Tips and tricks

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(stringr)
```

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(stringr)
```

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 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 Inflate multiple flat files ?

fusen::inflate("dev/flat_file1.Rmd")
fusen::inflate("dev/flat_file2.Rmd")
fusen::inflate("dev/flat_file3.Rmd")

If the main “dev_history.Rmd” file does not exists, you can create it with add_flat_template("dev_history")

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}
```