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2 changes: 2 additions & 0 deletions .Rbuildignore
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^grateful-refs\.bib$
^data-raw$

^\.github$
^CODE_OF_CONDUCT\.md$
126 changes: 126 additions & 0 deletions CODE_OF_CONDUCT.md
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# Contributor Covenant Code of Conduct

## Our Pledge

We as members, contributors, and leaders pledge to make participation in our
community a harassment-free experience for everyone, regardless of age, body
size, visible or invisible disability, ethnicity, sex characteristics, gender
identity and expression, level of experience, education, socio-economic status,
nationality, personal appearance, race, caste, color, religion, or sexual
identity and orientation.

We pledge to act and interact in ways that contribute to an open, welcoming,
diverse, inclusive, and healthy community.

## Our Standards

Examples of behavior that contributes to a positive environment for our
community include:

* Demonstrating empathy and kindness toward other people
* Being respectful of differing opinions, viewpoints, and experiences
* Giving and gracefully accepting constructive feedback
* Accepting responsibility and apologizing to those affected by our mistakes,
and learning from the experience
* Focusing on what is best not just for us as individuals, but for the overall
community

Examples of unacceptable behavior include:

* The use of sexualized language or imagery, and sexual attention or advances of
any kind
* Trolling, insulting or derogatory comments, and personal or political attacks
* Public or private harassment
* Publishing others' private information, such as a physical or email address,
without their explicit permission
* Other conduct which could reasonably be considered inappropriate in a
professional setting

## Enforcement Responsibilities

Community leaders are responsible for clarifying and enforcing our standards of
acceptable behavior and will take appropriate and fair corrective action in
response to any behavior that they deem inappropriate, threatening, offensive,
or harmful.

Community leaders have the right and responsibility to remove, edit, or reject
comments, commits, code, wiki edits, issues, and other contributions that are
not aligned to this Code of Conduct, and will communicate reasons for moderation
decisions when appropriate.

## Scope

This Code of Conduct applies within all community spaces, and also applies when
an individual is officially representing the community in public spaces.
Examples of representing our community include using an official e-mail address,
posting via an official social media account, or acting as an appointed
representative at an online or offline event.

## Enforcement

Instances of abusive, harassing, or otherwise unacceptable behavior may be
reported to the community leaders responsible for enforcement at awesome.tingwei@outlook.com.
All complaints will be reviewed and investigated promptly and fairly.

All community leaders are obligated to respect the privacy and security of the
reporter of any incident.

## Enforcement Guidelines

Community leaders will follow these Community Impact Guidelines in determining
the consequences for any action they deem in violation of this Code of Conduct:

### 1. Correction

**Community Impact**: Use of inappropriate language or other behavior deemed
unprofessional or unwelcome in the community.

**Consequence**: A private, written warning from community leaders, providing
clarity around the nature of the violation and an explanation of why the
behavior was inappropriate. A public apology may be requested.

### 2. Warning

**Community Impact**: A violation through a single incident or series of
actions.

**Consequence**: A warning with consequences for continued behavior. No
interaction with the people involved, including unsolicited interaction with
those enforcing the Code of Conduct, for a specified period of time. This
includes avoiding interactions in community spaces as well as external channels
like social media. Violating these terms may lead to a temporary or permanent
ban.

### 3. Temporary Ban

**Community Impact**: A serious violation of community standards, including
sustained inappropriate behavior.

**Consequence**: A temporary ban from any sort of interaction or public
communication with the community for a specified period of time. No public or
private interaction with the people involved, including unsolicited interaction
with those enforcing the Code of Conduct, is allowed during this period.
Violating these terms may lead to a permanent ban.

### 4. Permanent Ban

**Community Impact**: Demonstrating a pattern of violation of community
standards, including sustained inappropriate behavior, harassment of an
individual, or aggression toward or disparagement of classes of individuals.

**Consequence**: A permanent ban from any sort of public interaction within the
community.

## Attribution

This Code of Conduct is adapted from the [Contributor Covenant][homepage],
version 2.1, available at
<https://www.contributor-covenant.org/version/2/1/code_of_conduct.html>.

Community Impact Guidelines were inspired by
[Mozilla's code of conduct enforcement ladder][https://github.com/mozilla/inclusion].

For answers to common questions about this code of conduct, see the FAQ at
<https://www.contributor-covenant.org/faq>. Translations are available at <https://www.contributor-covenant.org/translations>.

