Three month post

A bunch of good things.

First of all, I have finished my first "real" project, a prognostication tool that compares multiple prognostic models in advanced cancer patients.  I have it hosted on pythonanywhere.com which has been great, and I actually bought a real domain name for it as well.

The website is here, not that anybody is reading this blog or really going to find it through here:

www.predictsurvival.com

I learned quite a bit more about how setting up a site works, more html, a lot more css, a fair bit of easy flask and python (I haven't yet really taken advantage of the power of flask to make a dynamic site or use databases).  In reality, this site is just a calculator.

With respect to reading, JT has been making great strides.  I think it has helped that I have consciously backed off on pushing him to read and will just read to him.  Having books that he likes to read over and over again help a lot too.  Some books he has recently read by himself:

The Berenstain Bears and the Spooky Old Tree (he is really on a Berenstain Bears kick)

He still has a tendency to try and guess a word based on the first couple of letters and the context rather than sound things out. He has quite a sight word registry as well which is mostly what he uses, but he is also more open to sounding out words and does a pretty good job of it.

We've also been working on some new games that I thought I'd share.

"Word Builders"

-We are trucks who go to the pile of letters and bring them to the boss, who asks for a word to be made.  The boss usually asks for limiting factors like "three letters" or "has the letter H in it".  Then he sounds out the word

Another Month Goes By

I feel that my worst concerns about pushing reading too hard have come true.  I don't think he likes reading.  I haven't seen him spontaneously read a book for months.  I know he can read all the words in Endless Reader, and I know when I'm reading to him if I point to a word he will read it, but when he does look at books I think he is just looking at the pictures.  I miss the pride he had when he would read "Just a Little Sick".

I am just trying to back off and let him rediscover it, but I'm not sure if I should come at him laterally with different things to reengage him or just wait for it to return spontaneously? I'll probably just make it worse.

On a positive note, he is really good at rhyming words now, and we often play "name a word that rhymes with ...."  Today I was even able to get him to play that with the added condition of the word starting with a certain letter.

In other avenues of life, I have made a new little calculator website for predicting impending mortality based on some some papers.  We'll see how it goes and what to do next.  I am happy that I learned the basics of flask with it and the next step will be doing something more dynamic.  Maybe a log in members only kind of deal.

In work I had a man younger than me die of acute liver failure and now I want a redo against death.  Maybe I should more strongly consider CC because the opportunities to make a big difference in hospital medicine seem few lately.

I also finished reading the Three Body Problem series (all three novels) by Cixin Liu.  Very good and each sequel was not a let down unlike some other SF series I've read lately.

Almost Election Day

Not that I'm going to write anything about it.  I'm just trying to vary the titles of the posts from just simply being variable descriptions of how reading is going.  Of course, that is exactly what the content is going to be.

I've made the rounds back to the "Flesch Cards", only we've simply been doing them on the computer.  I zoom in on the text files so that only one full word is seen on the screen and I'll either tape a piece of paper over half the screen or cover it with a book so that he can't see the picture.  I went through all the old ones that we had previously printed out and he got all of them right on the first try (I think that is 1 through 3 or 4).  We are up to number 8 and he can read ~90% of the words on the first try without any hesitation.  What's nice is that if he isn't sure he will default to sounding out the letters which I like to see him use rather than just guessing on the word based on context and the first and last letters (which he will often do).

As far as independently reading things on his own, I would say he is still on a GRL C or D level, where these books are completely readable by him alone on the first try.  Sometimes I do have to remind him that the other page has words too as he often seems more interested in the pictures.  I've been checking out a lot of the "Holiday" publishing company's children books since they are pretty consistent.

I have definitely noticed him reading things like signs or maps in the real world more often, so hopefully his interested in self-guided reading will pick up (which is what I would really like, as it would allow me to sort of just pop in when he has trouble with a word).  I'm excited to get to the concept of two syllable words because I think it will change his method a lot when he realizes how modular English can be (emphasis on the can).

To remind myself in the future for benchmarking with our other children:  a couple weeks ago I revisited a youtube video of frequent sight words and he knew all of them without hesitation, but I can't remember exactly when that was.  It may have even been before the last post.

