According to this report, despite the vaccination and other efforts, the daily new COVID-19 cases has reached the 200,000 mark on August 17 in the US. It appears that a new wave of the pandemic has begun.

# Shige's Research Blog

## Wednesday, August 18, 2021

## Wednesday, August 11, 2021

### Obsidian

I have been searching for a note taking/management tool for some time. From a book, I encountered Roam, which looks exactly what I need. After some research, I realized that is is a proprietary software using proprietary data storage format, and store all data on a remote cloud server. This, along with its not so modest price tag, raises a red flag.

Then I discovered Obsidian, which is itself proprietary (as opposed to open source) but it works on local, plain text (including Markdown) files, which can be opened and modified by any text editors. For now, it looks really promising!

## Tuesday, April 06, 2021

### NetLogo code for Party Competition

Today I spent some time to manually convert the NetLogo code for Party Competition from version 5 to version 6.

Fascinating book, by the way.

## Friday, February 26, 2021

### Thunderbird conversation mode

Just discovered Thunderbird conversations extension that displays Thunderbird emails like Gmail. Very cool.

## Thursday, February 25, 2021

### Convert email to event or task

I just found out that Thunderbird can convert an email into an event or task with deadline. This is extremely useful for me.

## Monday, February 15, 2021

### Using tikzDevice in R Markdown document

When I was LaTeX user in the past, I like TikZ and tikzDevice a lot. After switching to R Markdown, however, I gradually forgot about them. Today I spent some time figuring out how to make TikZ and tikzDevice work for R Markdown. Here is some simple code:

title: "Using tikzDevice"

output:

pdf_document:

latex_engine: xelatex

keep_tex: yes

includes:

in_header: setup.tex

---

```{r setup, include=FALSE}

knitr::opts_chunk$set(echo = FALSE)

```

```{r, fig.cap="Without tikzDevice"}

x<- rnorm(10)

y<-x +rnorm(5,sd=0.25)

model <- lm(y~x)

rsq<- summary(model)$r.squared

rsq<- signif(rsq,4)

plot(x, y, main='Hello \\LaTeX!')

abline(model,col='red')

mtext(paste("Linear model:$R^{2}=",

rsq, "$"), line=0.5)

legend('bottomright',legend=paste("$y = ",round(coef(model)[2],3),'x +',round(coef(model)[1],3),'$',sep =''), bty ='n')

```

```{r, echo=FALSE}

library(tikzDevice)

```

```{r, echo=FALSE, message=FALSE, results='hide'}

tikz('latexEx.tex',width=7,height=4.5)

x<- rnorm(10)

y<-x +rnorm(5,sd=0.25)

model <- lm(y~x)

rsq<- summary(model)$r.squared

rsq<- signif(rsq,4)

plot(x, y, main='Hello \\LaTeX!')

abline(model,col='red')

mtext(paste("Linear model:$R^{2}=",

rsq, "$"), line=0.5)

legend('bottomright',legend=paste("$y = ",round(coef(model)[2],3),'x +',round(coef(model)[1],3),'$',sep =''), bty ='n')

dev.off()

```

```{r, fig.cap="With tikzDevice", message=FALSE, engine='tikz'}

\input{latexEx.tex}