Hey folks,

At long last the {phylotypr} R package is on CRAN! I posted a video on Wednesday describing the process of submitting the package. Then on Thursday, I submitted a manuscript to Microbiology Resource Announcements that describes the package. Hopefully, it will be published soon.

MRA is a pretty nifty journal that published short (~500 words) articles describing resources that microbiologists might find useful. There aren’t supposed to be any results, just a description of the rationale for the resource and a description. I encourage any microbiologists to use the journal as a forum for publishing data, protocols, software, etc. After many people asked me for a way to cite my YouTube Channel, last year I finally published an article describing the videos as a resource. The submission and review process was pretty straightforward. Give it a try!

You may have noticed I also posted videos on Monday and Thursday of this week that touched on the content of a previous newsletter from August 23rd. My hope is to return to posting videos twice a week. One will take the written description I’ve been narrating in the newsletter and turn that into R code. The second will be me representing the data either how I would go about doing it or trying to show off something in R. I hope to get to a point where the videos follow the newsletter by a week or two (I’m behind, so you’ll occasionally get newsletters like this one). Please let me know what you think of the new format! Also, if you have any figures - simple or complex - that you would like me to give my treatment, reply to this email with a link or a copy of the picture.

After posting two videos this week and recording two videos for next week I wanted to share two early observations.

First, I never cease to be amazed by how much I learn by producing these newsletters and videos. Teaching forces me to practice my own craft and explore parts of R that I am not familiar with already. Is there someone around you that you could teach? Even if you feel like you are just getting going with R, teach someone else what you have learned. I can guarantee you will learn what you still don’t know, you will be impressed by how much you do know, and you will be able to retrieve that information more easily in the future. If you don’t believe me, give it a try!

Second, a thought occurred to me. Why do I bother remaking other people’s figures? Take for instance this week’s video showing how to make a scatter plot. I’m fairly certain that the original figure used GraphPad Prism. It has thick lines and bold fonts. The overall appearance feels chunky to me. But by reproducing the original as faithfully as I could allowed me to get more practice with manipulating and creating axes and the text that goes with them.

In the video I worried about the points falling on top of the y-axis in the original, but behind the axis in R. I could have let that slide, but that would have been lame. Right? That forced me to consider removing the default y-axis and creating my own. Along the way, I used the clip argument from coord_cartesian() and the expand argument from scale_*_continuous(). Even if I never make this same type of y-axis again, this practice helped me get more practice with those functions and arguments. Spoiler: I use clip and expand in next week’s videos too :).

What I hope you take away from this discussion and my videos isn’t how to make a specific type of plot that suits your specific needs. Rather, I hope you learn how to use a powerful set of tools to do anything you want. I have observed many learners over the year want to know how to make a specific plot with a specific type of data. But what will that get them in 5 years when they’ve moved on to a new type of plot and a different type of data? Learn to use the tool and how its parts work. Then you’ll become a master of your craft. That’s what I want for you. I’m certain you are capable of it!

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