Wednesday 22 December 2021

False positives

There are two kinds of error in medical diagnostic tests: the test indicates negative when there is disease present, or positive when there isn't.   Given that a person either has the disease or doesn't, and tests positive or negative, these four are the only possible outcomes:

  • Patient has the disease and tests positive - GOOD
  • Patient has the disease and tests negative - BAD
  • Patient doesn't have the disease and tests negative - GOOD
  • Patient doesn't have the disease and tests positive - BAD
The error rate for a diagnostic test is therefore fully specified by two statistics, labelled as % false positives and % false negatives.   Fine so far.

The problem is that the % false positives is not the percentage of positive test results that are false, although it sounds like it should be.  It is the (average) percentage of people who don't have the disease who none the less test positive.  The two things are very different.

To illustrate, let's consider an imaginary diagnostic test - a good one.   Let's suppose our test has a false positive rate of 1% and a false negative rate of 0%.   This would be an extraordinarily good test - I don't know if any tests available today meet these criteria.

Let's now suppose that we roll out this test on a population where the true rate of infection is, say 500 per 100,000.  (That is, 5 per 1000, or 1 for every 200 people) This kind of infection rate has our political leaders losing control of their anal sphincters, so it's a "bad" scenario. 

Let's test 200 of these people, chosen at random.  On average there will be one person infected, and our excellent test always indicates positive for that person.  But we also get around 2 false positives (1% of 199).  So if you are a member of this population, and you test positive, the chance that you actually have the disease is about 1 in 3, that is 33%, and the chances that you don't are about 67%.

If the false positive rate of our test was 10% (a more realistic figure), a positive test result would mean you had only a 5% chance of having the disease.   If the true infection rate were lower, the chances of having the disease if you test positive would be (even) lower. 

Wednesday 15 December 2021

Accordeon at Le Mans

Richard Galliano is a renowned accordeon player, and he gave a concert recently at the Palais des Congrès et de la Culture in Le Mans.   He was playing alongside the strings from the Orchestre Nationale de Pays de la Loire, conducted by Mme Alexandra Cravero, in what was billed as a tribute to Piazzolla, an Argentinian composer who is remembered for introducing the tango into the classical music repertoire.

We had decided to make a day of it, and went in time for lunch at the Auberge des Sept Plats, and then did some random shopping.   We had booked a room at a Chambres d'Hôtes just down the road from the concert, to minimise walking, and to avoid a long drive home late at night.

The official check-in time for the Chambres d'Hôtes was 5 PM, and we had some time to spare, so we found the place and Anita went and asked the man there if we could check-in a bit earlier.  He said there would be no problem after 4:30, and to park outside.  So we did.  Surprise.  After we rang the bell, a woman opened the window, told us we couldn't park there, and we couldn't stay anyway because she was ill.  And besides, she runs the place, and not the gentleman Anita had spoken to earlier.  I don't think I've ever experienced a more hostile reception.   We sat in the car and phoned the Ibis just down the road, and, being assured that they had plenty of rooms, drove there and checked in.

The concert was excellent.  Richard Galliano provided the musical excellence that one expects of a master; he played an accordeon for most pieces, and a bandoneon for Piazzolla's concerto for that instrument.   

The Ibis hotel to the north of the railway station was very friendly,  and with a bit more comfort and character than one might expect of a hotel aimed primarily at the business traveller.   It also provided a superb breakfast that lasted me nearly all day.

Thursday 9 December 2021

Submarine museum

I didn't know that there is a submarine museum at Gosport, but I saw a poster for it on the way from Portsmouth dock to my sister's place.  I decided to take a look.

I think that I was the only visitor at the time, so I got a personal guided tour of the big sub on display, HMS Alliance.  I expected it to be cramped inside, but when you think that a crew of 64 men was on board, that water was scarce and they didn't wash much, I can't imagine what they smelt like when they came ashore.

There were many interesting exhibits, so here's just a few that I found especially interesting:  A B40 communications receiver.  When I was a kid, I had a friend who had one of these, and we listened in to the radio hams around the world.   The wonders of SSB transmissions, and the strange sounds of the wireless world.  Actually the sub had a B41, but it was as I remember the B40, although smaller than I thought.

How about these for a bunch of push rods and rocker arms?  I bet the make a racket when they're going.

Apparently, submariners would keep the beer in the torpedo tubes to keep it cool.  I was sadly informed of The Great Beer Tragedy when the tube was evacuated without checking for beer first.