[homepage]: https://www.contributor-covenant.org
11 changes: 7 additions & 4 deletions README.Rmd
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Expand Up @@ -24,15 +24,16 @@ knitr::opts_chunk$set(
[![lifecycle](https://img.shields.io/badge/lifecycle-maturing-blue.svg)](https://lifecycle.r-lib.org/articles/stages.html)
[![saythanks](https://img.shields.io/badge/say-thanks-ff69b4.svg)](https://github.com/AlphaPrime7/normfluodbf)
[![test-coverage](https://github.com/AlphaPrime7/normfluodbf/actions/workflows/test-coverage.yaml/badge.svg)](https://github.com/AlphaPrime7/normfluodbf/actions/workflows/test-coverage.yaml)
[![R-CMD-check](https://github.com/AlphaPrime7/normfluodbf/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/AlphaPrime7/normfluodbf/actions/workflows/R-CMD-check.yaml)
[![license](https://img.shields.io/badge/license-GPL--3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0.en.html)
[![Maintenance](https://img.shields.io/badge/Maintained%3F-yes-green.svg)](https://github.com/AlphaPrime7/normfluodbf/graphs/commit-activity)


The goal of [`{normfluodbf}`](https://github.com/AlphaPrime7/normfluodbf) is to normalize fluorescence data obtained from liposome flux assay experiments via the FLUOstar microplate reader. Input or source file is a .dbf file that is not ready for analysis without processing through {normfluodbf}. There is a ShinyApp for this as well.
The goal of [`{normfluodbf}`](https://github.com/AlphaPrime7/normfluodbf) is to normalize fluorescence data obtained from liposome flux assay experiments via the FLUOstar micro plate reader. The Input file is a .dbf file that requires cleaning and normalization using [`{normfluodbf}`](https://github.com/AlphaPrime7/normfluodbf), before insightful analysis can be conducted. .

## &darr; Installation

You can install the development version of normfluodbf from [`{normfluodbf}`](https://github.com/AlphaPrime7/normfluodbf) with:
The development version of [`{normfluodbf}`](https://github.com/AlphaPrime7/normfluodbf) can be installed as illustrated below:

``` {r, eval = FALSE}
install.packages("devtools")
Expand All @@ -46,20 +47,22 @@ library(normfluodbf)

## Example

This is a basic example which shows you how to solve a common problem:
This is a basic example which illustrates package usage:

```{r example, eval=F}
library(normfluodbf)
liposomes_214 <- system.file("extdata", "liposomes_214.dbf", package = "normfluodbf")
normalized_data <- normfluodbf(liposomes_214)
```

## R packages used
## R packages Imported
- tidyr
- data.table
- foreign
- tibble

Vist [`{my page}`](https://alphaprime7.github.io/normfluodbf/articles/normfluodbf.html) for details on the concept behind the project.

# References
[@datatable]
[@foreign]
Expand Down
84 changes: 26 additions & 58 deletions README.md
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Tingwei Adeck
August 21, 2023
Tingwei Adeck August 22, 2023

<!-- README.md is generated from README.Rmd. Please edit that file -->

# normfluodbf <img src="man/figures/logo.png" align="right" width="180" />

[![Project
status](https://www.repostatus.org/badges/latest/concept.svg)](https://github.com/AlphaPrime7/normfluodbf/commits)
[![Project
Status](https://www.repostatus.org/badges/latest/active.svg)](https://github.com/AlphaPrime7/normfluodbf/commits)
[![Project
Status](https://www.repostatus.org/badges/latest/wip.svg)](https://github.com/AlphaPrime7/normfluodbf/commits)
[![lifecycle](https://img.shields.io/badge/lifecycle-maturing-blue.svg)](https://lifecycle.r-lib.org/articles/stages.html)
[![saythanks](https://img.shields.io/badge/say-thanks-ff69b4.svg)](https://github.com/AlphaPrime7/normfluodbf)
[![test-coverage](https://github.com/AlphaPrime7/normfluodbf/actions/workflows/test-coverage.yaml/badge.svg)](https://github.com/AlphaPrime7/normfluodbf/actions/workflows/test-coverage.yaml)
[![license](https://img.shields.io/badge/license-GPL--3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0.en.html)
[![Maintenance](https://img.shields.io/badge/Maintained%3F-yes-green.svg)](https://github.com/AlphaPrime7/normfluodbf/graphs/commit-activity)

The goal of
[`{normfluodbf}`](https://github.com/AlphaPrime7/normfluodbf) is to
normalize fluorescence data obtained from liposome flux assay
experiments via the FLUOstar microplate reader. Input or source file is
a .dbf file that is not ready for analysis without processing through
{normfluodbf}. There is a ShinyApp for this as well.
# normfluodbf <img src="man/figures/logo.png" align="right" width="180"/>

[![Project status](https://www.repostatus.org/badges/latest/concept.svg)](https://github.com/AlphaPrime7/normfluodbf/commits) [![Project Status](https://www.repostatus.org/badges/latest/active.svg)](https://github.com/AlphaPrime7/normfluodbf/commits) [![Project Status](https://www.repostatus.org/badges/latest/wip.svg)](https://github.com/AlphaPrime7/normfluodbf/commits) [![lifecycle](https://img.shields.io/badge/lifecycle-maturing-blue.svg)](https://lifecycle.r-lib.org/articles/stages.html) [![saythanks](https://img.shields.io/badge/say-thanks-ff69b4.svg)](https://github.com/AlphaPrime7/normfluodbf) [![test-coverage](https://github.com/AlphaPrime7/normfluodbf/actions/workflows/test-coverage.yaml/badge.svg)](https://github.com/AlphaPrime7/normfluodbf/actions/workflows/test-coverage.yaml) [![R-CMD-check](https://github.com/AlphaPrime7/normfluodbf/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/AlphaPrime7/normfluodbf/actions/workflows/R-CMD-check.yaml) [![license](https://img.shields.io/badge/license-GPL--3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0.en.html) [![Maintenance](https://img.shields.io/badge/Maintained%3F-yes-green.svg)](https://github.com/AlphaPrime7/normfluodbf/graphs/commit-activity)

The goal of [`{normfluodbf}`](https://github.com/AlphaPrime7/normfluodbf) is to normalize fluorescence data obtained from liposome flux assay experiments via the FLUOstar micro plate reader. The Input file is a .dbf file that requires cleaning and normalization using [`{normfluodbf}`](https://github.com/AlphaPrime7/normfluodbf), before insightful analysis can be conducted. .

## ↓ Installation

You can install the development version of normfluodbf from
[`{normfluodbf}`](https://github.com/AlphaPrime7/normfluodbf) with:
The development version of [`{normfluodbf}`](https://github.com/AlphaPrime7/normfluodbf) can be installed as illustrated below:

