JP Monteagudo

Lissajous Curves   Lissajous curves are created by plotting two oscillations on perpendicular axes  and ​​​. These oscillations, represented by sinusoidal functions, intersect to create different patterns. When the ratio of these frequencies is equal to — the oscillations are equally phased— the curve is a straight line.

Beautiful movement—the music and beauty of Lissajous(Liss–uh–joo) curves

Visualization &amp; Pearson’s correlation coefficient   The 30DayChartChallenge is a data visualization community that hosts daily challenges for April. Today’s challenge involves dinosaurs. I used the Datasaurus package to create an animated visualization to demonstrate the importance of graphing data, and the effects of outliers on statistical properties.

Animating the Datasaurus dataset as part of the 30 Day Chart Challenge

TL; DR:   Don’t be an absolutist– use relative paths. Use the here package instead of setwd() or getwd() to increase reproducibility and avoid wasting your and other people’s time.

Don’t be an absolutist. Use the here package for reproducible workflows

monthly changes in her circle orb
<i>
</i>
Tip  If you’re wondering where I’m getting my titles and headings, they come from Shakespeare’s sonnets.  The moon has always fascinated me. Eversince I was a child, I was entranced by it; her constant pursuit everywhere I went and her sneaky tactics during the day. This year, before the solar eclipse, I decided to do a little digging and replicate one algorithm used to determine the phases of the moon.

swear not by the moon, the fickle moon

not so quickly! Recently, I become intrigued by game theory algorithms, not because I absolutely love playing games, but because it offers a quantifiable, systematic way to understand human relationships. I find the certainty of science and systematization reassuring to some degree so when I learned about this game called “the prisoner’ dilemma”, I thought it would fun to experiment and figure out the answer to this classic scenario.

the iterated prisoners’ dilemma

Quantile Beta Regression   The quantile beta regression model discussed in the 2021 paper by Running Code   When you click the
<strong>
 Render
</strong>
button a document will be generated that includes both content and the output of embedded code.

A parametric quantile beta regression for modeling case fatality rates of COVID-19. Building models using the betareg and RBE3 packages

RQ: What exactly is the CLT and what’s the deal with n  30?   CLT - mathematical definition and simple terms definition  How we use CLT  How to know when empirical distribution converges to normal distribution? How did we come up with n $ $ 30?  Cohen (1991) Taught that at least 30 observations were needed to use critical-ratio approach used in t-tables when comparing groups.

“{Can I have the CLT, please– a straightforward explanation of the Central Limit Theorem and the magic (n )}”

JP's blog

::: {#tl-dr .section .level2}
## TL; DR: {.anchored anchor-id="tl-dr"}

Don't be an absolutist-- use relative paths. Use the `here`
[package](https://here.r-lib.org/) instead of
[`setwd()`](https://rdrr.io/r/base/getwd.html) or
[`getwd()`](https://rdrr.io/r/base/getwd.html) to increase
reproducibility and avoid wasting your and other people's time.
:::

::: {#whats-the-problem-with-setwd .section .level2}
## What's the problem with `setwd()`? {.anchored anchor-id="whats-the-problem-with-setwd"}

Since I created this website, I've been coding, writing, and reading a
lot more which has unequivocally led to a mountain of new files and the
forging of new paths-- quite literally​ :smile:. At first, I kept things
pretty organized, but now it's nearly impossible to know where I saved
`such_and_such.txt` file without wasting at least 5 minutes of my day.

This is what I used to do:

::: {.cell layout-align="center"}
::: {#cb1 .sourceCode style="background: #f1f3f5;"}
``` {.downlit .sourceCode .r .code-with-copy}
url1 <- "https://somefile_online_data_source_here.com"
download.file(url1, destfile = "./data_file_here.zip")
unzip("data_file_here.zip", exdir = getwd())
Dat <- readRDS("summaryDat.rds")
Dat2 <- readRDS("SummaryDat2.rds")
```
:::
:::

My directory will be anywhere on my device unless I have previously
specified it using [`setwd()`](https://rdrr.io/r/base/getwd.html), but
this strategy will soon be an obstacle to saving new information in an
organized and reproducible way. If, later on, I change my `R` scripts to
a different folder the original file path won't work anymore.
:::

::: {#here-is-the-solution .section .level2}
## `here` is the solution 📁 {.anchored anchor-id="here-is-the-solution"}

The `here` package allows you to set up a relative path mapped onto your
R project directory on every device regardless of your absolute path.

