Keep moving

When I first got my job in August, I’d intended to join the gym on campus, but never got around to it. My birthday came, and I said, “After I talk to the doctor about my symptoms.” The winter holidays and new year came and I said, “After the colonoscopy, when I have a clean bill of health.” Then the need for surgery, and it’s not a good idea to start working out at that time. So, again, I put it off.

Now. . . What I really like to do is lift free weights. That’s going to still be out for some time, I think. Maybe if I had been lifting, I could modify the routine to maintain muscle, but I haven’t been.

Being active is necessary to maintaining health through chemo, so I’ve started walking again. I got a new fitbit Alta to try to track how I’m doing, at least on my good days (connect with me at fitbit here and MyFitnessPal here). Since I’ve been pretty sedentary, I set my daily goal fairly low at 5,000 steps. I met that goal 4 days and came close on one day in the past week. I’m bumping the goal up by 500 this week, at least on the before chemo days.

I keep saying I’m going to do yoga, but haven’t gotten the mat out yet. Now that the port site is healed, though, I should.

Yesterday, my roommate wanted to get out of the house and walk by the river, which was nice.

I complained about being tired after such a short walk. Then he reminded me: surgery, chemo, etc. He made me feel better about just doing what I can for now. It still bothers me that I’m getting tired when I don’t really think I’ve done much. I mean, I’ve only had one treatment. I’d expect to feel that tired in a couple months, but not now.

My appetite is back to normal, but I’ll be hitting chemo again in a few days. My weight is fluctuating as you might expect from a widely varying appetite.

Starting chemo

I started writing this on Wednesday, March 23rd after my first treatment, with the intention of finishing it up an publishing on Thursday or Friday. That didn’t happen. 😛

On Tuesday this week, I had a port put in my chest. It goes under the skin, with a line inside my body going along the jugular vein to sit just above the heart. Apparently, this is the most efficient way to get the medication into the body.

When this is done, they put you into a light sedation. I was aware of people talking. I could feel pressure where they were working, but no pain. By bedtime, there was some pain, but some ibuprofen helped.

Wednesday, I had my first treatment. The medication combo I’m taking is known as FOLFOX 6.

One of the medications is oxaliplatin. Apparently a very well known side effect of this is cold sensitivity. I was listening to the nurse talk about this one. She placed a lot of emphasis on it.

Don’t drink or eat anything cold like ice cream. Don’t put ice in your drinks. Use a straw. No chilled drinks. It seemed redundant. Don’t take food out of the freezer without gloves. It seemed excessive, and I was thinking the whole the time, “Yeah, right” and internally rolling my eyes. “Like that’s gonna happen.” I’m normally much more sensitive to heat than cold. I can wear short sleeves or tank tops when other people are bundled up.

Before I left the hospital, I was running my hand along a wooden banister in the hallway. My fingers felt like I’d touched an ice cube long enough to start to burn. WTF? When we got home, I was climbing the stairs to my apartment and couldn’t grip the metal railing. It hurt! The metal doorknobs in my apartment, the flush handle on the toilet. Cold water from the tap to wash my hands. All feel way colder than I know they are, only hours after the first treatment. Holy shit.

So this is gonna suck.

I’ve ordered some cotton gloves and I’m looking through my knitting patterns to see if I can find some cute ones I can make in cotton or linen.

I am carrying the 5-FU medication around until Friday morning, but I’m determined to go to work today. I’m letting my roommate take the car, so if I feel sick, he can come get me. That way, I won’t have to drive if I’m not up to it.

When we got home, I made a grocery list for him, including some cleaning supplies we’d need and stuff. He hasn’t lived with me long, but he’s starting to pick up on my likes and dislikes. He knew I wouldn’t be able to eat the frozen juice pops I’d bought for snacks, so he picked up some mint Milano cookies that I like. 🙂 I thought that was sweet.

Thursday wasn’t a bad day. I carried the pouch, worked, took the nausea medication. Went to bed at a normal time. Slept ok.

