Tips and tricks

Can I be lazy in names used?

Can I knit the content of the flat template ?

Yes. Although this is not the real goal, the flat template can be filled and run like any other Rmarkdown file.
However, you need to keep in mind that this will be transformed as a R package, which requires some specific attention.

```{r dev}
library(glue)
library(stringi)
```

Note that this will not be used anywhere in the package. A development chunk is only there for your code exploration, during development.

How to declare packages with library() for the future vignette ?

If you use a classical chunk, without any specific name, it will be copied as is in the vignette.

```{r}
library(glue)
library(stringi)
```

How to include examples that cannot be run ?

I created a chunk example but I do not want the example to be run in the function example and I do not want it to be run in the vignette.

```{r function-myfunction}
myfunction <- function(x) {x}
```

```{r example-myfunction, eval=FALSE}
# Will be run in example but not in vignette
myfunction(10)

# Will not be run in example
#' \dontrun{
myfunction(12)
#' }

#' \dontrun{
#' myfunction(12)
#' }
```

Document your internal datasets in a function chunk as usual

To document datasets, pkgdoc, special R files, you can write them as is in the function chunk.
If {fusen} does not detect the keyword function() or R6Class() in the function chunk code, then the chunk is copied as is in a “R/” file.

```{r function-cars}
#' cars
#'
#' data in 'datasets'.
#'
#' @format A data frame with 50 rows and 2 variables:
#' \describe{
#'   \item{ speed }{  numeric }
#'   \item{ dist }{  numeric }
#' }
#' @source Ezekiel, M. (1930) Methods of Correlation Analysis. Wiley.
"cars"
```

How to ignore some chunks ?

All chunks named dev or development will not be used in the package.
Use them for your exploration that you do not want to keep at the end of the process.
This won’t affect your package.

```{r dev}
# Some code exploration
```

How to create a vignette with different title and Index Entry?

You can use inflate(vignette_name = c("Super title" = "01-Super Slug")) for vignette title different from vignette Entry

inflate(vignette_name = c("Super title" = "01-Super Vignette Index Entry"))

How not to create a vignette?

inflate(vignette_name = NA)

How to get a pre-filled template for a specific function name ?

If it is the first function of the flat template:

If this is the second function inside an existing template:

How to pre-fill multiple functions in one template

This can be added in the “dev_history.Rmd”, and will replace a place holder in your flat rmd (HERE in this case) with proper fusen chunks for all your future functions to be.

# Path of the flat file
path_flat_rmd <- here::here("dev/flat_minimal.Rmd")

# Name of future functions to add - example
fun_nms <- c(
  "get_contract_by_country_of",
  "get_contract_subsidies_of",
  "get_contract_effort_of",
  "get_contract_fees_of",
  "get_contract_target_countries_of",
  "get_contract_all_info_of"
)

# Create content
l_chunks <- purrr::map_chr(fun_nms, fusen:::build_fusen_chunks)
chunks <- paste(l_chunks, collapse = "")

# Add in the flat file
flat_rmd <- readLines(path_flat_rmd)
flat_rmd <- sub("^HERE$", chunks, flat_rmd)
writeLines(flat_rmd, path_flat_rmd)

How to Inflate multiple flat files ?

Read the dedicated vignette “inflate-all-your-flat-files”

vignette("inflate-all-your-flat-files", package = "fusen")

How to store multiple functions in a unique R file ?

There are multiple ways of doing it. Choose one of: use the section title structure, use roxygen tags or use chunk parameter.

All functions under one title section

Use the 3-set of chunks (fun, example, test) twice, under the same title section of the Rmd

# One title for both groups of chunk

The code and tests for the first function

```{r function-fun1}
```

```{r example-fun1}
```

```{r test-fun1}
```

The code and tests for the second function

```{r function-fun2}
```

```{r example-fun2}
```

```{r test-fun2}
```

Use same @rdname in function roxygen

# Title 1 for function 1

```{r function-fun_rdname1}
#' My fun_rdname1
#'
#' @param x Vector of Numeric values
#' @inheritParams stats::median
#'
#' @rdname same_rdname
#' @return
#' Median of vector x
#' @export
#'
#' @examples
#' my_fun_rdname1(2:20)
my_fun_rdname1 <- function(x, na.rm = TRUE) {
  if (!is.numeric(x)) {stop("x should be numeric")}
  stats::median(x, na.rm = na.rm)
}
```