``` r
install.packages("devtools")
Expand All @@ -41,52 +24,37 @@ library(normfluodbf)

## Example

This is a basic example which shows you how to solve a common problem:
This is a basic example which illustrates package usage:

``` r
library(normfluodbf)
liposomes_214 <- system.file("extdata", "liposomes_214.dbf", package = "normfluodbf")
normalized_data <- normfluodbf(liposomes_214)
```

## R packages used
## R packages Imported

- tidyr
- data.table
- foreign
- tibble

- tidyr
- data.table
- foreign
- tibble
Vist [`{my page}`](https://alphaprime7.github.io/normfluodbf/articles/normfluodbf.html) for details on the concept behind the project.

# References

(Dowle and Srinivasan 2023) (R Core Team 2022) (Wickham et al. 2019)

<div id="refs" class="references csl-bib-body hanging-indent">

<div id="ref-datatable" class="csl-entry">

Dowle, Matt, and Arun Srinivasan. 2023.
*<span class="nocase">data.table</span>: Extension of
“<span class="nocase">data.frame</span>”*.
<https://CRAN.R-project.org/package=data.table>.

</div>

<div id="ref-foreign" class="csl-entry">

R Core Team. 2022. *<span class="nocase">foreign</span>: Read Data
Stored by “Minitab,” “S,” “SAS,” “SPSS,” “Stata,” “Systat,” “Weka,”
“<span class="nocase">dBase</span>,” ...*
<https://CRAN.R-project.org/package=foreign>.

</div>

<div id="ref-tidyverse" class="csl-entry">

Wickham, Hadley, Mara Averick, Jennifer Bryan, Winston Chang, Lucy
D’Agostino McGowan, Romain François, Garrett Grolemund, et al. 2019.
“Welcome to the <span class="nocase">tidyverse</span>.” *Journal of Open
Source Software* 4 (43): 1686. <https://doi.org/10.21105/joss.01686>.
::: {#refs .references .csl-bib-body .hanging-indent}
::: {#ref-datatable .csl-entry}
Dowle, Matt, and Arun Srinivasan. 2023. [*data.table*]{.nocase}*: Extension of "[data.frame]{.nocase}"*. <https://CRAN.R-project.org/package=data.table>.
:::

</div>
::: {#ref-foreign .csl-entry}
R Core Team. 2022. [*foreign*]{.nocase}*: Read Data Stored by "Minitab," "S," "SAS," "SPSS," "Stata," "Systat," "Weka," "[dBase]{.nocase}," ...* <https://CRAN.R-project.org/package=foreign>.
:::

</div>
::: {#ref-tidyverse .csl-entry}
Wickham, Hadley, Mara Averick, Jennifer Bryan, Winston Chang, Lucy D'Agostino McGowan, Romain François, Garrett Grolemund, et al. 2019. "Welcome to the [tidyverse]{.nocase}." *Journal of Open Source Software* 4 (43): 1686. <https://doi.org/10.21105/joss.01686>.
:::
:::
12 changes: 8 additions & 4 deletions _pkgdown.yml
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- icon: fa-code
text: Output and Analysis
href: articles/example_redirect.html
- icon: fa-newspaper
text: News
menu:
- text: Version 1.0 (Pre-release)
href: news/index.html

structure:
right:
- reference
- NEWS
- github
- email
- mail
- Linkedin
components:
email:
mail:
icon: fa-envelope
href: mailto:awesome.tingwei@outlook.com
Linkedin:
icon: fa-linkedin
href: https://www.linkedin.com/in/tingwei-adeck-52b963164/

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