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Posts tagged “science

Start of summer experiments

Well today is the day! I’m just hours away from collecting my first dataset for my summer project. I’m excited, it’s a cool project and I get to be first author on the paper. The topic is impressive to me so I think it will be a good way to get my name out there in the field since this will be my first paper in my Co-PI’s lab (well first, first author paper). It’s a lot of responsibility and of course I don’t have any time to prep. The first experiment is always the hardest…

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Learning is sneaky

Three years ago this fall I walked into my main-PI’s lab for the first time and I knew nothing about the work we did. I was a mechanical engineer and had machining, solid modeling, and control experience. None of which helped me in my new position. Learning something new is a slow process. The more you learn the more you realize you don’t know anything and it feels like three years later I’m just as clueless as I was when I first set foot into the building. Learning is sneaky that way, you don’t always realize how far you’ve come.

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The start of a busy week

Splitting your time between two labs should be pretty straightforward, on one hand my two PI’s have come to an agreement about how my time should be split and in a 40 hour work week, each should get roughly 20 hours of my time dedicated to the things they are working on. Easy, except it isn’t. Both are used to 40 hours to their lab and I’m not complaining, I enjoy being wanted, but as my Co-PI pointed out I have a lot going on and I need a break. Literally he told me to take a break, it’s bad enough that my Co-PI is telling me to go home.

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Intro to MATLAB – Part 2

I’m teaching an intro to MATLAB class and if it’s one thing I hate it’s hording knowledge so I’m sharing it here for all of you to enjoy! If you missed the first part, fear not you can find it here. I’ve also created a special category (the Intro to MATLAB category) where you can find these posts and a whole lot of other things I’ve taught, like my 10 week solid modeling for beginners classes and my incredibly detailed and surprisingly popular, know your spinal cord series (my personal favorite). Okay enough plugging my classes, let’s talk MATLAB.

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Intro to MATLAB – Part 1

Not MATLAB, but it looked nice.

Per my usual routine, I’m teaching a class and instead of hording the knowledge I’m putting it here for all of you to use! I’m even going to attach the example code I wrote, which has enough comments to fill a small book, to help everyone just starting out. As I explained to my students, this is an intro to MATLAB course so my focus is on showing how things are done in MATLAB and less on how to problem solve using MATLAB. Although the last two lectures have not been created yet so they may focus on problem solving, who knows.

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Competing projects

With summer upon us I still have a few things to wrap up, but I am hoping that by the end of the month I should be able to take a breather for a few weeks/month we’ll have to wait to find out. The issue now is that my main-PI and my Co-PI both have projects for me to do and both of those projects are incredibly time consuming. Oh and they both want them done at roughly the same time. Sounds fun, right?

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My talk is today and you’re all invited!

Okay so I wanted to update everyone on how my first lecture went yesterday since I only had a few short days to throw everything together and it was a mad panic to the end. Unfortunately we cannot go into detail today! That’s because today is my “I’m giving a talk” talk (which I wrote about here). It’s free to watch, my talk is roughly four minutes long and is a nice little rundown of some of the work I do. So today I figure I will go into a bit of detail and should you be so inclined to attend you’ll get the chance to chat with me in person about my work! Yep, I’m breaking anonymity yet again, but it’s for a good reason.

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Pre-class disaster

What’s the rule? If something can go wrong, it will? I’m fairly sure that applies in this case. I am just hours away from teaching my first class of four and nothing seems to be going right. So I need to step away before I throw something (okay not really, but I wish I could). It’s frustrating and part of the issue is that this was thrown together so quickly without any sort of prep beforehand. So what’s the backup plan, well that’s the topic of the day.

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Surprise class prep time

Between the bout of depression and the fact that I have some weird thing going on that bloodwork apparently cant figure out I have accomplished roughly zero of the prep I need for my surprise class (more here). So how do I come up with four classes worth of material in just a few hours… magic! I wish, but really I think the best thing for me to do is come up with an outline and then just focus on the first lecture (of four). Since I try to write daily, I figure we can go through my thought process together!

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On designing experiments

After meeting with my Co-PI and discussing the super cool experiment he wants me to do (here) it sounds like I’m in control here. Scary thought, right? This is that whole working WITH my Co-PI and not FOR my Co-PI, he trusts me to make good choices. I mean either way he’s going to need to sign off on it when I finish the design, but it’s kind of interesting to be the one who gets the say in how we do this.