::: {#the-here-function .section .level3}
### The `here` function {.anchored anchor-id="the-here-function"}

Suppose my directory is located in the Project folder. The `here`
package is going to look for the `.Rproj` file and establish the root
directory there.

::: {.cell layout-align="center"}
::: {#cb2 .sourceCode style="background: #f1f3f5;"}
``` {.downlit .sourceCode .r .code-with-copy}
# Project/
#    |
#    |__ data/
#    |    |___  summaryDat.rds
#    |    |___  summaryDat2.rds
#    |
#    |__ blog/
#    |    |_____index.qmd
#    |    |
#    |    |__ post/
#    |    | |______ 2024/
#    |    |       |____ 02/
#    |    |          |____  index.qmd
#    |    |              |____  dat3.R
#    |    |__ img/
#    |      |_____  plots.png
#    |
#    |__ scripts/
#      |____ ind.R
#      |____ cond.R
```
:::
:::

Here you can see my root directory and how that changes with each
iteration of the `here` command.

::: {.cell layout-align="center"}
::: {#cb3 .sourceCode style="background: #f1f3f5;"}
``` {.downlit .sourceCode .r .code-with-copy}
library(here)
here::here()
# [1] "C:/Users/jpmonteagudo/Desktop/R/Project"
  here::here("blog")
# [1] "C:/Users/jpmonteagudo/Desktop/R/Project/blog"
  here::here("2024")
# [1] "C:/Users/jpmonteagudo/Desktop/R/Project/2024"
  here::here("02")
# [1] "C:/Users/jpmonteagudo/Desktop/R/Project/02"
  here::here("post")
# [1] "C:/Users/jpmonteagudo/Desktop/R/Project/post"
  here::here("scripts")
# [1] "C:/Users/jpmonteagudo/Desktop/R/Project/scripts"
#| I'll point R to the actual document by providing the full relative path
here::here("blog","post","2024","02","dat3.R")
# [1] "C:/Users/jpmonteagudo/Desktop/R/Project/blog/post/2024/02/dat3.R"
```
:::
:::

I can also go up several folders at once by using the full relative
path. However, when I call the `here` function again, it sends me back
to my root directory.

::: {.cell layout-align="center"}
::: {#cb4 .sourceCode style="background: #f1f3f5;"}
``` {.downlit .sourceCode .r .code-with-copy}
here::here()
# [1] "C:/Users/jpmonteagudo/Desktop/R/Project"
```
:::
:::

I would use the `here` function to get or write files and not just be
there. If I don't need anything from my subdirectory, then `R` will go
back to its root, the `.Rproj`. For example, saving a `.png` file with
multiple plots involves specifying the relative path using
[`here::here()`](https://here.r-lib.org//reference/here.html).

::: {.cell layout-align="center"}
::: {#cb5 .sourceCode style="background: #f1f3f5;"}
``` {.downlit .sourceCode .r .code-with-copy}
ggsave("plots.png",arranged_plots, 
       path = here::here("blog","2024","02","post","img"),
                width = 800,
                height = 600,
                units = "px",
                dpi = 72)
```
:::
:::
:::

::: {#the-set_here-function .section .level3}
### The `set_here` function {.anchored anchor-id="the-set_here-function"}

If I want to "just be somewhere" anytime I open my project, I would use
another function-- the `set_here` function. Basically, this function
creates a `.here` file anywhere in your project so you can use this
directory as your `root`. Here's the description in the function's
syntax

> When `here` encounters such a file, it uses the directory that
> contains this file as root. This is useful if none of the default
> criteria apply. You need to restart the R session so that
> [`here()`](https://here.r-lib.org//reference/here.html) picks up the
> newly created file.

