---
title: "Files"
author: "Rory Nolan"
date: "`r Sys.Date()`"
output: rmarkdown::html_vignette
vignette: >
  %\VignetteIndexEntry{Files}
  %\VignetteEngine{knitr::rmarkdown}
  %\VignetteEncoding{UTF-8}
---

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

Here are some useful things which `filesstrings` makes easier than `base` or `fs`.

First let's load the library: 
```{r load}
library(filesstrings)
```

## Remove spaces from file names
"A space in your file name is a hole in your soul." - Jenny Bryan

`remove_filename_spaces(replacement = "_")` replaces them all with underscores for all files in a directory. By default, they are replaced with nothing.
```{r, remove_filename_spaces}
file.create(c("file 1.txt", "file 2.txt"))
remove_filename_spaces(pattern = "txt$", replacement = "_")
list.files(pattern = "txt$")
file.remove(list.files(pattern = "txt$"))  # clean up
```

## Messed up file numbering
The microscope I use numbers files with 3 numbers by default, i.e. `file001.tif`, `file002.tif` and so on. This is a problem when the automatic numbering passes 1000, whereby we have `file999.tif`, `file1000.tif`. What's the problem with this? Well, sometimes you need alphabetical order to reflect the true order of your files. These file numbers don't satisfy this requirement:
```{r nice_nums setup}
file.names <- c("file999.tif", "file1000.tif")
sort(file.names)
```
so `file1000.tif` comes before `file999.tif` in alphabetical order. The function `nice_nums()` returns the names that we'd like them to have:
```{r nice_nums}
nice_nums(file.names)
```
The function `nice_file_nums` applies such renaming to all the files in an entire directory. It wraps `nice_nums`.

## The name of a file without the extension
```{r before_last_dot}
before_last_dot("spreadsheet_92.csv")
```

## Ensure that a file name has a given extension
Add a file extension if needed:
```{r add file extension 1}
give_ext("xyz", "csv")
```
If the file name has the correct extension already, it's left alone:
```{r add file extension 2}
give_ext("xyz.csv", "csv")  
```
Change a file extension:
```{r change file extension}
give_ext("abc.csv", "txt")  # tack the new extension onto the end
give_ext("abc.csv", "txt", replace = TRUE)  # replace the current extension
```