did for other metrics from this dashboard, I made a chart of what seemed the cumulative total cases, differentiating staff (who are stuck working there) and residents (who stuck living in these facilities):

COVID-19 inequalities in Maryland

Sat, 13 Jun 2020 01:54:42 +0000

The recent Black Live Matters protests made me think a lot - as a white man, as a husband and dad, as a biologist by training, as a health economist by day, as someone interested in COVID-19 data where I live by night … as a human, in summary. I don’t have grandiose pieces of advice or any deep thoughts, not for here (but if you call me, we can talk ;-)). Here, let’s continue our exploration of COVID-19 data in Maryland.

Weekly seasonality in COVID-19 deaths reported in Maryland

Wed, 03 Jun 2020 21:58:48 +0000

On its dashboard, the Maryland Department of Health is reporting confirmed deaths due to COVID-19 in two ways: by date of report and by date of death (updated as amendments to the death record are received). The definition of confirmed death is:

A death is classified as confirmed if the person had a laboratory-confirmed positive COVID-19 test result.

What I was intrigued is that reporting seems to follow a pattern influenced by the day of the week (see figure below). The top chart (cumulative) is just an addition. A plateau would be welcome: it would indicate death rate is slowing down. Today, the COVID-19 death rate is 41 / 100,000 population. The bottom chart shows the number of deaths due to COVID-19 reported each day: the black line represents the number of deaths each day they were reported; the grey line represents the number of deaths each day they occurred.

A glimpse at COVID-19 cases in some Maryland ZIP codes

Sun, 31 May 2020 03:24:47 +0000

A publicly-available MD COVID-19 metrics that I didn’t investigate much is cases per ZIP code. I created a dashboard where you can highlight one zip code at a time. Tyler Fogarty built a cool Treemap Explorer. Silver Chips has a nice heatmap of all zip codes as part of their extensive dashboard (a bit like the MDH dashboard). How can we make sense of all this?

A classical way to see it is to look at the daily number of positive cases, similarly to what I did for counties or the state.

Will it be the end of Stage 1 in Maryland?

Sat, 30 May 2020 21:00:18 +0000

Since May 14, 2020, Maryland is carefully reopening from an easy lock-down caused by coronavirus spreading thru the community (and all over the world). In this post, I’ll go through all the variables we have on the MD Health Department dashboard. But first, the official data comes from the MD dashboard and if you want scientific information about COVID-19, please consult the CDC website. If you are interested, you can read my previous posts on COVID-19 in Maryland from this page.

No visible impact yet of different COVID-19 Stage 1 strategies in Maryland

Thu, 21 May 2020 06:25:25 +0000

In my previous post, I was wondering if Maryland was ready to reopen, ready to enter Stage 1 of COVID-19 recovery. I also mentioned, in the end, that if Gov. Hogan announced the reopening of Maryland, he also gave counties the power to “fully” open, to be partially open or even to remain closed. You can see more info about Maryland Strong: Roadmap to Recovery: there is a map of what Counties decided.

Is Maryland ready to reopen?

Sun, 17 May 2020 03:59:11 +0000

A visual analysis of Governor Larry Hogan’s decision to enter Stage 1 of reopening Maryland.

(This will be a post based on a thread of tweets I posted on May 14 with updated graphs for today - one days after the start of Stage 1 - and more)

Maryland is in state of emergency since March 5, 2020 due to COVID-19. Governor Larry Hogan announced on May 14 that Maryland will " gradually reopen with flexible community-based approach" ( the official declaration is here). The MD Strong plan said " a 14-day downward trajectory of benchmark metrics - or at least a plateauing of rates - is required before recovery steps can begin". This Phase 1 started yesterday, May 15, 2020. So, are we there already?

MD counties COVID-19-specific death rate

Sun, 17 May 2020 02:32:22 +0000

Since a few weeks, I report the raw number of COVID-19 deaths in Maryland counties. If this gives an idea of the cumulative number of deaths - which is interesting - it doesn’t reflect the fact that some counties have more inhabitants than others. That’s why I plotted below the number of COVID-19 deaths adjusted for the population (i.e. the COVID-19-specific death rate):

Today (May 16, 2020), in terms of absolute number of deaths, Montgomery, Prince Georges and Baltimore County are the top 3 counties (this is the same for cases but not in the same order). In terms of confirmed deaths per 100,000 population, the top 3 counties are Kent, Prince Georges and Montgomery.

