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The long data processing road

Okay I’m taking another break from the “in statistics” posts, at least for today since the next topic is going to be a long multi-day post worth of stuff and I need an easier post for today. I have way too much stuff going on at the moment to organize a long post! In any case, I figure I could give an update to the data I’ve been working with and how that whole mess is going. It’s mind numbing and exhausting work, but not in the way you would think.

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The Bonferroni correction in statistics

Well we’re doing it, today we’re talking about the Bonferroni correction, which is just one of many different ways to correct your analysis when you’re doing multiple comparisons. There are a lot of reasons you may want to do multiple comparisons and your privacy is our main concern so we won’t ask why. Instead we’re going to talk about how to adjust your alpha (chances of making a type 1 error) so you don’t end up making a mistake.

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One-tailed vs. two-tailed tests in statistics

Sit right back because we’re telling a troubling tale of tails full of trials, twists, and turns. The real question is, will we run out of words that start with t during this post? It will be tricky, but only time will tell. When do we use a two-tailed test vs. a one-tailed test and what do tails have to do with tests anyway? With a little thought, I think we can tackle the thorny topic. In short, let’s talk tails!

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The p-value in statistics

We’ve been dancing around the p-value for some time and gave it a good definition early on. The p-value is simply the probability that you’ve made a type one error, the lower the p-value the less chance you have of making a type one error, but you increase your probability that you’ll make a type two error (errors in statistics for more). However, just like with the mean, there’s more than meets the eye when it comes to the p-value so let’s go!

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The z-score in statistics

Okay, time to get back to statistics, if only for today! P-value, z-score, f-statistic, there are a lot of ways to get information about the sample of data you have. Of course, they all tell you something slightly different about the data and that information is useful when you know what the heck it is even trying to tell you. For that reason we’re diving into the z-score, it’s actually one of the more intuitive (to me anyway) measurements so let’s talk about it!

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Freedom of speech

I didn’t expect to have to talk this out, but here we are. Freedom of speech applies to the government, not private entities such as (but not limited to) twitter, facebook, schools, work, and basically any private place you congregate. Freedom of speech also does not mean freedom from consequences of that speech, you can’t talk about blowing up a school for example without consequences, even if it was a “joke.” More importantly, the government already ruled that certain hate speech isn’t protected. Why is this important? Well it’s a good reminder for the internet in general, but this time it’s a little closer to home reminder, namely the lab I work in.

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VA healthcare in a pandemic

With the pandemic stretching now over a year, which really feels like twenty, eventually healthcare was going to be an issue for me. I’ve already had to have a surgery during the pandemic, which was nerve wracking not because of the surgery, but because of COVID. Well it’s become a struggle to keep trying to put off getting care when I’m someone who needs pretty regular care. I went from bi-weekly appointments to once every 6 months or more, not ideal.

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EEG cleaning progress

Yesterday’s coding work went better than expected! That may or may not bode will for the rest of the week, but hey at least I’m sort of ahead of schedule. Today I figure we can take a quick look at what I’ve been doing with the data and why. This will be part informative and part me complaining about how everything has to be so damned hard (basically the usual around here). Mostly it will just be some visuals of the things I’ve had to change to get everything looking like my main-PI wants, he’s got a particular style he likes so a lot of large text, bolded labels, etc.

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The juggling act

The middle colorful plot, it’s called a spectrogram and if you notice the colorbar to the right has values ranging up to 25,000, that’s not right…

Blogging and coding and writing, oh my! There’s a lot to get done, seems like a running theme around here doesn’t it? If it were possible to clear some of it off my plate it wouldn’t be so bad, but the sad truth is deadlines seem to like to group together and there are quite a few coming up. Most of them are for my class so I can’t really miss those even if I wanted to. My research deadlines I can’t really miss either, not without some consequences anyway. So we’re back to juggling everything, but as we’ve seen in the past, I’m pretty good at this.

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The new to-do list

It’s been busy! So busy I was trying to find time to write while working on the million other things I have going on. Since I have a moment, I thought now would be as good a time as any to go over the big list my main-PI gave me to do before next week. It’s a long, long, long list and as you may expect, he’s pretty far removed from the situation, so I don’t think he realizes how difficult it is to do what he’s asking, but we’re doing any anyway! Thankfully I’ve gotten pretty good at coding, the bad side is that it’s not my code I’m working with, so that’s the start of my struggles.

