Posts

Note: sometimes I write these posts to teach myself a better way to do things in R. I have been avoiding tidyeval somewhat, because I seem to have a bit of a learning block about it. I’m going to try to write some posts that help me understand what’s going on with Tidy Evaluation. Using sym() in a Shiny App One fairly simple Shiny Application might be selecting a column of the dataset and then doing something with it, such as using it in a select() or filter() statement.

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I’m still in the process of recovering from my current bout of depression and anxiety. I’d like to talk about what is currently helping me moderate my anxiety. I have been practicing mindfulness and meditation for the past three years and I’m beginning to realize how necessary it is in our information dense age. Many of my symptoms of anxiety are really from an information overglut. I’m currently on way too many projects and am teaching as well.

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I decided to write this post in celebration of my newest album, [Tiny Fugues, being released](). I consider myself a scientist and I am a musician in almost equal parts. There has been a lot of talking about the role of creativity in science. Honestly, I rarely try to cross the streams of science and music, mostly because it really hasn’t been encouraged in my career. I do think that I do use the same problem solving skills that I do in science that I also use in composition.

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I want to thank everyone who has reached out to me after I wrote my post on struggling with my depression and self-care. I am incredibly grateful for everyone’s concern about me. I wrote that at a low point in my life because I had to. I was suffering too long in silence, and I needed to do something. Writing that post was incredibly scary. I am still worried that it may be used against me somehow down the line when I am reviewed for tenure.

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Motivation A few weeks ago, as part of the [rOpenSci Unconference](), a group of us (Sean Hughes, Malisa Smith, Angela Li, Ju Kim and me) decided to work on making the UMAP algorithm accessible within R. UMAP (Uniform Manifold Approximation and Projection) is a [dimensionality reduction technique]() that allows the user to reduce high dimensional data (multiple columns) into a smaller number of columns for visualization purposes (Usually two). It is related to both Priniciple Components Analysis (PCA) and t-SNE, which are techniques often used in the single-cell omics world to visualize high dimensional data.

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Well, Cascadia-R 2018 has come and gone. This year we tried our best to make it as inclusive, welcoming, and friendly as we could. Considering we had 224 participants this time around, I’d say it was a success. I just thought I would do a little write up of some of the things we did and why we did them in our conference. I’m hoping it will be useful for other conference planners to create a welcoming environment.

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Note: I am not writing the following to complain, or excuse any past behavior. I am writing this just to be honest and transparent about my current struggles in academia. I hope it helps someone, or encourages other to seek help. I have to confess that I haven’t really been feeling all that well the past few months. Right now I am plagued with feelings that I am doing my work as an Assistant Professor wrong.

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Even though I’ve been using the tidyverse for a couple of years, there’s always a couple new applications of tidyverse verbs. This one, in retrospect, is pretty simple. I had a one to many table that I wanted to collapse, tidy-style. Let’s look at the diamonds dataset: diamonds %>% select(color, cut) ## # A tibble: 53,940 x 2 ## color cut ## <ord> <ord> ## 1 E Ideal ## 2 E Premium ## 3 E Good ## 4 I Premium ## 5 J Good ## 6 J Very Good ## 7 I Very Good ## 8 H Very Good ## 9 E Fair ## 10 H Very Good ## # .

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In academia, it’s inevitable to have to travel and present at conferences and meetings. As an introvert, I’ve been trying to compile a few tips that have helped me navigate large conferences so I don’t feel overwhelmed. It is unfortunate that though the academic community has many introverts, conference and meeting structure is heavily biased towards extroverts. (No offense to extroverts, but some of you can sometimes seem like blowhards to us introverts.

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Sorry for the lack of posts. I have been busy with co-teaching our Health Informatics course (HSMP410) for the OHSU/PSU School of Public Health. I’m trying to make most of my lectures activity-driven for my students, who are Community Health Education and Nursing majors. I believe that you can teach mathematical concepts visually, so I am experimenting with using LearnR/Shiny to teach the basics of data literacy. I’m also using datacamp-light to show my students a simple intro to data science.

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