Publications by Posts | Joshua Cook
R Markdown animated GitHub corner
This is an incredibly easy way to spice up any R Markdown file. It adds an animated link to GitHub in the top corner of the HTML output, just like you see at the top of this page. Mouse over the icon to make it wave. All thanks and praise should go to the creator Tim Holman. The first step is to create a new file called “header.html” and past...
1627 sym R (1662 sym/2 pcs)
Rmarkdown animated GitHub corner
This is an incredibly easy way to spice up any Rmarkdown file. It adds an animated link to GitHub in the top corner of the HTML output, just like you see at the top of this page. Mouse over the icon to make it wave. All thanks and praise should go to the creator Tim Holman. The first step is to create a new file called “header.html” and paste...
1623 sym R (1661 sym/2 pcs)
Setting axes to integer values in ‘ggplot2’
The problem I stumbled across this problem as a TA for an introductory R course. It was a minor question on a Problem Set focussed on creating a Shiny app that the instructor had seeminly dismissed as trivial and not bothered to include in his solution guide. Anyways, I needed to be able to grade the problem set, so I gave it a shot. Like any goo...
2445 sym R (1023 sym/6 pcs) 6 img
Setting axes to integer values in ‘ggplot2’
The problem I stumbled across this problem as a TA for an introductory R course. It was a minor question on a Problem Set focussed on creating a Shiny app that the instructor had seeminly dismissed as trivial and not bothered to include in his solution guide. Anyways, I needed to be able to grade the problem set, so I gave it a shot. Like any goo...
2445 sym R (1023 sym/6 pcs) 6 img
Lithops
Lithops is one of my favorite type (specifically, genus) of plant. I find them charming and fascinating. For this reason, I own several adult specimens and am growing several species of Lithops from seeds: [Lithops from seed]() and [Lithops from seed (II)](). Below is some information on these interesting plants including their natural history an...
2654 sym
GitHub Actions for Compiling and Converting LaTeX
Introduction I am preparing a manuscript for submission to a scientific journal and decided to compose it in $\LaTeX$ using Overleaf. While Overleaf, an online $\LaTeX$ editor, has many collaboration features (including live, multi-person editing and review) many people, namely my PI, dislikes both $\LaTeX$ nor Overleaf, and instead prefers MS Wo...
3995 sym R (736 sym/1 pcs) 2 img
GitHub Actions for Compiling and Converting LaTeX
Introduction I am preparing a manuscript for submission to a scientific journal and decided to compose it in $\LaTeX$ using Overleaf. While Overleaf, an online $\LaTeX$ editor, has many collaboration features (including live, multi-person editing and review) many people, namely my PI, dislikes both $\LaTeX$ nor Overleaf, and instead prefers MS Wo...
3986 sym R (736 sym/1 pcs) 4 img
OncoTree Tidygraph
Introduction Cancers are often first classified by their tissue of origin, but there are several types of cancer for each tissue. Further, each of these can have several subdivisions. For example, head and neck cancers can be further divided into seven cancers, including head and neck squamous cell carcinoma (HNSC). HNSC itself has six subtypes, ...
8267 sym R (8631 sym/24 pcs) 10 img
OncoTree Tidygraph
Introduction Cancers are often first classified by their tissue of origin, but there are several types of cancer for each tissue. Further, each of these can have several subdivisions. For example, head and neck cancers can be further divided into seven cancers, including head and neck squamous cell carcinoma (HNSC). HNSC itself has six subtypes, ...
8266 sym R (8631 sym/24 pcs) 10 img
‘mustashe’
The purpose of the ‘mustashe’ R package is to save objects that result from some computation, then load the object from file the next time the computation is performed. In other words, the first time a chunk of code is evaluated, the output can be stashed for the next time the code chunk is run. ‘mustashe’ can be installed from CRAN or fr...
5436 sym R (1803 sym/14 pcs)