---
title: "Introduction to annotater"
output: rmarkdown::html_vignette
vignette: >
  %\VignetteIndexEntry{Introduction to annotater}
  %\VignetteEngine{knitr::rmarkdown}
  %\VignetteEncoding{UTF-8}
---

```{r, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)
```

```{r setup, include = FALSE}
library(annotater)
```

`annotater` came to be while teaching workshops or helping peers and realizing that many issues relate to package installation failures and dependency issues for packages that were not even used in a problematic script. Scripts get passed around, code is copied and pasted, and we might not know what certain packages are for. Additionally, it is often useful to specify a package's source and version within a script, for reproducibility purposes and to keep a record of where any of the packages can be obtained.


## Package functions

This package works around a suite of functions that match package load calls (i.e. `library` and `require`) in a character string with one line per element, and replace them with annotated versions. As of version 0.2.0, loading packages with `pacman::p_load` is also supported. 

First, `match_pkg_names` produces a tibble of package load calls and package names.

```{r}
pkgs_string <- c("library(boot)\nrequire(Matrix)")
match_pkg_names(pkgs_string)
```

The values in this tabular output are then passed to 
`utils::packageDescription`, which parses and returns the 'DESCRIPTION' file of an installed package. Fields of interest from these descriptions are then used to build the annotations.

The 'Title' field from a package's description makes for a good summary of what it does, so `annotate_pkg_calls` uses it to build annotations. These titles are inserted after each package load call, separated by a commenting symbol.

```{r}
pkgs_string <- c("library(boot)\nrequire(tools)")
annotate_pkg_calls(pkgs_string)
```

A similar approach is used by `annotate_repo_source` to paste the repository source and version number.

```{r}
pkgs_string <- c("library(boot)\nrequire(lattice)")
annotate_repo_source(pkgs_string)
```

Titles, repositories and version numbers can be annotated together in the output from `annotate_repostitle`.

```{r}
pkgs_string <- c("library(boot)\nrequire(lattice)")
annotate_repostitle(pkgs_string)
```

To annotate which functions are being called from each loaded package, use `annotate_fun_calls`.

```{r}
testcode <- c('library(purrr) 
x <- list("a", 1, c("bo","bi","bu"))
pluck(x, 1)
map(x, pluck, 2)')
annotate_fun_calls(testcode)
```

To annotate which datasets are being called from each loaded package, use `annotate_pkg_datasets`.

```{r}
testcode <- c('library(tidyr) 
summary(household)
plot(fish_encounters)')
annotate_pkg_datasets(testcode)
```


## A note on the `tidyverse` and other metapackages
The `tidyverse` package is a meta-package with few exported functions of its own, so the annotation tools provided here (`annotate_fun_calls`) will not match the functions from the various individual packages (such as `dplyr` or `readr`) that get attached when loading `tidyverse`. As of version 0.2.2, load calls for metapackages can be replaced with separate calls to each of the core metapackage components as defined by their respective _attach.R_
files.

## Usage in RStudio

These main package functions can be called through their respective RStudio addins, written to work on the active .R or .Rmd file open in the Source pane.

#### Annotate package calls in active file
Describes the packages being loaded by calling `annotate_pkg_calls`.

#### Annotate package repository sources in active file
Adds the source and version by calling `annotate_repo_source`. This addin aligns the commenting symbols vertically for aesthetic purposes.

#### Annotate titles and repository sources in active file
Adds titles, sources, and versions by calling `annotate_repostitles`.

#### Annotate each package's function calls
Adds all the unique functions being called by each loaded package, calls `annotate_fun_calls`.

#### Annotate each package's datasets
Adds all the datasets being called by each loaded package, calls `annotate_pkg_datasets`. Works for lazy loaded data, namespaced data, or objects called with `data`.

#### Expand metapackages
Replace a call to a metapackage with multiple calls to each of its core components.