MD counties COVID-19 cases adjusted for population

Tue, 12 May 2020 04:42:23 +0000

Since a few weeks, I report the raw number of COVID-19 cases in Maryland counties. If this gives an idea of the cumulative number of cases - which is interesting - it doesn’t reflect the fact that some counties have more inhabitants than others. That’s why I plotted below the number of COVID-19 cases adjusted for the population:

Evolution of COVID-19 confirmed cases in Maryland counties, adjusted and not adjusted for population, on May 11, 2020

Trend in Coronavirus cases in Maryland (3)

Mon, 27 Apr 2020 16:12:00 +0000

Following up on my two previous posts ( here and here), I am writing a third post on COVID-19 in Maryland because I believe we enter a new phase.

Before continuing, please note that the same disclaimer as in my previous post applies here (in short: read the CDC and MDH websites for official information).

In the first phase, the importance was to detect and make sure COVID-19 patients were treated (also: make sure not to overwhelm the healthcare system, flatten the curve, lower the baseline, & stay at home!). My two previous posts were following these efforts, thanks to daily data released by the Maryland Department of Health (MDH) on its dashboard. My second post will still be updated with the latest data from there, go read it!

Trend in COVID-19 cases by Zip code in Maryland

Mon, 27 Apr 2020 00:43:35 +0000

Since the Maryland Department of Health (MDH) started to display number of COVID-19 cases for each Zip code in its dashboard, I was wondering how to display this information in a nice way. The MDH display the information as a map - very nice but it lacks from where each Zip code came from: is the number of cases increasing or decreasing?

Following on my busy chart with the evolution of all Zip codes (and highlighting just one of them - that may not be the one you are interested in, see previous post), I created a simple dashboard where you can select the Zip code you are interested in and see how cases are evolving. You can play with it here: https://jepoirrier.shinyapps.io/md-coronavirus-zip-app/ (screenshot below). Enjoy!

Trend in Coronavirus cases in Maryland, USA (2)

Sun, 29 Mar 2020 03:12:18 +0000

This post was last updated on April 26, 2020.
A new post from April 27, 2020 is here.

Following up on my previous post, here are updated trends in Coronavirus cases in Maryland (USA), the state I live in. I am writing a second post because the Maryland Department of Health (MDH) updated its dashboard with way more data than before (more on this below). Before continuing, please note that the same disclaimer as in my previous post applies here (in short: read the CDC and MDH websites for official information).

Trend in Coronavirus cases in Maryland, USA

Mon, 16 Mar 2020 23:17:29 +0000

Disclaimer: Although I work in infectious diseases, I’m not a specialist in Coronavirus. For the most up-to-date information on Coronavirus in the US, please visit the CDC website. For the most up-to-date information on Coronavirus in Maryland, please visit the Maryland Department of Health. That being said, now you can proceed at your own risk ;-)

This post was updated by one post on March 28 and another one here on April 27. Read the latest one here.

283 tweets about flu today

Wed, 14 Nov 2018 05:01:54 +0000

I wanted to use the TwitteR package for R since a long time, I tried but didn’t do much of it. Today I found a few minutes, followed simple recipes (I admit), and looked at the number of tweets about flu today (November 13, 2018). Result: 283 tweets in English (I wanted to focus on the USA but, for some reason, I couldn’t … yet!). That’s not a lot. But remember we are only at the beginning of the influenza season 2018-2019 in the Northern hemisphere.

Time commuting in Belgium

Mon, 06 Aug 2018 18:41:19 +0000

DISO1 - Data I Sit On, episode 1. This post is the first of a series of a few exploring data I collected in the past and that I found interesting to look at again … (I already posted about data I collected, see the Quantified Self tag on this blog)

Life is short and full of different experiences. One of the experiences I don’t specifically enjoy but is integral part of life is commuting. Although I tried to minimize commuting (mainly by choosing home close to the office) and benefit(ed) from good work conditions (flexible working hours, home working, etc.), a big change occurred when I took a new opportunity, in 2015, to work in the Belgian capital, Brussels.