In programming news I thought it might be fun to make a little python program to help diagnose impending death in actively dying patients based on research of David Hui and his group at MD Anderson (see the Cancer and Oncologist papers for their signs and symptoms).  It's been a nice little review in applying likelihood ratios to pre-test probabilities and how to calculate them.  The huge problem I keep running into is how to accurately assess a pretest probability.  For one thing it can have a larger affect than any positive or negative LR.  Secondly, if it seems that by objectively finding a good pretest probability, I'm already most of the way there to answering my question in the first place!  Otherwise, what does it really mean when I'm saying a patient has a 30% vs a 70% chance of dying in the next 3 days?  Both are quite "large" numbers, yet after a positive LR of 10.0, the former post test prob is 81% and the latter 95%.  How useful is telling a family that their loved one has an 81% vs 95% chance of dying in the next 3 days?  I guess that might actually show some usefulness because no matter what it shows that a positive sign means death is likely.  On the other hand, let's take 1% pretest vs 10% pretest.  The absolute difference in these numbers is small but the resultant post test probs (9% vs 51%) actually tell very different stories.  How confident can I be that a patient has a 1% chance of dying vs a 10%?  This is where I am stuck and looking for answers in the research.

Nice Day at the Park

Today we went out to our local park, which is probably the nicest park I will ever within walking distance of.  As we approached the swings I saw a man with three young kids, the youngest a baby in a stoller.  "Poor guy, having to deal with all that I thought."  JT wanted to go on the swings by them and we struck up some small talk and it turned out that the man was a Transplant Cardiologist, visiting from Australia while his Heme/Onc wife did some training!  He is on a sabbatical for the next three months and it sounded like this was the first time was going to be the primary caregiver.

In hindsight, I probably should have had a ready made pamphlet, entitled "How to be a physician and Dad while taking care of your children full time."  Or something better titled, you must understand that this is maybe my specialty!

One thing he mentioned to me that struck me as a very good logical place to start was this: "I've decided to divide my days into thirds, one third we spend outdoors doing something, one third inside, and then the last third my wife comes home and she gets them!".  I think this is a good idea, however the problem I think he will run into after a while is that that final third might cause some difficulties with his wife, who is probably tired from her full day and may want some time with him as well.  I sometimes struggle with the ever increasing amount of "me" time that I can spend on things like this, or probably more commonly wasting it on Reddit, reading the news, or the occasional Minecraft binge.

The second interesting point about this encounter was I had recently read a Reddit post of a young doctor asking for advice on whether/how to tell strangers/first dates/barbers one is a doctor without it affecting the interaction too much.  In this case I'm glad he asked me what I did because it gave us an opportunity to connect, and I think it being honest about it is always the best policy.  I do try and take the focus off of being a doctor somewhat though, by usually framing it as:  "I work for ____ hospital as a hospitalist/nocturnist/doctor" (the last word depending on what I assume the listeners familiarity with medical speak is).  I like this way because it puts the focus more on the hospital system which allows them an easier follow up question.  Just saying "I'm a doctor", usually leads to: "what kind?"

In reading news, I should upgrade my assessment of JT's progress.  I think he can read GRL C-E books without issue on the first try, probably almost 80% of an F or G book too I would reckon.  We are overdue for a library visit (pun intended, and yes we owe them money) to get some new books.

My concerns with how reading is going

Another month between posts.  I will regret this someday when I am looking back and trying to look for clues.

JT continues to make progress with his reading, however I have noticed a few things that nag me.  One is that I feel that his method of reading is one where he now shies away from sounding out words and instead relies on his bank of sight words.  For example, we were reading and came to the word "skin" and he said "snack" (this happened two times in a row on separate reading). This leads me to think that his thought process is: "OK, I don't know this word 100% but it has 's', 'k' and 'n' in it, and so does 'snack' so that is probably it".

Furthermore, he is resistant to trying to sound out words with me, but when I sound them out for him, even if I put a lot of space between the individual sounds, he rapidly can say the word.  Isolating the problem, it seems that he has some new resistance or doesn't trust himself to sound out the letters.  I don't know why this is the case or if it is really new. IIRC, in the past I was complaining that with the flash cards he would ONLY sound out the words and not memorize them.  Still haven't done any flash cards for months, and maybe it would be beneficial to try them again to introduce more word grouping and sounds.  I feel like maybe with the introduction of 'ee' and 'oo' words he is starting to feel less secure about the 'basic' vowel sounds.  He was really upset when we read a book and I tried explaining the 'ph' in phone didn't make the 'p' sound.  What are you trying to pull Dad? He doesn't seem to have any problem reading the word "know", however.