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Twice the work, half the… fun?

I work with… Braiiiiins!! Well yesterday I touched on an experiment I did waaaay back in October-ish of last year! With the way things are going it feels like five years not 5 months, but what can you do? My main-PI has started to not so gently or subtly push me to process the data to his satisfaction and start working on the publication of the results. There’s been a lot going on that has pulled me away from the project, from the end of December to the middle of February I was working on grants, but now there isn’t a whole lot stopping me from working on this project almost exclusively… if you don’t include the other grant I’m writing and the fellowship I’m supposed to apply for.

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A PhD proposal defense

Not mine, at least not yet. A colleague of mine is defending his PhD proposal today and while I was going to wait until I did mine to go over the details about how that works and why we do it, I figured today was as good a time as any to do it. Besides I probably (definitely) repeat myself a lot around here, but that’s the catch with blogging daily. So let’s get into what a proposal defense is and why it’s important, shall we?

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COVID variants and our future

Awhile back I wrote a post on everything you needed to know about the COVID vaccine (here), I talked about the science, my experience with it (as someone who got vaccinated very early on), and more importantly why you should feel safe getting your shots too. Very ominously I mentioned that the target for the vaccine was the spike protein because it would (ideally, but not for sure) be conserved across mutations, well it’s time for an update and the news isn’t great.

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The mean in statistics

Yeah it seems simple, I mean (no pun intended) the mean is just the average! Yet as with so many different things in statistics there’s more to the mean than meets the eye! We’re going to go into why the mean is important, why it’s our best guess, why it may not always be your best option, and why we work so hard to find the mean sometimes! It seems simple, but I promise today we’re answering a lot of the big “why’s” in statistics, so let’s go!

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The Tukey test in statistics

No, not turkey, Tukey, although they are pronounced very similar (depending on who you ask I guess? I’ve seen people pronounce it “two-key”). Any way, today we’re saving our job and the wrath that comes with failure. The mad scientist boss of ours tasked us with testing mind control devices and determining statistically which one (if any) worked. After the last failure, we now had four new devices to test, so we couldn’t use the same method as before. However, an assistant’s work is never done, we didn’t finish the job! That’s what we’re going to do today.

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The ANOVA in statistics

Image from: Listening a great sci-fi movie (in my opinion)

Our mad scientist is back and this time they are not taking any chances! After statistical failure in the last example, they created not just one, but four mind control prototypes! We’ve been tasked with determining if they are working or face certain DOOOOOOOM! Sure, working for a mad scientist can be stressful, but we can do this… right? I’ve been dreading this post and you’ll see why, there’s a lot to cover before we solve the mystery, so let’s dive into it!

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Significance in statistics

That feeling when your p-value is lower than your alpha, aww yeah! But what does it really mean? It’s one thing to say there is significance and on the surface it means the two things are different “enough” to be considered two things, but I think there’s a simpler way to explain it. So today we’re going to talk about what significance actually means in the practical sense. Maybe it’s super obvious, but it never hurts to state it anyway.

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The f-test in statistics

Yep, we’re getting right back into it. I’m still working out things from yesterday, so we can just talk more statistics. This will be an interesting one and hopefully it will be pretty straightforward. The f-test, which in this case is really the f-test to compare two variances. You may have guessed, but the t-test uses the t-distribution (sort of like the normal), well the f-test uses the f-distribution, which is nothing like the normal! Let’s dive in, shall we?

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A roadblock

I haven’t spoken with my Co-PI about this yet because I’m angry. Like fist balled, white knuckled, want to scream into some endless void angry. This was not the post for today, but I’ve learned a long time ago that I should get things out instead of bottling it up and letting it eat me alive. It’s the reason I’m still here today and one minor step to my success in not falling into the abyss that is depression. I am angry and I need to chose my next words carefully, because as you’ll see, I have no power here.