Increasing certainty in flu vaccine effectiveness

Fri, 23 Feb 2018 16:48:18 +0000

According to CDC data, studies are getting better at estimating the influenza vaccine effectiveness.

With the 2017-2018 flu season still going on in the USA, there are already some indication that vaccines have some effectiveness (although its target strains were mismatched). The CDC reports how it measures vaccine effectiveness here and I was interested in their confidence intervals (the interval that takes into account uncertainties to extrapolate to the broader, unknown population).

Euthanasia in the Netherlands and Belgium, 1990-2015

Fri, 18 Aug 2017 23:24:59 +0000

While parsing the general literature, I found this paper from van der Heide et al. (2017) giving some numbers about end-of-life decisions in the Netherlands these past 25 years. I was wondering if one could see similar evolution in Belgium. And I didn’t have to look very far: van der Heide cited another NEJM paper with Belgian numbers ( Chambaere et al., 2015 ; an attentive reader will notice “Belgian” data is “only” about Flanders, not the whole Belgium).

Activity tracker: waist vs. wrist

Thu, 17 Aug 2017 16:03:36 +0000

A few weekends ago, I was challenged by a friend to do more steps than him. Of course, I won ;-) But I noticed he was wearing his activity tracker on his wrist while I was wearing mine on my waist. As I noticed several times before, when I had an activity tracker on my wrist, these devices tend to capture some movements even if you don’t actually walk (while typing energetically on the computer or while driving for instance).

So I took the opportunity of a small trip to wear 2 activity trackers, one Fitbit One on my waist and one Fitbit Charge HR on my wrist.

Digitize you charts with Engauge Digitizer

Fri, 04 Aug 2017 16:31:39 +0000

A few words of appreciation for an open source software that can help you a lot in your work, Engauge Digitizer (ED) from Mark Mitchell. ED is a simple, straightforward curve digitizer: it takes images with graphs like the one below and transform them (with a little help) in data you can use later on.

Counting steps is the easiest way to reduce cardiovascular risk

Thu, 16 Feb 2017 01:42:00 +0000

After abandoning my Fitbit device in January because using it didn’t see improvement in my weight (see previous post), I was wondering if I could still measure my risk to develop cardiovascular diseases and other preventable chronic diseases (diabetes e.g.). So, still sitting at my desk (something I do for more than 8 hours a day in theory - probably more in practice), I looked into the ways to monitor my risk for these diseases …

Evolution of the number and causes of death in Belgium (2010-2014)

Fri, 20 Jan 2017 01:37:18 +0000

Statbel, the Belgian governmental organisation for data and statistics, just released mortality data for 2014 ( press release in French, dataset). The headline of their press release was that, for the first time, tumors were the first cause of death for Belgian men. Diseases of the circulatory system remains the main cause of death in Belgium, for women and for both sex together.

While the death of someone is a bad news in itself, I’m more interested here in the evolution of death causes. I’m interested in the evolution of causes of death because it might be a consequence of the evolution of the Belgian society and, as a proxy, of any (most) developed, occidental countries.

2013 in review: how to use your users' collected data

Sun, 19 Jan 2014 11:11:56 +0000

With a few days of interval I received two very different ways of reviewing data collected by users of “activity trackers”.

The first one came from Jawbone (although I don’t own the UP, I might have subscribed to one of their mailing-lists earlier) and is also publicly available here. Named “2013, the big sleep” it a kind of infographics of how public (and mostly American) events influenced sleep of the “UP Community”. Here data about all (or at least a lot of) UP users were aggregated and shown. This is Big Data! This is a wonderful and quantitative insight on the impact of public event on sleep! But this is also a public display of (aggregated) individual data (something that UP users most probably agreed by default when accepting the policy, sometimes when they first used their device).

