path: root/2022/captions/emacsconf-2022-health--health-data-journaling-and-visualization-with-org-mode-and-gnuplot--david-otoole--main.vtt

WEBVTT captioned by sachac

NOTE Introduction

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Hi, this is Dave O'Toole, and today

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I'll be giving a presentation on tracking health data

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with Emacs, Org Mode, and Gnuplot.

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So Gnuplot is the well-known scientific

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and mathematical plotting application.

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You feed it text files full of names, dates, numbers,

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data points, and you get out a nice graph.

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You can spit out SVG. You can spit out PNG graphics.

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In this case, we're using an SVG.

NOTE How to take daily health journal items

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What I'm going to show you today

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is how to take daily health journal items:

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in other words, things like I exercised

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such and such number of minutes today,

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I got X hours of sleep last night,

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I used such and such number of pieces of nicotine gum,

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say five pieces. So let's see,

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we've got this whole picture here, all right,

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and I've tracked here...

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This is a month of data from my life.

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This is... I'm not showing all the variables,

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but this is what I felt comfortable sharing

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in order to help people who might have a need to track,

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either because of a chronic condition,

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or just because of a health improvement goal

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or what have you, people who might need to

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track health data in a way

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that's a little bit more robust

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than just one or two variables

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and just weight or just blood pressure.

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So in this case, I've got exercise,

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I've got the number of hours of sleep,

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the number of doses of nicotine,

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(that's the yellow line here),

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and this is referring to nicotine gum.

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What we're going to be talking about

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is looking at connections, the idea

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that plotting your data can actually

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help you figure out what's going on.

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This is just one month.

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I've been doing this for a couple of months now,

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but I felt comfortable showing one month

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with a limited subset of the variables.

NOTE How to set up your org templates

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What I'm going to be doing in this presentation

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is showing you how to set up your org templates

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so that you can, you know, hit a hotkey

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to capture today's data with an org template--

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or in this case yesterday's. Usually I'm saying, okay,

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yesterday this happened,

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because you don't know until the day's over

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how many pieces of nicotine gum you ate

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or how many hours you slept.

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So usually we're recording data for the previous day.

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We can set up a capture template

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so that it fills a little org entry. One for exercise,

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one for sleep, one for nicotine, one for distress.

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Here distress is just 1 to 10:

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how bad do you feel today?

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It's not a scientific measure, but you know,

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many, many things ask you to rate

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on a scale of 1 to 10, how bad is the anxiety,

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how bad is the general level of stress,

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and so without a lot of complication,

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I just rate that one to ten.

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Pain, okay, we won't have to get into any details,

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but if there is a level of chronic pain, well,

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I put that between 1 and 10. As we can see here,

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during the period that I've shown you, it's pretty low.

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There's some. If you miss a dose of medication,

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you can track that, in this case

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with a big ugly red triangle, you know.

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You can see, I can see here that in mid-, in late September,

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sorry, in early to mid-October,

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I stopped using the nicotine gum

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and probably should have cut down more gradually

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because my sleep suffered. Look at this.

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The sleep line is down here, okay?

NOTE How to do it in GNU Emacs

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What I'm going to do now,

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now that I've shown you the graph

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and some of the things that are useful about it,

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I'm going to actually take a step back

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and show you from start to finish how you can do this

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in GNU Emacs, and I have a little template generator

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that you can use if you'd like.

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All right, so let's go back.

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Let's step back from this file.

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We're going to split the screen, and on the left side,

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I'm going to put the underlying Org file

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that generates this graph.

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Let me shrink that a little bit.

NOTE Overview of the presentation

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All right, I'm going to work my way backwards

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from the template to the template generator,

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meaning that you'll be able to spit out,

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given your own specification of health variables,

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you'll be able to have it spit out

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a custom Gnuplot script like this

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that's preset up with the definitions

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for the column view in Org mode.

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I'm assuming a little bit of familiarity

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with Org mode and Gnuplotting,

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but I'll try to explain as much as I can as I go along.

NOTE The journal

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The journal here is where... okay, okay, one moment.

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So as you can see, there's a sub-entry here

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for each day that I've included from my data set

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starting on September 13th of this year

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and ending on October 17th.

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And there's an Org property drawer with

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the corresponding names of each field and the value.

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Now the idea here is that the columns specify...

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if you know a little bit about Org mode,

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what happens is that you...