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A meeting with my two PI’s

Yeah it feels pretty dangerous…

If I could make a comedy TV show about my life, I would call it my two PI’s and I would get into hilarious situations while trying to make both of them happy. Mostly you would see me get a lack of sleep and sort of feel like I’m running on a treadmill, going as fast as I can, but getting nowhere. It’s not all bad and I respect my two PI’s, but there’s a saying about having too many hands in the cookie jar and sometimes it feels like that’s what is happening. It’s a lot like the old game “telephone” where I’m given information to pass along between the two, so we’re all going to meet… *cue dramatic music*

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First project deadline!

I didn’t have anything particularly lined up for today to add to the “in statistics” posts I’ve been doing, so today I thought it may be better to outline what I’m doing in the statistics course I’m taking. At the very least it may help me get it done, because as usual around here, the project is due… today. Yep, it’s yet another mad dash to the finish. Will I make it? Will I ever figure out what statistics is? Will I learn to stop asking questions in this format? Find out all this and more!

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Confidence intervals in statistics

Wait… this is the wrong kind of confidence!

Well since our mad scientist from yesterday’s post is on a short break, today we’re going to fill in some of the gaps that post brought into view. First up is the confidence interval. There are some subtle points here, so this should help clarify a few things that may not have been clear yesterday. We’re going to do a somewhat deep dive into what the heck we’re doing when we talk confidence interval and why the standard deviation of our data is important in determining the values.

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The t-test in statistics

mind reading

Welcome fellow mad scientist enthusiasts, the last time we talked statistics, we found ourselves in an interesting situation and we need to figure out if the mind control device that was developed is actually working. We introduced the idea of a two population problem and today we’re going to use something called a t-test to determine if our mad scientist succeeded.

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We interrupt your regularly scheduled programing…

This is not the post you are looking for. Error, please try again. Okay, seriously I need to get some work done today and I don’t have time to solve our mysterious mind control device problem that I posed yesterday, so today I’m going to give some quick thoughts on something totally unrelated because there isn’t time for anything else and while trying to figure out a header for this post (where I was originally going to say hey can’t talk today) I was reminded of max headroom. I genuinely don’t know that I’ve ever said that before, but here we are…

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Two populations in statistics

As a mad scientist, or maybe just a grumpy scientist, you want to test a new mind control technique! To do this you decide that you want to test this works by having people select one of two objects set in front of them. *Insert evil laugh* Using your mind control technique you want your unwitting participants pick the object on the left. You don’t get 100% success, but suspect it’s working, how do we know for sure?

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A fair coin in statistics

It has been a busy day, but the show must go on so to speak and I’m here today to tell you I have a nice shiny new coin for us to flip! The catch you may ask? Well it could be a fair coin or I may have just swapped it out for a coin that was not fair! Our goal is to see if I’m being sneaky and to do that we’re going to need some statistics!

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The central limit theorem in statistics

Today we’re gonna push it to the limit! The central limit theorem that is. It’s a cornerstone in statistics and the short and dry version is that it lets us turn any distribution we have into a normal distribution. If it wasn’t for the central limit theorem statistics would hurt far worse than it does now (speaking as someone taking a stats class now). For the longer version we need to discuss why a normal distribution is needed, why we prefer to work with them!

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Effect size in statistics

Imagine our population data is the red curve and our sample data is the blue and the post will help you make sense of it.

We’ve been talking statistics for the past few days and today we’re talking effect size. The short explanation is effect size is the difference between two conditions! The bigger the effect size, the easier it is to tell the two conditions apart, easy… right? There’s a lot that goes into determining effect size, after all it’s hard to know what your effect size is without having some prior knowledge about what you’re groups look like, so let’s go into some detail.

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Errors in statistics

type 1 erro

Everyone makes mistakes, that’s okay! In day to day life there are a lot of different ways you and I could make mistakes. In statistics however, there are just two ways for you to make a mistake. That may sound like a good deal, but trust me when I say two ways to make a mistake is two too many. To think, you spent all that time picking the right statistical test, did the experiment, analyzed the data, just to make an error in the end. Don’t worry, it happens to the best of us, but knowing what they are will help you prevent them!

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The hypothesis in statistics

As promised today we’re talking statistics for experiments! It’s more interesting than it sounds… okay it’s exactly as exciting as it sounds. Depending on who you are that’s a lot or not at all. No matter where on the spectrum you fall, knowing how it works is useful. So we’re starting at the beginning and discussing what a hypothesis is and how we test it.