The number of books he reads on his own continues to grow. I would estimate that he can read any GRL C book by himself on the first try now, and most of GRL D books.  Almost all of these books are library books so we have to return them after he has "memorized" them.  I do wonder if it would be better if we kept some longer because the books he seems to like to read the most on his own spontaneously are the ones he can read easily on his own and have mastered.  That way, he would have more opportunities to spontaneously read on his own.  I haven't yet seen him independently pick up a book that challenges his reading capabilities.  If I saw him do this, it would allay some of my fears that I'm conditioning him to read as work, not as fun.

Recently I've taken to reading him a book with no pictures to help him go to bed (which has worked miraculously well, probably helped by the sad fact that naps have not been working out since his little sister joined us in June).  It is one of my childhood favorites: Susan Cooper's "The Dark is Rising".  Earlier in the year we did make it through "The Hobbit" as our night/nap book, but it was an edition with illustrations, so it was often interrupted with him asking me if there was a picture.   I regret not starting him on non-picture books earlier.

Reading taking off

I can't believe it's been two months since I've last put something here.  It is a shame because with the passage of time it will be hard to pinpoint exactly when JT started, what I call, officially reading.

For at least the last month he has been able to read books completely on his own, even ones he's never read before.  With respect to the GRL (Guided Reading Level) classification, at this point if it is B he can read it on his own the first time, if it is C-D he will read it on his own after I help him with any new words in it (but he will still read the majority of it and try to sound out or guess the new words). 

I haven't used any Flesch cards for a long time, and we haven't used the lightsaber reading for a long time as well.  In fact, we have pretty much tried to remove any blatantly sword or saber things because he tends to get more riled up with those around.  This hasn't stopped him from unscrewing the antennae and using them as swords or unscrewing the handles on his rocking giraffe and placing it inside a foam rocket to make a sword either.  At least he will have to creatively work to get his fill of violence.

His favorite books to read are ones that are funny, in his opinion.  "Robot Burp Head Smartypants" had him ridiculous with the "E-I-E-I-Errrp" burping.  We also read one called "Stalling" last night that had a similar reaction ("Stack some blocks, smell my socks", stinky socks are hilarious).  I think the first book he really read on his own and enjoyed was "Go To Bed Blue".

In retrospect, part of me thinks that I was pushing early reading books on him too early (such as the Bob books). For Emilia, I think I will try to first get to the "lightsaber reading" level before introducing a lot of "reader" books, and just focus on reading a lot to her books that she enjoys.  On the other hand, "Go To Bed Blue", was a book we had checked out months before he was really reading, and I think some of the familiarity with it may have made it easier for him?  Perhaps it's just that he likes the book.

At this point we are just working on learning other patterns of how words sound out.  Sight words seem to be getting picked up as we go along with repetition.  Aside from the "basic" vowel sounds (such as ahhh for a, ehhhh for e, etc...) I have shown him "double o words" and he now has that down pretty well.  We've also done "double e words make the eeeeee sound", as well as "sh", "ch", and "th".  I'm wondering when to point out the silent e rule?  What amazes me is that even if we go over something for 5 min and I don't feel like he really picked anything up, the next time I go over it it's much easier, which really is a well known.

I've also been trying to be more formal in teaching him math (I know, probably going to ruin it for him as well).  I had picked up a cheap Target Pre K math workbook and he really enjoyed it.  It gave me several ideas of what he knows and what he doesn't (for example Most is an easy concept, Least or Fewest, not so much).

In other news, with respect to programming, I have been going through a book called "Think Stats" which covers statistics while implementing all of the concepts in Python.  It's actually been really good because the level of coding is great for me (most of it so far is simple but occasionally there are things I have to really sit down and think about or look up).  Plus, it is very hands on with lots of exercises that really cement and build up my code base which I can refer to or use later.

Lightsaber reading

I had an idea a couple months ago about taking a chopstick or other pointer and attaching an LED circuit with a push button to make a more interesting pointer for reading.  It turns out that the dollar store and the interventions of the grandparents did this for me by getting my son a bunch of cheap key chain light sabers, although it took me about a month to realize their true potential.  Using this yesterday he was pointing at the words and read a book pretty much entirely himself (a Biscuit book, which are pretty simple and a lot of them he has partially memorized).  This was a somewhat arbitrary step that I had been waiting for.  He has no problem sounding out new words if they are on a card but when he looks at sentences he has a tendency to say "this is too hard, you read it".  With the light saber he is able to focus more easily on the word at hand.