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Surprise teaching, seriously.

Well this is awkward. My main-PI just asked me to teach a course on MATLAB to our new summer interns. Most of them have never used MATLAB before and those that have probably know very little about it. To fix this my main-PI told me that I was going to teach a course on it. At first I thought it was one, but it turns out he want’s four classes (two hours long each) on it. I was trying to have a light summer, but that doesn’t look like it will happen.

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Journal papers update!

Not a typo, journal papers as in multiple. This year I’m planning on submitting three different journal papers. I’ve already submitted two and got feedback on them, so technically resubmit those. The third is still a work in progress and to be honest, there could be a fourth that I submit this year as well. Basically there’s a lot going on and it’s all pretty mindboggling that I can’t seem to get any of this off my plate. It’s a process for sure, but even though I’m still hard at work, there’s been some progress.

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Surgical shadow update!

Well I finished my surgical shadow today. Frankly I’m exhausted, maybe I was just too excited, but I got roughly zero sleep last night. That said, it went better than the last shadow where I had just gotten my second dose of vaccine the day before. Now that was not my idea of a fun time! So per the usual I cannot go into the details, but I can talk vaguely about what happened and what’s next.

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Another surgical shadow

Just FYI, I didn’t take this and I’m pretty sure it’s just a stock photo, but it works for the post. I wouldn’t want to cause any privacy issues.

Well it’s officially on the books! Monday (super early) morning I will be shadowing my second surgery. For those new around here this was the first. It was an awesome experience and I’m excited to do it again. Today we’ll talk about why I, as someone who does non-invasive research, is even attending surgeries and what I get out of them. There is an actual practical reason to attend, but it’s also just super interesting!

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The best laid plans…

The full quote is “the best laid plans of mice and men often go awry” and is from a poem, but also inspired the book title, “Of mice and men”

Well this week has been a serious rollercoaster of emotion. There have been incredibly high highs and extremely low lows. It’s so bad I’m not even sure what’s going on at the moment and it’s throwing my entire life into chaos. I wish I were exaggerating, but unfortunately I am not. So what has me so out of sorts? My academic plans are entirely up in the air now. For the next few months (up to 6 months) I will have to sit and wait to figure out what I can do about it. Let’s just start at the beginning.

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Intro to ICA

Independent component analysis, probably not something you hear about all that often unless you’re in a field that uses it. If you’ve found this via google or the such, then you’re probably looking for an explanation on what the heck ICA is and how to use it. Fear not, today we’re going over the why of ICA, why it works, why we use it, and why it isn’t the perfect tool we wish it was. Hint, the reason it isn’t perfect is because of math, stupid math. Quick note, I’ll be focusing on EEG uses for ICA, but there are tons of other applications and this knowledge will still apply to them as well.

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First class of the summer

I’m teaching again! Okay, I didn’t exactly stop, I mentor and do other things, but tomorrow is the first class of the summer that I’m teaching. Which means today I need to finish the slides I’m using, review the materials, and get everything ready so everything will go smoothly. There’s a lot of moving parts that have to happen and while I’m not particularly new to this, it will be the first time teaching the topic. What topic is that? Well…

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Journal problems

I feel like I’m playing the how many journal papers can I have in review at once game and I hate it. Since there’s so much going on I think it would be a good idea to discuss a little bit on what I have up in the air at the moment, why I’m so freaking annoyed about the situation, and what comes next. Most of this is just me being frustrated and venting about the process, but what the hell, sometimes it’s okay to complain. I think that’s pretty much what grad school is anyway, getting better at complaining.

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The hunt for funding

Funding, a running theme around here. When I started my PhD it was clunky, I had no clue what I was doing, but I new that I needed to have some money because the first rule of doing a PhD is that you DO NOT pay for your PhD. That much I knew from my Masters (which I was lucky enough to not have to pay for because my PI at the time was just starting out and had funding for me). The rest was up in the air and has been up in the air for a little bit now, so today I’ll be talking about my funding history and where I’m at now. It’s all a little up in the air at the moment, but I’m optimistic.

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Surprise summer project!