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The last PhD requirement

Real photo of me determining significance between two samples. It’s scarier than it looks.

We’re already at the end of the month, how the hell did that happen? It’s been close to a month and a half since the term started and it feels like it’s flying by. I realized that when I first started this project I covered a lot of the stuff I was learning at the time. In fact one of my previous class notes posts was in my top 10 highest viewed blog posts for 2020. Somewhere along the line I stopped doing that, so today we’re going to talk about what I’m taking this term, why I’m taking it, and why I’ll probably be adding a few step by step instructions for how you can do what I’m learning too in some of my upcoming posts.

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Great expectations

What did you want to be when you grew up? Sometimes the question ends in hilarity, a dinosaur, a unicorn, or maybe some other type of animal. Sometimes it leads to dreams of a sci-fi future, deep space traveller, Mars colonist, maybe a superhero. Whatever the answer is, they all have something in common. No one dreams of being average, but the average exists because so many people fall into it. Most of us have our dreams die as the reality of our existence becomes clear. I say fuck that, dream big until your last breath, why not?

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A look ahead

With the weather trying to kill everyone, the pandemic trying to kill everyone, and just life in general I feel like things are moving…. slooooow. I have a weekly meeting with my main-PI who reminded me that I’m behind and while he agreed it was probably due in part to the pandemic, it’s time to try and catch up. There is a lot going externally and internally, but I’m hoping that by covering a few things here I will have a nice little list I can refer back on and keep me on track. That’s the idea anyway.

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What is good outreach?

Yet another outreach event in the books! I have two more events this week and I believe that’s the last for my skype a scientist commitment. Since this term I was assigned classes practically all at once, I may re-volunteer to get a few extra classes in this term. Normally requests for my specific field don’t happen, but they’ve become more frequent, which is interesting to see because biomedical engineering, or my subset neuroengineering, isn’t a widely known field, but it is growing. All this recent outreach has gotten me thinking about what makes a good presentation, so let’s talk about it.

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Outreach as a hobby

I reference this photo later in the post, but it’s my robot foot!

It feels like only yesterday I was fighting to stay alive and stay warm, but now like a bad dream it’s gone before it settled. Sure I’m still stiff from sleeping on the floor and the water isn’t on yet, but life has quickly thrown us back into “normal.” I don’t understand how people can shift so suddenly like the last week didn’t happen, but here we are, and here I am getting ready for another round of outreach.

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On water

Water, it’s easy to take for granted when, with the flick of a wrist, you can get it pumped directly into your sinks, your showers, your toilets. The human body can survive for a substantial amount of time without food, that number varies depending on body composition and other factors, but it’s typically estimated anywhere from 8 to 21 days. That isn’t to say food is unimportant, just that on the hierarchy of needs, water is king. Depending on the circumstances, you may not even last a full day without it, so what do you do when you don’t have any?

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Full speed ahead

Neither rain, nor sleat, nor pandemic, nor freezing to death stop us from moving forward. I think that’s how the PhD motto goes anyway. Since the past week we’ve been struggling to simply live, we’ve had the whole city sort of on pause. That pause has come to an end, there is no recovery period here, it’s straight back to work. That’s a feature of capitalism, not a bug and it isn’t limited to getting a PhD, but we’re definitely included in the back to work group.

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Surviving catastrophe: A how to guide

Well what a crazy time to be alive, a time where everything is trying to kill us. Okay I acknowledge that nature is one ruthless force, but a lot of what has happened in the past few days has been almost completely due to human greed. Between the global warming causing this “once in a lifetime” storm — that is certainly not once in a lifetime — and power companies more concerned about profit than human lives, it’s been a trial. People, real people like you or I, but with far more money, are trying to kill us. Don’t give them the satisfaction.

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I lived!

What a combo breaker, two years of dedication and daily blogging down the toilet because the government was trying extremely hard to kill me. I’m not mad, just disappointed, okay I’m very mad (in the government stuff, not my streak that’s not a big issue). Technically I’m not through the storm quite yet, the power could still go back out, but I have had power longer now than I have in the past few days. Long enough to write a quick update anyway.

