---
title: "Package Development Day 1"
author: "Joyce Robbins"
output: github_document
---

```{r setup, include=FALSE, cache=FALSE}
knitr::opts_chunk$set(fig.align='center', echo = TRUE, eval=FALSE)
```

# Welcome

Joyce Robbins [jtr13\@columbia.edu](mailto:jtr13@columbia.edu) Twitter: \@jtrnyc

Thank you to Emily Dodwell and Erin Grand of RLadiesNYC for organizing.

Thank you to Mine Çetinkaya-Rundel and Emma Rand of RForwards for developing package development workshop modules.

```{r, echo=FALSE}
knitr::include_graphics("images/ty.jpg")
```

# Misha update

```{r, fig.width=5}
knitr::include_graphics("images/misha.jpeg")
```

# What are packages?

-   Collections of code

# Where are they stored?

-   CRAN

-   GitHub

-   BioConductor

-   Your hard drive

# How to install

-   from CRAN:

```{r}
install.packages("assertthat")
```

```{r}
install.packages("RLadivmhgfkjhgljkhklhgjesnyc")
```

-   from GitHub:

```{r}
devtools::install_github("jtr13/ggformat")
```

```{r}
devtools::install_github("jtr13/ggformat", force = TRUE)
```

Many packages are available both on CRAN and GitHub:

"dev version"

```{r}
devtools::install_github("tidyverse/forcats")
```

- from your hard drive:

```{r}
devtools::install("~/ggformat")
```

Regardless of the method, the packages are *installed* -- see Packages -->

# What is a "source" package?

```{r}
fs::dir_tree("~/ggformat")
```

```{r}
list.files("~/ggformat")
```

# Why use projects?

So you never have to use `getwd()` or `setwd()` again. You're always just in the right place.

# Loading vs. installing

Usually we use `library()` to load packages into memory. While developing a package we use `devtools::load_all()`.

-   It doesn't show up in the list of packages (or at least the version under development doesn't.)

-   The functions are in memory and will disappear if we restart R.

# Creating a package

We need some essential files: `DESCRIPTION` and a folder called `R` with `.R` files.

The easier way to create the structure is with `create_package()`:

```{r}
library(devtools)
create_package("~/covidtime")
```

# YOUR TURN

See [Day1_lab.md](Day1_lab.md)

# Using the package in another project / script

Before we can use the package elsewhere we need to:

-   add function documentation by clicking "Code... Insert Roxygen Skeleton" (or at a minimum include `@export`)

-   edit DESCRIPTION

-   document with `devtools::document()`

-   install the package with `devtools::install()`

# YOUR TURN

See [Day1_lab.md](Day1_lab.md)

# Package states

```{r, echo=FALSE}
knitr::include_graphics("images/installation.png")
```

Source: <https://r-pkgs.org/package-structure-state.html#installed-package>

Key points:

-   `devtools::install()`: source --> installed

-   `install.packages()`: binary --> installed

-   Developers submit *bundles* to CRAN, CRAN builds and distributes *binaries*

# Closer look at package files

DEMO

# Adding git/GitHub

```{r}
usethis::usegit()
usethis::usegithub()
```

To set default branch from master to main, execute the following in the terminal:

`git config --global init.defaultBranch main`