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let's say that I hit the key for my journal template,

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which... Mine is very similar.

NOTE The capture buffer

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This is the capture buffer for today's date,

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and if you're recording yesterday's date,

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you can just flip it like that if you need to.

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Then I say, yesterday, I remember

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I went for about a one-mile walk,

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so that's probably about 20 minutes,

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and that I had such and such,

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I had eight and a half hours of sleep, let's say.

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I estimate how many pieces of nicotine gum I have.

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I try to count as closely as I can, how much distress,

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you know what I mean,

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whether or not I missed a dose of medication.

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Then when you hit C-c C-c,

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it captures that to the end of your Org file.

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Now what this shows is that... I cut and paste it in.

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I've been keeping these entries every day for months,

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and that I cut and pasted in a month of data.

NOTE The columnview table

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Now I'm going to dig in a little bit to the Gnuplot script.

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This here, all this stuff, is one component of the graph,

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and I'll go over how it works.

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First, the items through this column declaration here,

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and the id:myid, this columnview table here,

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#+BEGIN: columnview, this whole bit here,

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is going to get filled in with the corresponding columns,

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exercise minutes, sleep hours, nicotine doses.

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And then it gets pumped out by Org mode into a file

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that looks like this: tab-separated values

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with an ISO-style date at the beginning.

NOTE Gnuplot

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So what we're going to do is we're going to go through

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the Gnuplot portion of this,

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and I'm going to enlarge the font a little.

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I'm going to go line by line through the Gnuplot portion.

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Now, my template generator will give you one like this.

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You don't have to write this from scratch.

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But I'm going to go through it line by line

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because if you do use the template,

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then it'll help to have gone through it line by line,

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because you're probably going to have to modify it.

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So first, we're going to clear the graphics

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from any previous runs

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so that if we reuse the same Gnuplot process,

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we're not overwriting the old--

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that we are completely overwriting the old image.

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So that's the purpose of this line here.

NOTE Output parameters

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The output parameters: we want to put out an SVG file.

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Font Arial, that's funny,

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but I don't know what font it's actually ending up choosing,

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but it looks fine.

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Then we want it to be square,

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so I'm giving it 900 by 900 pixels,

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even though it is a scalable vector graphic.

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We're putting it in the same folder as the org file,

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example.svg.

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These lines here set it up to use the Org mode format

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that we showed in the other file over here.

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The time format is four-digit year, two-digit month,

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two-digit day.

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The time format doesn't specify here the time,

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but that doesn't seem to mess it up.

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This line "set datafile separator" means that

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the separators between that

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and between all the other fields are tabs,

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which is what Org mode does

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when it spits out a table by default.

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Okay, along to the next lines.

NOTE Time series data

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We're going to set up for time series data,

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meaning that the x-axis is going to be time,

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x2tics 1 format.

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I believe this means that every day has one tick

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and that this tells it that the first--

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unfortunately, I forget the exact meaning of this one line.

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I'm just going to move on. We want one X tick per day,

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and because X is in seconds,

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it's 24 hours times 60 minutes times 60 seconds.

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This line "set grid xtics" gives us

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a vertical line on each day of the graph.

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I'll pull up the graph

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just so that it's a little easier to see.

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All these vertical lines, one on each day,

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that's given to you by "set grid xtics".

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One Y tick every five points.

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So here at five pieces of nicotine,

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we've got a five, at ten pieces – well,

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we don't want to eat ten pieces, but ten, fifteen, twenty.

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Rotating the labels to make them fit a little bit better,

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that's this part here where the labels are sideways,

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and even with just one month of data,

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they're getting a little crowded.

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This "set key box lc" just makes the line around the key,

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the legend here, a little bit less severe.

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set xtics format: this makes it so that, for example,

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I've done a United-States-style date here

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with the month and then the day.

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You don't necessarily have to do that.

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You can have whatever you want.

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This xtics format,

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that relates to how the dates are printed.

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Remember that over here, this set timefmt,

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that relates to how the dates are formatted

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in the Org mode output.

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So remember, those are two...

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You don't want to mix those up.

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All right, "yrange [0:40]".

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Thus far, my exercise sessions have all been

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less than 30 minutes, and nothing's gone over 30.

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If you have a health variable

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that is in a significantly different range,

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you may need to get a slightly more complicated

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Gnuplot script because it is possible to plot

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multiple yranges in one plot

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if you have a variable that uses a different range.