In programming news, I can't remember if I already mentioned this in the last post but I was trying to make a physiologically accurate simulation of a person.  The problem is that this is too complex and I'm stuck with a basic model that can't even get oxygen delivery (DO2) correctly modeled compared to real experimental data.  Plus after discussing via email with the author of some renal physiology papers (thank you Dr. Bengt Redfors) there are still too many unknowns on what even causes something as "simple" as hypoperfusion related AKI. 

Currently I am just working on better understanding the basics of flask, so that I can apply this to a project in the future.

New Child

A month and a half since my last post and a couple of notable events.

In May I worked 3 out of the four months, including 14 nights straight.  A new record that actually wasn't too terrible.  The switch back to days was the same as with any other week of work.

About one week after the above workload we had a new addition to the family.  I am now a parent with two children.  This is a girl so as my wife noted we have officially replaced ourselves.  I added that evolutionarily (perhaps not the best term) we have fulfilled our purpose in life, though statistically the number of children needed for population replacement is slightly higher due.  I guess we will need at least one more.

My project of teaching my son to read continues to be going well.  He likes the "Flesch" cards now and we play with them usually every day.  The way he likes to play is to have the cards "attack" him by running across the table and he has to read the card before it gets him or his food.  He also likes to play our version of "Munchkin" which I've detailed in older posts.

I was actually working on a programming project as well.  It originated as trying to come up with "Dwarf Hospital" (you can easily assume the influence).  It started as two independent projects.  One was doing the libtcod python tutorial to make a rogue like.  At this point I have made a turn based map with a character and I was going to try and make patients that you would see. 

The second prong was trying to come up with as accurate a physiological model of the human body as possible.  After diving in I quickly realized that there are hundreds if not thousands of PhD's around the world who devote their life to making just one model of, say, the kidney's response to ischemic acute kidney injury.  So far I have model that is two organs, the kidney and "other" (represents rest of the body).  The heart is really just a continuous flow rate, only systemic circulation (no lungs yet, just an SaO2 value).  I'm running into issues getting the correct predicted oxygen delivery values (only off by about 50%) so I'm troubleshooting it still.  Not sure where this will go.  A fun side effect is that I've been reading more renal physiology.

Out of the water

The last time I posted things were in a rut, but now they have turned around a bit.  I can't exactly pinpoint what changed but I'll list a couple things.

First, we have been playing more of our version of "Munchkin", and he seems to enjoy the cards more.  I've noticed that he still gets lower case "b" and "d" (and sometimes "p") mixed up.  I fixed our printer (ie had the printer clean the nozzles) and printed out the next set of "Flesch Cards".  In hindsight, it was long overdue to move beyond the first set.  He liked cutting out the new cards (we got him scissors and he's all about cutting paper) and wanted to read the new cards.  He also understands now a lot more when I explained to him the theme of the cards (ie, these all have "e" in them, so they make the "ehh" sound).

Next is that I was at Costco and saw that they had a deal on six "Biscuit" books for 10 dollars.  I had read that these were great reading introduction books from reading a flyer at one of our local libraries so I went ahead and got them. Actually, I had previously borrowed from the library the first "Biscuit" book a couple months ago but didn't think it was that special at that time.  This time, however they have been really great for getting him to read independently.  The vocabulary in the books is more extensive than a "Bob" book, but interspersed throughout each story is the voice of Biscuit, who invariable says "Woof", or "Woof, woof!", or "Woof, woof! Woof, woof!".  This might sound boring but actually I saw it give a lot of confidence in pointing to the words and knowing what they said, so much so that it is easy for him to slide into the next sentence and read that out as well.

Thirdly to my surprise he's picked up how to spell simple CVC (consonant vowel consonant) words.  We discovered this on accident by spelling some words and he said them.  Today, I quizzed him because I didn't really believe my wife, and he was able to tell me what C/B/R/S-A-T and G-O and M-O-M.

Now, if only I could find a way to get him to stop saying "butt, butt, butt, butt" every time he wants to be funny....

Treading Water

I don't think that there has been much of a significant change since the last time I posted two weeks ago. I worked a week of nights and so I wasn't able to do as much reading with my son. He's still in this phase where he can sound out individual words when asked, but doesn't really have a large memorized sight word vocabulary.  Sometimes it is a struggle to get him to read what the books actually say rather than what he is guessing them to say. To help with this, I'm trying have him focus more on pointing to each word as he reads it so that he has to register.  I haven't done the flash cards for over a month now.  I made an excel sheet to record the number of "memorized" sight words he knows because I thought it might be fun to look back at it someday.  So far, it's been a plateau.