More sleep with Fitbits

Wed, 08 Jan 2014 21:05:58 +0000

After a bit less than 2 hours, jepsfitbitapp retrieved my sleep data from Fitbit for the whole 2013 ( read previous post for the why (*)). Since this dataset covers the period I didn’t have a tracking device and, more broadly, I always slept at least a little bit at night, I removed all data point where it indicates I didn’t sleep.

So I slept 5 hours and 37 minutes on average in 2013 with one very short night of 92 minutes and one very nice night of 12 hours and 44 minutes. Fitbits devices do not detect when you go to sleep and when you wake up: you have to tell tem (for instance by tapping 5 times on the Flex) that you go to sleep or you wake up (by the way this is a very clever way to use the Flex that has no button). Once told you are in bed the Flex manages to determine the number of minutes to fall asleep, after wakeup, asleep, awake, … The duration mentioned here is the real duration the Fitbit device considers I sleep (variable minutesAsleep).

Getting some sleep out of Fitbits

Sun, 05 Jan 2014 00:11:21 +0000

After previous posts playing with Fitbit API ( part 1, part 2) I stumbled upon something a bit harder for sleep …

Previous data belong to the “activities” category. In this category it is easy to get data about a specific activity over several days in one request. All parameters related to sleep are not in the same category and I couldn’t find a way to get all the sleep durations (for instance) in one query (*). So I updated the code to requests all sleep parameters for each and every day of 2013 … and I hit the limit of 150 requests per hours.

Do you climb more floors when moving from an apartment to a house?

Wed, 25 Dec 2013 22:47:08 +0000

I continue to explore data about my physical activity in 2013 ( see part 1). We moved from an apartment (on the third floor of a building) to a house (with two floors) on July 1st, 2013. I was wondering if the change would have an impact on the number of floors I climbed: I now have to climb to reach bedrooms and go down to go in the living room. A standard house.

2013 with Fitbits

Mon, 23 Dec 2013 23:22:46 +0000

2013 is near its end and it’s time to see what happened during the last 360 days or so. Many things happened (graduated from MBA, new house, holidays, ill a few days, …) but I wanted to know if one could quantify these changes and how these changes would impact my daily physical activity.

For that purpose I bought a Fitbit One in March 2013. I chose Fitbit over other devices available because of the price (99 USD at the time) and because it was available in Europe (via a Dutch vendor). At that time the Jawbone Up was unavailable (even in the USA) and the Nike Fuelband couldn’t track my sleep.

Belgium doesn't score well in the Open Data Index (not speaking about health!)

Mon, 11 Nov 2013 23:00:35 +0000

The Open Knowledge Foundation (OKF) released the Open Data Index, along with details on how their methodology. The index contains 70 countries, with UK having the best score and Cyprus the worst score. In fact the first places are trusted by the UK, the USA and the Northern European countries (Denmark, Norway, Finland, Sweden).

And Belgium? Well, Belgium did not score very well: 265 / 1,000. The figure below shows its aggregated score (with green: yes, red: no, blue: unsure).

Is it so difficult to maintain a free RSS reader?

Mon, 05 Aug 2013 12:04:10 +0000

A few months ago Google decided to retire its Google Reader (it stopped working on July 1st, 2013). As it was simple, effective and good-looking, a lot of people complained about this demise. A few days ago The Old Reader, one of the most successful replacement for Google Reader, also announced it will close its gates, only to keep early registered users. And today Feedly, another successful alternative, announced it is introducing a pro version at 5.00 USD per month.

Will we see more babies named George in England and Wales?

Thu, 01 Aug 2013 19:13:18 +0000

A few days ago Prince William and Duchess Catherine of Cambridge gave birth to Prince George. Today at the office we were wondering if we will see more babies names George in UK. Very important question indeed!

So I went to the UK National Statistics website and looked for baby names in UK. Let’s focus on England and Wales only. There are two datasets for what we are looking for: one for the period 1904-1994 (by 10 years steps) and one for 2004 (if we want to be consistent with the 10 years step in the first dataset). I extracted the ranking relevant for us here: for babies called William, George (and Harry, William’s brother). The data is here.