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It's just a little trickier.

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These parts here, aside from the fact

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that you might make some changes that relate to

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the date and your country format,

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are going to be the same.

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This is like boilerplate for almost anything.

NOTE Health variables

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Now here are the parts that are going to vary

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depending on what health variables you want to store.

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There are three main sections here.

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One is setting the different line types that are used.

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Setting linetype 1 with line width 2, line color RGB.

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Unfortunately, Gnuplot is a little bit cryptic,

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which is why I've made this template generator

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that I'll show you in a moment.

00:13:38.000 --> 00:13:43.039
I pick a color. So this is exercise, forest green.

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Point size 1, meaning you get

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these little green triangles about that size.

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But the point type 9 is the pointing up triangle.

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Line type 2, purple. So that's the sleep line.

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So we're just establishing these different line types

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that we've given arbitrary numbers.

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Now onto the next section.

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Oh, before I move on here,

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you can see point type 11 for line 5, which is red.

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And that's the missed medications line,

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so you get a triangle that's upside down

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because that's point shape 11.

NOTE Goal lines

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All right. The next section here is the goal lines.

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There are horizontal dashed lines here

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at 8 purple hours of sleep, because 8 hours is the goal.

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So there's a horizontal line at Y = 8.

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For pieces of nicotine gum,

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I'm trying to keep it to around 5 right now.

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So my goal line is at 5. So these...

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Here, a goal of at least 20 minutes of exercise.

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Sometimes I get more, sometimes I get less.

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There's a green line and a 20, showing that that's the goal.

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These lines here are actually the goal lines.

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You can specify the goal for each one

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in the template generator that I'll show you.

NOTE The Gnuplot command

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The last part is the actual plot command.

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So the dependent... So okay,

00:15:30.200 --> 00:15:34.919
these all start with 1, "using 1" against this variable.

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So $2... This is a ternary operator here

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that says if the value of the second column is zero,

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then don't plot a point. In other words,

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not a number means it won't plot a point.

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The template generator lets you skip over

00:15:58.920 --> 00:16:02.119
the details of that. It sticks this in there.

00:16:02.120 --> 00:16:02.759
I'll show you.

00:16:02.760 --> 00:16:09.399
So we only want to plot a point when the value is non-zero.

00:16:09.400 --> 00:16:12.479
If there was no exercise, we're not plotting a point.

00:16:12.480 --> 00:16:15.759
The with construct means we'll plot data

00:16:15.760 --> 00:16:21.340
using date against exercise with points,

00:16:21.341 --> 00:16:25.519
the title is "exercise (minutes)", line type 1.

00:16:25.520 --> 00:16:29.839
Remember, we established line type 1 up here

00:16:29.840 --> 00:16:35.079
as being forest green, point style 1,

00:16:35.080 --> 00:16:37.599
point type 9, green triangles.

00:16:37.600 --> 00:16:42.399
Now I'm going to show 1 against column 3,

00:16:42.400 --> 00:16:43.919
which is "hours of sleep".

00:16:43.920 --> 00:16:46.039
This one is plotted with lines,

00:16:46.040 --> 00:16:48.599
so we don't specify a point type or point size,

00:16:48.600 --> 00:16:51.719
just a line type 2. And remember, you can see

00:16:51.720 --> 00:16:55.240
that line type 2 is defined as purple

00:16:55.241 --> 00:16:57.359
with point type 1, point size 1.

00:16:57.360 --> 00:16:59.959
Okay, so I did specify point size and point type,

00:16:59.960 --> 00:17:01.479
but because I'm not plotting with points,

00:17:01.480 --> 00:17:02.279
those are ignored.

00:17:02.280 --> 00:17:08.799
Here we come to the line with nicotine.

00:17:08.800 --> 00:17:11.559
The fourth column is the nicotine number,

00:17:11.560 --> 00:17:13.199
the fourth column from the Org mode file.

00:17:13.200 --> 00:17:16.007
So here you can see how we're telling Gnuplot

00:17:16.008 --> 00:17:19.799
to take each column of the tab-separated Org mode file

00:17:19.800 --> 00:17:21.119
and put it into the graph.

00:17:21.120 --> 00:17:25.959
The line types are set up here.

00:17:25.960 --> 00:17:30.799
The goal lines are set up here.