I’m super excited! My Co-PI sent me an email late yesterday asking me if I had time to help with an experiment. I absolutely love my Co-PI’s lab and all the stuff they do (throw back to this post), so of course I wanted a project! Well I read over the proposal and what he wanted me to do and let’s just say that I am in for a fun summer. I cannot wait to get started, since I can’t go over the details about what I’ll be doing, I think I’ll talk about the consequences.

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On having two PI’s

My two PI’s, a comedy/drama TV show I want to make one day which just happens to be based on my life. Yep, for those who are unaware I have a dual appointment in a hospital where I do a lot of my research. It’s amazing and it really makes me excited to focus more on the clinical side of things, but it means that I have not just one, but two PI’s and that isn’t a bad thing! It’s just a bit of work and can feel like being caught in the middle.

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How to find the right lab for your PhD

Going into a PhD program is a confusing whirlwind of stress, new experiences, and the general feeling of being lost. You do belong there… right? You know what’s harder than making the choice to get your PhD? Finding the lab you want to call home for the next five or more years. Inspired by advice I gave to one of the undergrads I’m mentoring, today we’re going to talk about how you should hunt down a lab you want to be a part of. It’s that time of the year again, but don’t worry, finding the right lab for you doesn’t need to be scary.

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The start of summer teaching

Today is the start of our labs summer classes. This marks the beginning of roughly 12 weeks worth of lectures on the stuff we do in the lab for our undergrad and high school students. It will be a chance to teach them how to use some of the techniques they will be working with during their summer with us and it will also be a good refresher for everyone in the lab, because we tend to focus on very specific analysis when we do our research it helps teaching each other some of the things we do well.

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A data detective

You did a cool experiment, you have some interesting data, and you found something unexpected! Great, but what does it mean? Sometimes the answer isn’t as straightforward as you may hope. That’s the problem for the day, I found something in my data that makes no sense and the worst part is I have no idea what it means. It’s definitely something, so now I need to go through the steps of making sense of it. That’s the problem with doing something new, you have no frame of reference for the result.

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Summer teaching

It’s that time of the year again! We’re taking on undergrad and high school students for the summer research program! An exciting chance for people to get their hands dirty and learn what it’s like to work in a lab. The best part is that most of the people attending are paid! That’s right, undergrads are paid to be there. That also means I get to put on my teacher hat, which I absolutely love. Today we’re going to talk about what I’m teaching and I’ll probably spend a bit of time talking about how much I enjoy teaching, let’s go!

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The last day of the conference

Today’s the day! The last day that is, the final day of the conference I’m attending. The past few days I’ve talked about different aspects of conferences in general and I’ve touched on why virtual conferences are important, needed, and should be the norm. I’ve also talked about the difficulties presenting at a live conference when you have disabilities that make public speaking a challenge. Today I figure we can round out the topic by covering some of the good things about conferences and why you want to attend when you can.

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Presentation anxiety

Today is day two (of three) for the first conference of the year for me (more here). Presenting live is always a challenge and the difference between a good presentation and an okay presentation (any attempt is at least an okay attempt in my opinion) is a combination of planning, practicing, and luck. Of course there are things that can make this particularly difficult, for example one of the issues I have is aphasia, so while I can write normally (mostly), speaking can be a challenge. This is particularly apparent when I’m stressed, so presentations are a challenge.

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The first conference of the year

Today marks the start of the first conference of the year for me. This was the one that was unfortunately named far too similarly to the other conference I was awarded a slot to speak at (here). It’s three days long and is completely virtual (thankfully!) so I won’t be traveling just yet even though things are relaxing (far too early in my opinion). I figure today since I’ll be doing that we can discuss why I’m happy that we made the switch to virtual and why I am angry that it’s going to change soon.

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The CDC guidelines and you

The CDC announced that YOU NO LONGER NEED TO WEAR A MASK… if vaccinated. Yep they put the important part in nice tiny font and after a year of people actively putting others at risk because they would rather throw a fit about wearing a mask than help stop the spread. Roughly just over a third (~36% as of this writing) of the population has been vaccinated. What’s troubling is the large number of epidemiologists and scientists in general were shocked by the CDC announcement. So what now?

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The first in-person meeting

Well today we met as a lab for the first time since the pandemic hit in person. I wasn’t a fan, still am not a fan, but didn’t get a choice in the matter so I went. Thankfully everyone was masked and agreed that it was probably for the best since in my case specifically, I work with a very vulnerable population. It was nice to see everyone, but it was mostly a waste of time, mostly.