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Well… the US is frozen

It’s beginning to look a lot like Christmas… not in the fun way either. Here in the US we’re almost completely blanketed in freezing weather and in most cases, lots of snow. Which of course means power outages, rolling blackouts, and generally trying to prevent the state from letting me freeze to death. It’s a whole lot of fun, I highly recommend it. When the temperature drops like this I’m reminded of times in my life where I couldn’t find a warm place to stay and that makes me nervous for the people stuck outside right now.

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On the stories we tell

It’s been a busy week, there was so much to do that I was worried it wasn’t going to all get done, but here we are! Things got done, mental health was prioritized, and I figure it’s a good time to talk about words. Or rather the stories they form, it’s a complex topic and this is really more for me than anything, a friendly reminder that I really enjoy writing. After all, while this blog is meant to help others, it’s also a message in a bottle to my future self, a reminder that I was really here and actually did the work. An ever growing time capsule of my thoughts if you will.

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My scicomm video is done!!

I finally finished my video for the outreach project my main-PI tasked me with (this was the last post talking about it). There was a lot of time, effort, frustration, and I will admit, some not so kid appropriate language I was using during the editing process of the video. Mostly because I’m an idiot who had to find the most difficult way to do this project. Today we’ll cover what I did, how I hate myself enough to do it, and the end result. Let’s just say I’m not going to be a movie director or actor anytime soon…

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The road to a PhD program

In hindsight this post should’ve happened a long time ago, like year one and day one of my 365 days of academia project. Things have… evolved in ways I didn’t understand when I started this, originally the project was simply going to be a notebook for my classes, then it turned into my journey as a whole, and even what I do in my spare time. Like anything we create it took on a life of its own and I’m reminded I should touch on the process to getting accepted into a PhD program.

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Paper submission!

This morning I woke up to some good news! I got an email letting me know that the journal paper I’ve been working on has been submitted. It’s not the end, it’s only the beginning really. It needs to be reviewed before we know the outcome, but I’ve spent the past ten months or so writing this damned thing, so this is a huge moment for me.

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The tightrope of mental health

My mental health is like walking on a tightrope, one slip and I’m done. Getting back up could take years for someone like me. The truth is, things are hard on the best of days. Getting out of bed, shaving, cutting my hair at regular intervals, things that would come easy to some require sheer force of will to accomplish. All the small choices through the day eat away at what little energy I have until I’m drained before breakfast. Yet here I am, pushing forward. It’s days like today remind me that for all the progress I’ve made, it’s still just a tightrope I walk.

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Back to outreach

Just hanging out with the bots.

Today was the finish line, like it or not the R21 grant had to be finished. My Co-PI seems happy enough about the outcome, so we’ll have to wait and see what the result is, it could be several months before we know anything. It was a marathon of work, data process, experimenting, and now… nothing. I’m finally done so I can actually focus on other projects, which is the topic of the day!

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R21 Deadline

Today is the FINAL day for me draft before we send the R21 proposal off for internal review. Technically I think we have all day tomorrow too, but I need to get this back to my Co-PI for review and his final edits before we can submit it. The good news is the scientific writer was very thorough with their edits and suggestions, the bad news is I told my Co-PI I would get it back to him tonight before realizing how much there was to do!

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The zero factorial

Permutations and combinations and math, oh my!

Today I’m doing some stats homework and was reminded of an odd quark in math, the zero factorial. It’s not very intuitive and I absolutely love weird math, so I thought I would share the fun. I never said I was normal… Anyway today we’re going to go over why 0! (zero factorial) is so interesting!

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A clear path!

The easy path to getting your PhD…

That was quick! I have an update regarding yesterday’s funding debacle already… it’s good news, but that’s all the hint you’re getting for now! Things are happening fast and frankly they need to I only have a few more days to finish the grant before its due for internal review and I don’t know how my Co-PI is feeling right now, but I’m stressed out!

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Trouble on the horizon

I did not see this one coming… or maybe I did and just wanted to pretend it wasn’t going to be an issue. There’s been a difference of opinion to put it lightly. I received an email this morning from my main-PI asking if we could meet to discuss my funding options and he also casually mentioned that the R21 might not get submitted.

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