00:17:30.800 --> 00:17:35.559
And then the actual plot command is set up here.

NOTE The template generator

00:17:35.560 --> 00:17:41.319
So now we're going to work further backwards

00:17:41.320 --> 00:17:42.959
from this Gnuplot template

00:17:42.960 --> 00:17:46.559
to the template generator that I used to make it.

00:17:46.560 --> 00:18:01.959
Now I'm not going to go into

00:18:01.960 --> 00:18:03.759
all of the details of the code,

00:18:03.760 --> 00:18:06.159
but what I am going to show you is that

00:18:06.160 --> 00:18:10.679
there's a variable called `health-factors`.

00:18:10.680 --> 00:18:15.839
And what this does, this `health-factors-from-list`

00:18:15.840 --> 00:18:20.919
lets you specify, with a property list

00:18:20.920 --> 00:18:22.679
of keyword and value pairs

00:18:22.680 --> 00:18:24.799
(here's the keyword name and the value is exercise),

00:18:24.800 --> 00:18:28.199
the goal that I want 20 minutes of exercise,

00:18:28.200 --> 00:18:30.199
that the unit is minutes,

00:18:30.200 --> 00:18:36.159
that the color is forest green, and so on.

00:18:36.160 --> 00:18:39.439
The aspects of the Gnuplot setup

00:18:39.440 --> 00:18:43.559
have been abstracted here.

00:18:43.560 --> 00:18:49.279
Eight hours of sleep is the goal here.

00:18:49.280 --> 00:18:54.039
The hours are units. What color,

00:18:54.040 --> 00:18:55.119
what thickness of the line.

00:18:55.120 --> 00:19:00.079
Here we specify the number of points.

00:19:00.080 --> 00:19:01.279
There's references online

00:19:01.280 --> 00:19:05.199
that show you what point types are what shapes in Gnuplot,

00:19:05.200 --> 00:19:11.479
and so on and so forth.

NOTE The code that creates a template

00:19:11.480 --> 00:19:17.399
I'll walk through the code a little bit that does this,

00:19:17.400 --> 00:19:20.439
that actually takes these pieces,

00:19:20.440 --> 00:19:24.399
that takes this specification of what your variables are

00:19:24.400 --> 00:19:30.439
and turns it into a template.

00:19:30.440 --> 00:19:37.959
First, I'm using EIEIO,

00:19:37.960 --> 00:19:41.719
the object system that's included with GNU Emacs.

00:19:41.720 --> 00:19:45.119
It's a reasonable facsimile

00:19:45.120 --> 00:19:47.319
of the Common Lisp Object System.

00:19:47.320 --> 00:19:51.239
What I'm going to be doing here

00:19:51.240 --> 00:19:56.199
is defining a class with each of those items,

00:19:56.200 --> 00:19:58.479
those properties that we talked about in that list

00:19:58.480 --> 00:20:01.319
that lets you specify name, what the goal is,

00:20:01.320 --> 00:20:04.239
what the units are, and the Gnuplot things

00:20:04.240 --> 00:20:06.559
(the Gnuplot parameters like thickness,

00:20:06.560 --> 00:20:13.239
plot type, and all that) into a class that will then

00:20:13.240 --> 00:20:16.519
spit out the template once you feed it

00:20:16.520 --> 00:20:27.759
some of these health factor objects. So just a moment.

00:20:27.760 --> 00:20:34.479
For example, you can see that this template

00:20:34.480 --> 00:20:46.319
originally came from being generated by this code here.

00:20:46.320 --> 00:20:52.959
To use the template,

00:20:52.960 --> 00:20:55.399
to use this little template generator...

00:20:55.400 --> 00:21:06.279
See, here's where it spits out the line type

00:21:06.280 --> 00:21:07.439
given the pieces.

00:21:07.440 --> 00:21:09.679
This is all just text formatting.

00:21:09.680 --> 00:21:11.319
This is one of the things that Emacs Lisp

00:21:11.320 --> 00:21:13.159
just really excels at.

00:21:13.160 --> 00:21:19.519
I need to take a piece of data

00:21:19.520 --> 00:21:22.639
like a list of health information,

00:21:22.640 --> 00:21:25.679
a list of health variables, what their units are,

00:21:25.680 --> 00:21:28.119
and how they're supposed to be formatted in Gnuplot,

00:21:28.120 --> 00:21:30.199
and go from that to the nice template.

