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README.Rmd
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---
output: github_document
---
<!-- README.md is generated from README.Rmd. Please edit that file -->
# baRcodeR
<!-- badges: start -->
[](https://CRAN.R-project.org/package=baRcodeR)
[](https://CRAN.R-project.org/package=baRcodeR)
[](https://travis-ci.org/ropensci/baRcodeR)
[](https://app.codecov.io/gh/ropensci/baRcodeR?branch=master)
[](https://www.repostatus.org/#active)
[](https://cran.r-project.org/web/checks/check_results_baRcodeR.html)
[](https://github.com/ropensci/software-review/issues/338)
<!-- badges: end -->
baRcodeR generates labels for more repeatable workflows with biological samples
## Installation
You can install the released version of baRcodeR from [CRAN](https://CRAN.R-project.org) with:
```
install.packages("baRcodeR")
```
And the development version from [GitHub](https://github.com/) with:
```
# install.packages("devtools")
devtools::install_github("ropensci/baRcodeR", build_vignettes = T)
# for windows users to build vignettes
# install_github("ropensci/baRcodeR", build_opts = c("--no-resave-data", "--no-manual"), build_vignettes = TRUE)
```
> NOTE: Restarting RStudio is necessary for the addin for baRcodeR to appear.
## Quick Start
Text identifiers can be created in a sequential or hierarchical pattern.
```{r}
library(baRcodeR)
example_labels <- uniqID_maker(user = FALSE, string = "Example", level = 1:80)
head(example_labels)
```
Then the text identifiers can be printed out with a laser printer on sticker sheets.
```{r include = F, eval = F}
# generate the image shown in vignettes as png rather than pdf so it shows up in markdown
# pdf_file_name <- "man/figures/example_file"
# create_PDF(Labels = example_labels, name = pdf_file_name)
# pdf_file <- magick::image_read_pdf("man/figures/example_file.pdf")
# magick::image_write(pdf_file, path = "man/figures/example.png", format = "png")
```
```{r eval = F}
pdf_file_name <- tempfile()
create_PDF(Labels = example_labels, name = pdf_file_name)
```
```{r echo = F}
knitr::include_graphics("man/figures/example.png")
```
Th particular layout above defaults to ULINE 1.75" * 0.5" labels but other layouts can be specified through parameters in the `custom_create_PDF` function.
## Introduction
`baRcodeR` is a R package for generating unique identifier strings and printable 2D (QR) barcodes, with the aim of improving repeatability of labelling, tracking and curating data from biological samples. Specifically, users can:
* generate simple ID codes (Ex001, Ex002, Ex003 ...),
* generate hierarchical (i.e. nested) ID codes (A01-B01, A01-B02, A02-B01, A02-B02, A03-B01 ...),
* generate printable PDF files of paired ID codes and QR barcodes with default spacing for ULINE 1.75" * 0.5" WEATHER RESISTANT LABEL for laser printer; item # S-19297 (uline.ca)
* customize the PDF layout for any type of printable format (e.g, vinyl stickers, waterproof paper)
* generate reproducible code for archival purposes (e.g. in publications or online repositories)
* create CSV files to link unique IDs and sampling hierarchy with downstream data collection workflows. For example, the PyTrackDat pipeline can be used to set up a web-based data collection platform: https://github.com/pytrackdat/pytrackdat
Creating unique, scannable barcodes generally involves two steps:
1. Generate unique ID codes with `uniqID_maker()` or `uniqID_hier_maker()`
2. Create a PDF file containing unique ID codes coupled with 2D barcode using `create_PDF()`
If you already have ID codes saved in a CSV file, the csv can be read into a `data.frame()` in R. The `label` column, if it exists will be used as input to generate barcodes. Otherwise, the first column in the data frame will be used.
> NOTE: When printing from pdf, ensure that 'anti-aliasing' or 'smoothing' options are turned OFF, and that you are not using 'fit to page' or similar options that will re-scale the output.
### Cheat Sheet
A 2-page, quick-reference guide is available via [Figshare](https://dx.doi.org/10.6084/m9.figshare.7043309)
## Usage with RStudio addin
Please load the vignette "Use Addin".
```{r eval = F}
library(baRcodeR)
vignette("use-addin")
```
## Usage from the console
Please load the vignette "Using-baRcodeR" for console use.
```{r eval = F}
vignette("Using-baRcodeR")
```
# Contribution
Please note that the 'baRcodeR' project is released with a
[Contributor Code of Conduct](https://github.com/ropensci/baRcodeR/blob/master/CODE_OF_CONDUCT.md).
By contributing to this project, you agree to abide by its terms.
Please document issues with a description, a minimal reproducible example, and the `sessionInfo()`.
```{r}
sessionInfo()
```
# See also:
- [zintr](https://github.com/carlganz/zintr)is an R interface to the C zint library. Use zintr if you want to create single barcode images. zintr does not include functions for (i) automating the creation of biologically-relevant, unique ID codes or (ii) customizable layouts for printing multiple barcodes.
- [zint](https://zint.org.uk/) is a C library that generates a variety of different barcodes. Just like zintr, zint produces single barcode images.
[](https://ropensci.org)