::: {.cell layout-align="center"}
::: {#cb6 .sourceCode style="background: #f1f3f5;"}
``` {.downlit .sourceCode .r .code-with-copy}
here::set_here("blog/2024")
# Created file .here in C:\Users\jpmonteagudo\Desktop\R\Project\blog\2024. 
# Please start a new R session in the new project directory.
```
:::
:::

Next, I start a new `R` session here, and `RStudio` will automatically
set my directory to this folder. I don't need to open the `R` project to
reach this new directory. It will give me access to the folder's files,
and I can then set a relative path to other files.

::: {.cell layout-align="center"}
::: {#cb7 .sourceCode style="background: #f1f3f5;"}
``` {.downlit .sourceCode .r .code-with-copy}
# Checking directory in new R session
here::here()
# [1] "C:/Users/jpmonteagudo/Desktop/R/Project/blog/2024"
```
:::
:::

From this new directory, I can reach files anywhere by using the
[`here::here()`](https://here.r-lib.org//reference/here.html) function.
:::

::: {#the-confusing-i_am-function .section .level3}
### The confusing `i_am` function {.anchored anchor-id="the-confusing-i_am-function"}

This function has given me a headache. The `here` package is supposed to
be a tool that facilitates collaboration and connectivity, but I just
couldn't get it to work until now.

Call the [`here::i_am()`](https://here.r-lib.org//reference/i_am.html)
function at the top of your script in the first chunk of your markdown
file. It will accept a relative path and then establish the new project
root there. So far, it only works when I point R to a specific file I'd
like to work with. If I choose a file path that's not in my project
directory, it will just point to the original directory and throw an
error. If the current directory is outside of the project where the
current script is running, you'll get an error message:
`Could not find associated project in working directory or any parent directory`.

::: {.cell layout-align="center"}
::: {#cb8 .sourceCode style="background: #f1f3f5;"}
``` {.downlit .sourceCode .r .code-with-copy}
# You're in the scripts folder working on ind.R but need to access summaryDat2.rds.
#  Simply include the relative path to the data file at the top of your script:
library(readr)
data <- read_csv(here::i_am("data/summaryDat2.rds"))
# From my script I'm now pointing to a folder containing my Dat2.R
```
:::
:::
:::

::: {#the-dr_here-function .section .level3}
### The `dr_here` function {.anchored anchor-id="the-dr_here-function"}

The [`here::dr_here()`](https://here.r-lib.org//reference/dr_here.html)
shows a default message explaining why the current directory was chosen.
You probably won't use this function often-- unless you're curious and
want to understand how the package selects the root directory. However,
if you used `here::here("file_path")` and got an unexpected result, go
ahead and call
[`here::dr_here`](https://here.r-lib.org//reference/dr_here.html). It'll
most likely ask you to create a `.here` file or set your directory using
the [`here::i_am()`](https://here.r-lib.org//reference/i_am.html)
function.

In the end, the `here` package will make it easy to collaborate and work
on your projects on any device by using the
[`here::i_am()`](https://here.r-lib.org//reference/i_am.html),
[`here::here()`](https://here.r-lib.org//reference/here.html), and
[`here::set_here()`](https://here.r-lib.org//reference/set_here.html)
functions.
:::
:::

::: {#quarto-appendix .default}
::: {#quarto-citation .section .quarto-appendix-contents}
## Citation {#citation .anchored .quarto-appendix-heading}

<div>

::: {.quarto-appendix-secondary-label}
BibTeX citation:
:::

``` {.sourceCode .code-with-copy .quarto-appendix-bibtex}
@online{monteagudo2024,
  author = {Monteagudo, JP},
  title = {Don’t Be an Absolutist. {Use} the `Here` Package for
    Reproducible Workflows},
  date = {2024-03-17},
  url = {https://www.jpmonteagudo.com/blog/2024/03/here},
  doi = {10.59350/4a9fr-acc34},
  langid = {en}
}
```

::: {.quarto-appendix-secondary-label}
For attribution, please cite this work as:
:::

::: {#ref-monteagudo2024 .csl-entry .quarto-appendix-citeas}
Monteagudo, JP. 2024. "Don't Be an Absolutist. Use the \`Here\` Package
for Reproducible Workflows." March 17, 2024.
<https://doi.org/10.59350/4a9fr-acc34>.
:::

</div>
:::
:::