And vomited shortly after waking on Friday morning. Luckily, I had the day off already, since I had 2 medical appointments that day. They disconnected the pack. That was quick and easy. But I was tired and nauseous, despite the nausea medication. No food seemed appetizing.

The second procedure was taking a biopsy of my thryoid – a whole other issue.

According to my scale, between Thursday and Sunday, I lost 10 lbs. Only vomited 3 or 4 times, but simply couldn’t touch food and didn’t drink nearly enough water. I’ve gained 5-6 lbs back in the week since.

I managed to work all week, but I am pretty tired.

Different Direction – Colon Cancer

I’d originally intended this blog to be about learning data science and database systems. But things have changed since I started that path.

In August 2015, I started a new job with a federal agency as an IT specialist on the local help desk. After years of unemployment and underemployment, financial and emotional struggles, I finally had a job that was letting me live comfortably, pay my bills and start adding in some little luxuries.

But I was having some problems. I’m going to have to get a bit explicit here, to describe my symptoms. I was having intestinal pain. I’d experienced pain like this before, but only occasionally, and usually if I wasn’t consuming enough fiber. There was also blood in my stool.

And the symptoms didn’t go away.

I tried to be better about taking both a fiber supplement and Greek yogurt (for the probiotics). There was no change in the symptoms.

So, in November, I sent an email to my primary care doctor (the VA has secure messaging available so you can do that! It makes communicating so much easier than calling, leaving messages and hoping they contact you back). She asked a few questions and gave me a referral to a GI doc. Both she and the GI doc were thinking IBD – Inflammatory Bowel Disease. When I saw the GI doc in December, she suggested that I get a colonoscopy to rule out other things, just in case.

The colonoscopy was in January. By now, the pain was getting a bit worse. I was in the bathroom a dozen times a day, but I may only go a little bit or even not at all.

When they woke me up from the procedure, they pulled me into an office to tell me that they found something they didn’t expect. A 4 cm lesion that was highly suspicious for cancer in the sigmoid section of my large intestine. Biopsy confirmed an adenocarcinoma.

On February 11th, I had surgery to remove most of the sigmoid area (sigmoid colectomy or sigmoidectomy).

Recovery has been a little slower than I thought it would be. I’ve had a couple of abdominal surgeries before and bounced back faster. I’m 4 1/2 weeks post surgery and still very tender and moving a bit more slowly than I’d like.

This is a cancer that is much more common in people older than I am. I’ve seen age 69 as median age of diagnosis and 72 as a mean. I’m 46. Both the GI doc and the surgeon were convinced the surgery would be all that was needed. But they tested 15 lymph nodes and found cancer in 2.

So I need chemo.

Freaking out about that a little bit.

R, RStudio & Getting Started with swirl

I’d seen “R” in job descriptions (usually as “experience with Python or R”), but I didn’t really know what it was.

In the first course I took through Coursera, they had us install R and RStudio.

In short, R is a statistical programming language.

The “about R” page talks about it being a “dialect of S”, an older programming language.

R provides a wide variety of statistical (linear and nonlinear modelling, classical statistical tests, time-series analysis, classification, clustering, …) and graphical techniques, and is highly extensible. The S language is often the vehicle of choice for research in statistical methodology, and R provides an Open Source route to participation in that activity.

Also from the “About R” page:

R is an integrated suite of software facilities for data manipulation, calculation and graphical display. It includes: an effective data handling and storage facility, a suite of operators for calculations on arrays, in particular matrices, a large, coherent, integrated collection of intermediate tools for data analysis, graphical facilities for data analysis and display either on-screen or on hardcopy, and a well-developed, simple and effective programming language which includes conditionals, loops, user-defined recursive functions and input and output facilities.

It’s free and open source and expandable with “packages”. It seems to be very flexible in what it can do.

The first lectures in the R Programming course talk more about the history of the language.

As I mentioned in my first post, I didn’t feel like the lectures really explained what was needed for the course projects. The lectures and associated slides are good for providing some background and an understanding of why you’d want to do certain things, but are not really a how-to, at least not a step-by-step.