# Title  2 for function 2

```{r function-fun_rdname2}
#' My fun_rdname2
#'
#' @param x Vector of Numeric values
#' @inheritParams stats::median
#'
#' @rdname same_rdname
#' @return
#' Median of vector x
#' @export
#'
#' @examples
#' my_fun_rdname2(2:20)
my_fun_rdname2 <- function(x, na.rm = TRUE) {
  if (!is.numeric(x)) {stop("x should be numeric")}
  stats::median(x, na.rm = na.rm)
}
```

Use same @filename in function roxygen

@filename is recognized only by {fusen} as a proper roxygen tag to merge multiple functions in the same “R/” and “tests/” files.
This code line is removed in the resulting “R/” files to avoid any interference with Roxygenize.

# Title 1 for function 1

```{r function-fun_filename1}
#' My fun_filename1
#'
#' @param x Vector of Numeric values
#' @inheritParams stats::median
#'
#' @filename same_filename
#' @return
#' Median of vector x
#' @export
#'
#' @examples
#' my_fun_filename1(2:20)
my_fun_filename1 <- function(x, na.rm = TRUE) {
  if (!is.numeric(x)) {stop("x should be numeric")}
  stats::median(x, na.rm = na.rm)
}
```

# Title  2 for function 2

```{r function-fun_filename2}
#' My fun_filename2
#'
#' @param x Vector of Numeric values
#' @inheritParams stats::median
#'
#' @filename same_filename
#' @return
#' Median of vector x
#' @export
#'
#' @examples
#' my_fun_filename2(2:20)
my_fun_filename2 <- function(x, na.rm = TRUE) {
  if (!is.numeric(x)) {stop("x should be numeric")}
  stats::median(x, na.rm = na.rm)
}
```

Use chunk param filename = "the_comon_filename"

Add it in the function chunk only

# Title 1 for function 1

```{r function-fun_chunk1, filename = "fun_chunk1"}
#' The code of your function 1
```

```{r example-fun_chunk1}
```

```{r test-fun_chunk1}
```

# Title 2 for function 2

```{r function-fun_chunk2, filename = "fun_chunk1"}
#' The code of your function 2
```

```{r example-fun_chunk2}
```

```{r test-fun_chunk2}
```

How to read dataset that I usually put in “tests/testthat/” for my unit tests?

During checks, the tests are run relative to the “tests/testthat/” directory.
You will need to anticipate the two ways of reading the data:

# The path relative to the "tests/testthat" directory for tests
the_file <- "my_file.csv"
if (!file.exists(the_file)) {
  # The path to use during dev in the flat file
  the_file <- file.path("tests", "testthat", the_file)
  if (!file.exists(the_file)) {
    stop(the_file, " does not exist")
  }
}

my_file <- read.csv(the_file)

Can I load all functions of the current flat file during development without having to inflate()?

Yes. You can run and load function chunks only in the currently opened flat file with load_flat_functions().
With long flat file currently in development, and before inflate(), it is sometimes difficult to run all chunks needed after multiple modifications. This can also be useful when you start again your development the day after.

load_flat_functions() is like a load_all() for a flat file, although it does not account for dependencies.

In the console, run:

fusen::load_flat_functions()

You can also run function chunks of a specific flat file with:

fusen::load_flat_functions(flat_file = "dev/flat_full.Rmd")

Can I inflate a Quarto qmd file?

Yes you can. As long as what you include in your qmd flat file is good for a R package vignette, you can use the qmd format.
This will not really change the output of anything as the flat file is not meant to be rendered.
The vignette created from this flat file will still be a Rmd file. But why not!?

Hence, you can add a flat file and change its extension to “.qmd” if you like.

Can I use {fusen} with {golem}?

Of course ! That is even recommended as it allows to properly separate the business logic (in “dev/” directory) from the UI (in the modules of the “R/” directory).
Start by creating a {golem} project. Then you can start adding your flat files.
We recommend to create modules with names in relation to flat files, so that you can better navigate in your project.

golem::create_golem('my.golem.app')
fusen::add_minimal_flat(flat_name = "page1")
golem::add_module(name = "page1")

Although default {golem} “dev/” files already contain the main actions to maintain your package, you can still add the “0-dev_history.Rmd” file recommended with {fusen} using add_dev_history(). Note that some sections will be redundant with the {golem} dev files.