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Meetings and more meetings

Today was going to be about my meeting yesterday with my Co-PI, buuuut it turns out that I have even more news than that! How did that happen? Well I got an email from my main-PI asking me about my plans for the summer, when I wanted to finish the long, horrible, project I’ve been trying to work through, and more importantly, my funding situation. After some emailing back and forth things are looking dare I say good?

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So I shot myself in the foot

Ever say something dumb and immediately regret it? Yeah I made a huge mistake and ended up giving myself a ton of work for no reason. Well there was a reason, it just wasn’t needed. I don’t know why I do this to myself, but the good news is I got the work done. Okay, fine I’ll explain, it’s not a long story, but it is a funny one (at least now that the work is finished). It’s also a good reminder to never do that one again.

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Data mysteries

Data processing, it’s mind numbing sometimes. I guess it depends on the dataset you’re working on, but in this case it’s just a formatting thing. Literally copy, paste, rearrange, things like that. The issue is the volume of data you’re working with. The whole thing can take hours just to get done properly, but with any luck you’ll only have to do it the once. Most of the time I’m not that lucky, the last dataset I worked with for my Co-PI I reformatted five or six different times. While that isn’t the topic of the day, it’s a good way to start the conversation of the day.

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Journal paper update

With all the things going on I never got the chance to talk about some non-class news. The downside is it’s not good news, but on the scale of horrible things to happen recently it’s not that bad. Back in February I submitted a paper for journal publication and we got rejected. Not great news, but the reviewers were not super critical and with some minor changes we should be able to resubmit it. I figure today we can go over the stuff that needs to happen now since I’m the first author.

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Flexible coding for data visualization

My main-PI has an odd habit of wanting us to edit things as we’re presenting them. I’ve watched this happen and had to do it myself. Suddenly you find yourself editing a paper/grant/etc. and forgetting how to spell your name because you’re so flustered. It isn’t just papers though, it’s our visualizations that we make. He will ask us to go in and change things as they are being shown. This has happened to me several times already and more often than not I’m ready for it. So today I figured I would go over some of the things I do to make sure that I don’t spend the entire time sweating over edits to my code.

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Apparently I’m close?!

We’re talking about it again, the fact that every week for the past 5 weeks now I’ve been given tasks to do and then presenting on them the following week. It’s been… hard. However, my main-PI gave me hope that the end of all this is close, at least that’s the hope. He said I was close, so today we’re going to talk (as usual vaguely) about what I have left to do before this weeks meeting and why I cannot wait to be done with this.

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When you don’t want to say no

In undergrad I had a discussion with my advisor, or rather he was more of a mentor, he wasn’t technically an advisor. It went something like this, I don’t know what to do next because it all seems so interesting. He argued that it was a good problem to have and while I have generally narrowed down my focus (I am doing a PhD after all), I still have an issue with focusing my excitement. It’s like being at Disneyland and trying to force yourself to go on just a single ride your entire trip. I don’t wanna, I want all the knowledge!

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On the prefrontal cortex and abuse

Adulthood is often thought of as the point where you’re done developing. Most states for example don’t allow anyone under 21 to drink because that was where we drew the line, but we allow people as young as 18 (here in the US) to join the military, vote, etc. You may think that this would be roughly where we stop developing and that would explain the somewhat artificial line we’ve drawn. The truth is much stranger than that and when it comes to the brain you don’t develop evenly.

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Journal club

Okay, get this I completely skipped over the fact that my Co-PI started a “journal club” for our little lab. I say little because for the longest time it was just the two of us and the research coordinator (who is amazing by the way!), but now we have not one, but two others in the lab. It’s nice not having to do a lot of extra work, but different topic for another time. We formed a journal club a short 8 weeks ago and every other week one of us sends out a research paper they find interesting about a week prior to our biweekly meetings and then that person presents on it. This week it’s my turn and of course, the universe is against me.

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Fun with coding!

Yesterday I worked and worked, then I worked some more. By the time I called it quits it was well past my normal stopping time. The problem was that nothing was going right yesterday. When I finally gave up I had gotten exactly nothing done. It was one of those days as a collogue said sometimes you just have to power through it. The problem is I don’t have the time to just power through. Which reminded me of how I normally deal with stress, which is funny and I recommend others do this too.