Fortunately, the course offered extra credit for doing assignments in the swirl package.

I wouldn’t have had a clue where to start if it wasn’t for this package.

It’s essentially a self-paced tutorial on the language, starting from the very basic (assigning variables) and getting increasingly more complex.

This was more valuable than the lectures, at least to me.

I had a few hiccups where I didn’t understand what was necessary to create a couple of the scripts in the early lessons, but was easily able to find assistance online – there really is a blog for everything!

Right now, I’m trying to decide if buying any books about R would be helpful or if I should be able to mostly rely on material available online.

If you want to get started, you can download R here. You’ll see references to CRAN, which stands for: Comprehensive R Archive Network, which is:

a network of ftp and web servers around the world that store identical, up-to-date, versions of code and documentation for R.

R by itself looks like:

RStudio is a more user-friendly interface for R.

I started doing the first couple of things in the plain R, but moved to RStudio pretty quickly.

To use swirl to start learning R, you have to install the swirl package. There are step-by-step instructions here. (I’m using a Windows 7 machine, so the path name is in Windows).

> install.packages(“swirl”)
Installing package into ‘C:/Users/me/Documents/R/win-library/3.1’
(as ‘lib’ is unspecified)
trying URL ‘http://cran.rstudio.com/bin/windows/contrib/3.1/swirl_2.2.21.zip’
Content type ‘application/zip’ length 132575 bytes (129 KB)
opened URL
downloaded 129 KB

package ‘swirl’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in
C:\Users\me\AppData\Local\Temp\Rtmp08B97X\downloaded_packages

After it’s installed, you have to activate it by calling it from the library.

> library(“swirl”)

| Hi! Type swirl() when you are ready to begin.

And then it’s just a matter of following the directions.

swirl()

| Welcome to swirl!

| Please sign in. If you’ve been here before, use the same name as you did then. If you are new,
| call yourself something unique.

What shall I call you?

Learning: Data Science Specialization through Coursera

As I’m beginning to take my career into a new direction, I realize that I have a lot to learn.

I know math and basic statistics, but I need to know how to clean data, how to present it so businesses can use it to make decisions, and how to work with statistical programming languages.

I’m still trying to figure out if analysis or database administration is the better path for me, but to do that, I need more understanding of what is involved in each path.

In the last year, some of what I’ve really enjoyed doing was figuring out how to get information out of a database. That’s why I started studying SQL.

In my current position, I need to present information from varying sources (Google Analytics, Facebook Insights, other social media advertising and posting info, internal databases of customers, etc) in ways the company can use to make important decisions.

I started researching obtaining a Master’s degree or university extension certificate in Data Science, but the cost is beyond my capability for now.

When I heard that veterans can get a verified certificate through Coursera, I researched what was available.

The Johns Hopkins Data Science Specialization sequence seemed to be similar to the university extension certifications I was researching.

Each course in the sequence is 4 weeks long. Each course has video lectures, most with either PDF and/or HTML slides, a quiz each week, and programming projects.

So far, I’ve taken two courses in this sequence.

The Data Science Toolkit is an overview of the sequence, with an emphasis on getting the basic programs and accounts setup. It has you install R (an open source statistical programming language), RStudio (a more user-friendly interface for R) and Git (a version control program) as well as set up an account at GitHub.

GitHub is pretty interesting. It’s a place where you can share programmers share and crowdsource their software projects and documentation. I was unaware of this tool before the class. I’m looking forward to using it more.

R Programming is a brief, very brief, introduction to some of R’s capabilities.

Included in this course is a study “package” called swirl. This was probably the most useful part of the course – and was counted as extra credit.

The lectures seemed to prepare a person for the quizzes, but were really inadequate for the programming assignments, especially if you’re a novice programmer. There were many discussions on the forums for the course about this.

I found that I did ok with swirl and a little outside the course research, but I downloaded all the course material and want to walk through the programming assignments again on my own time.

Getting and Cleaning Data starts this week.

I’ll be adding the verified certificates to my LinkedIn profile as I receive them.