In a different part of the museum I came across this massive piece of ironwork.  It looked solid and must weigh several tons.  It is a chain tester; it was used to test the breaking strength of chains.  Here's the thing:  it was bought second-hand in 1901 and was in use until 2020.  That's more than one hundred and nineteen years of useful life.  I think we have become too complacent about things that stop working after 10 years or even less.

Finally, there was a squirrel in the grounds, cue my latest offering in my portfolio of wildlife pics, in an attempt to be accepted as a BBC wildlife photographer.

Wednesday 8 December 2021


While in England I decided to revisit some old haunts.   I have fond memories of wasting time along the river Meon, floating model boats that I had made, or just exploring.  It's less friendly these days, but still pretty, if only viewable now from the road.

Titchfield Abbey is still magnificent, spotlit in the evening, and the Fisherman's Rest, scene of many under-age drinking bouts, (at least, in my day) is still in business.

I wonder if I was a young teenager, I'd still be able to do what I used to there.  I doubt it.   I wonder what I'd do instead.

Tuesday 7 December 2021


This year I had the opportunity, not to be missed, of visiting the RAF museum at Tangmere before it closed for the season.   I took it.   I used to fly gliders there when I was a member of the Air Training Corps, and I have fond memories fo the place, so I went to see what they were up to.  The airfield itself has been turned over to growing vegetables, but some of the buildings remain.

I found it to be a fitting tribute to the people who flew and died, and learnt some interesting facts.   I didn't know that the RAF lost nearly 1,000 aircraft and the corresponding number of pilots in the evacuation of France, nor that Douglas Bader ran the training school at Tangmere towards the end of his career.

There was a lot of information about the pilots and the history of Tangmere, with example aircraft and flight sims that you could use.   Everything that you could reasonably hope for or expect in a museum of this kind.

I also noticed an atmosphere, a feel of the place if you like.   It was staffed, as far as I could tell, by ex-pilots and ground crew who were giving their time to help keep the memories alive.  They had "been there, done that", and had nothing to prove.  They were friendly and pleasant and knew their stuff.   I'm glad I went.

Monday 6 December 2021

There and back again

The trip to England was well planned, all sorted, until the Haunted Haystack announced that the arrival of the new MORONIC variant of our favourite bug warranted some changes to protocol.  He told us that we'd have to have to self-quarantine until our "day 2" covid test, now to be a PCR test and not the lateral flow test that we had booked and paid for, gave us a negative result.  But he didn't tell us when these changes might come into effect.

The problem was not just the waste of two days stuck indoors, out of a week in England, but the Tuesday of our planned arrival was the last day that the RAF museum at Tangmere would be open this year.  A lifetime ago, I flew gliders at Tangmere and wanted to go back to see what they had done.   This year we were visitng England early enough to go there.

The announcement was made on Saturday, and the necessary information appeared on government website on Sunday morning.  Shit!  The new rules took effect from 04h00 on Tuesday when we were scheduled to arrive at Portsmouth at 06h30.   Can we get an earlier ferry?  Departures from Caen were fully booked for the Monday, how about St Malo?   Yes, space on the ferry on Monday; it's a daytime crossing, can't be helped, book it.

And now the admin.  The cat boarding kennels are shut on Sunday, can we get him in?  Apologetic phone call, yes we can.  Piano lesson to cancel.  Can my sister put us up a day early?  Yes she can.  And while this is going on, Anita sends an email to the testing company -Prenetics-  and the conversation runs like this (paraphrased):

    - Is it possible to change the order from a lateral flow to a PCR?
    - Your request has been received and is important to us
    - Disregard my request because we don't need it
    - When the new regs come into effect you will have to upgrade to a PCR - feel free to contact customer support

But since we're now going early to avoid the new rules, we don't wish to, so we leave it at that, since we don't want to change the order.

Phew, now we're on the ferry.  Sorted, right?

Wrong.  Anita calls up Prenetics, just to confirm that all is well with the order for the Day 2 lateral flow test, and discovers that the order has been cancelled.   She then ends up in an argument with the person on the "help desk" who tries to tell her that the new testing rules apply right away (they don't)  and that a PCR test is now mandatory (it isn't).  Regardless, we can't buy the cheaper tests any more and have to get the more expensive ones.  *sigh*

So the bottom line is that we heard the news, changed the ferry to one that got in 6 hours earlier, and I got to visit the Tangmere museum.  It weren't that simple, though.

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