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Another week in review

A week ago exactly I gave a review of the week I had and a look at the week coming up. I thought it was so much fun I’m doing it again, because that’s what passes for fun around here. Who knows maybe I’ll do this regularly! Basically a lot has happened this week and now is a good time to catch everyone up on some of the oddball things I’ve done and things I may have missed in favor of freaking out about the work I’m doing. So let’s just jump into my semi-traditional introduction, then we can look back and ahead. It’s fun for everyone!

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I’m giving a talk!

Well I slipped through the cracks yet again! It hurts me to admit that I’ve probably earned this one. The 7th annual BRAIN initiative investigators meeting is coming (in June) and I was selected for a Trainee Highlight Award. Is it a big deal? Probably not, but I’ll take a win when I can get it. Today we’re going to dive into what exactly this means for me and why even little victories should be celebrated. Is it a little victory? I mean they did pick me, so what does that say about them?

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A week in review

I figure it’s a good time for the recap of the week. I mean there was a lot going on and while I want to spend some more time on my “in statistics” series, I also really need a break. So instead of spending a lot of time making sure the information I’m presenting is accurate, concise(ish), and (with luck) well thought out, I figure it would be easier to talk about the things I’ve had to do this week and the things I get to look forward to! Joy, welcome to life as a PhD candidate.

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Defining parametric tests in statistics

We’ve been throwing around the term a lot in this series. I’ve been saying in parametric statistics this, in parametric statistics that, but I kept putting off giving a definition. It’s not because it’s hard to understand, it’s just that typically when you’re doing statistics you already know if you’re using a parametric test, but because we try to make no assumptions in this series, we’re going to put this to bed once and for all. Today we’re talking about parametric statistics!

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Independence in statistics

A while back we introduced the central limit theorem, it was a way to take data and make it normal (gaussian) as if by magic, which is one of the assumptions needed for parametric statistics (the most commonly used kind). Today we’re introducing another assumption, that the data are independent. The idea of independent events is probably straightforward, but it’s yet another bedrock of statistics that we should talk about in depth to help us understand why things are the way they are.

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Variance in statistics

Sometimes you just want to kick a distribution right in the mean.

Variance, it’s one of those concepts that get’s explained briefly then you find yourself using it over and over. Now that I have a free moment, I figure it’s about time to revisit the “simple” concept and just take a minute to apricate why we have to deal with variance so often and why we try so hard to minimize it when we’re doing experiments. Just like the discussion about the mean, there’s some subtilty that goes into the idea of variance and it’s square root cousin standard deviation and we skip over it in favor of getting into more complex topics.

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Scientific figures are hard!

Well now, part of the work I needed to get done this week involved making some new figures. Actually I had added work dumped on me yesterday that I got done just as quickly thankfully. However, there’s a bunch of other figures I need to make that are due… tomorrow! Ah! So of course instead of actually making them I’m here to talk about how big a pain figures are and why we (the scientific community) stress out about them so much.

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Clinical research in a pandemic

Male and female characters scientists or lab attendants working in science laboratory using microscope, lab glassware, vector flat illustration. Scientific research, experiment, science and education.

One of the more interesting things about the pandemic is that everything at the university level shut down. They still send out emails suggesting that everyone wants to go back to in person classes, but they haven’t followed through with that threat. Human participant research has been halted and even though we’re probably going back to “normal” in the fall, right now nothing is happening. That’s at the university level though, clinical research is a different story.

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Another approaching deadline!

Well it’s going to be down to the wire this week. It’s good to know we’re keeping the theme, if you’ve been following along for awhile you already know it’s always down to the wire. This week is particularly challenging because I have competing interests for the time I have. There’s only 24 hours in a day, so there’s only so much work that can get done. I would prefer to not do it at the last minute, but here we are… again.

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Fun with Rstudio

Okay, not really. Having to use R is a pain. I’m not a fan and the structure they use is very confusing to me as someone who uses MATLAB on a regular basis. I understand matrices, I regularly make and successfully work with higher dimensional matrices ( > 3, which hurts your brain to think about a 20+ dimensional matrix, but hey whatever gets the job done). R on the other hand feels foreign and the commands feel clunky.

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