00:21:30.200 --> 00:21:31.719
So that's pretty much the whole thing.

00:21:31.720 --> 00:21:40.999
I want to see if there's anything I missed.

NOTE The power of the chart

00:21:41.000 --> 00:21:51.519
Bring up the chart.

00:21:51.520 --> 00:21:54.279
This has been really useful

00:21:54.280 --> 00:21:59.599
for communicating with healthcare professionals

00:21:59.600 --> 00:22:04.399
because you are both on the same page

00:22:04.400 --> 00:22:05.879
about exactly what is happening,

00:22:05.880 --> 00:22:10.679
what's been happening because if... Let's say

00:22:10.680 --> 00:22:15.239
that you're tired when you talk to your care provider.

00:22:15.240 --> 00:22:17.559
Well, if you have objective information

00:22:17.560 --> 00:22:18.839
that you've been recording every day,

00:22:18.840 --> 00:22:22.399
that you're ahead of the game, really,

00:22:22.400 --> 00:22:25.119
because you don't need, necessarily, the presence of mind

00:22:25.120 --> 00:22:27.679
to be able to give your care provider

00:22:27.680 --> 00:22:30.039
a complete picture of what's going on in your world.

00:22:30.040 --> 00:22:33.039
If you can find those few minutes a day to enter--

00:22:33.040 --> 00:22:34.399
not even a few minutes,

00:22:34.400 --> 00:22:37.759
really just a minute to enter the data

00:22:37.760 --> 00:22:39.839
and say what happened yesterday...

00:22:39.840 --> 00:22:42.759
I'm finding over these months

00:22:42.760 --> 00:22:45.039
that I've been more in touch with my health when I can--

00:22:45.040 --> 00:22:49.919
not forced, but when I have the habit,

00:22:49.920 --> 00:22:52.159
the consistent habit every single day

00:22:52.160 --> 00:22:55.839
of recording that data--I'm accountable to myself.

00:22:55.840 --> 00:22:57.359
It's interesting.

00:22:57.360 --> 00:23:01.039
I guess it gets into a little bit of ideas

00:23:01.040 --> 00:23:02.439
about the Quantified Self

00:23:02.440 --> 00:23:05.239
and how holding yourself accountable

00:23:05.240 --> 00:23:09.919
can change what you do and what the outcomes are.

00:23:09.920 --> 00:23:14.159
Just look at this here.

00:23:14.160 --> 00:23:17.279
Without getting into too much detail,

00:23:17.280 --> 00:23:19.679
one of the reasons I track my sleep is because,

00:23:19.680 --> 00:23:22.039
as you can see, my sleep

00:23:22.040 --> 00:23:26.759
is not as well-regulated as most people,

00:23:26.760 --> 00:23:31.439
and that's why I need to do that.

00:23:31.440 --> 00:23:34.440
This was a time... 10, 12,

00:23:34.441 --> 00:23:36.639
here's 14 hours of sleep, that's depression.

00:23:36.640 --> 00:23:43.519
It oscillates a little bit. But then below the goal line,

00:23:43.520 --> 00:23:45.639
the things are a little more normal here.

00:23:45.640 --> 00:23:46.919
This is a little more normal.

00:23:46.920 --> 00:23:52.079
But then, really, without thinking about it too much,

00:23:52.080 --> 00:23:56.239
I cut out the nicotine, and my sleep suffered.

00:23:56.240 --> 00:24:00.199
Just the fact that I'm able to look and see that connection

00:24:00.200 --> 00:24:01.359
is really amazing to me.

00:24:01.360 --> 00:24:02.759
Maybe I would have anyway,

00:24:02.760 --> 00:24:05.239
but looking at the whole months of data,

00:24:05.240 --> 00:24:07.399
there have been many things to discuss

00:24:07.400 --> 00:24:09.919
and many things to think about.

NOTE Thanks

00:24:09.920 --> 00:24:12.159
Because this is a short presentation,

00:24:12.160 --> 00:24:13.839
I probably should wrap up.

00:24:13.840 --> 00:24:18.239
I just want to thank the whole Emacs community

00:24:18.240 --> 00:24:23.319
for being there and for including me in the conference

00:24:23.320 --> 00:24:27.079
and I hope to participate next year as well.

00:24:27.080 --> 00:24:29.240
Thank you so much.