diff --git a/README.Rmd b/README.Rmd
index 0352588..124fcd0 100644
--- a/README.Rmd
+++ b/README.Rmd
@@ -13,42 +13,42 @@ knitr::opts_chunk$set(
)
```
-# Project creation with prodigenr: A component of reproducible and open scientific projects
+# Project creation with prodigenr: A component of reproducible and open scientific projects
-[](https://cran.r-project.org/package=prodigenr)
+
+[](https://cran.r-project.org/package=prodigenr)
[](https://github.com/rostools/prodigenr/actions)
[](https://lifecycle.r-lib.org/articles/stages.html)
-[](https://www.r-pkg.org:443/pkg/prodigenr)
+[](https://www.r-pkg.org:443/pkg/prodigenr)
+
-This [R] package is part of a [series][rostools-github] of (planned) packages that are aimed at
-creating a toolkit for doing reproducible and open science. Many researchers
-(especially in biomedicine, medicine, or health, which is my area of research)
-have little to no knowledge on what open science is or what reproducibility is,
-let alone how to do it. Our goal is create an [(opinionated) toolkit][rostools-manifesto] to automate
-and simplify the process of doing open and reproducible science.
-
-This package has a simple aim of being a *pro*ject *di*rectory *gen*erato*r*
-(prodigenr), with a simple focus on:
-
-1. Creating a standardized project folder structure with a few template files
-needed for beginning a data analysis project
-2. Following a "one project, one (main) output" principle, such as a
-report/manuscript in the case of scientific output or a book or website for things
-like courses or workshops
-3. Adhering to established best practices that make it easier for the project to
-be reproducible and open
-
-This standardized approach to how a scientific project is structured helps ensure
-that the final code and documents are fairly modular, self-contained, easy to share
-and make public, and be as reproducible as possible. The structure also
-makes use of the existing and established applications and workflows ([RStudio],
-[devtools], and [usethis]).
+This package has a simple aim of being a *pro*ject *di*rectory
+*gen*erato*r* (prodigenr), with a simple focus on:
+
+1. Creating a standardized project folder structure with a few template
+ files needed for beginning a data analysis project.
+2. Following a "one project, one (main) output" principle, such as a
+ report/manuscript in the case of scientific output or a book or
+ website for things like courses or workshops.
+3. Adhering to established best practices that make it easier for the
+ project to be reproducible and open.
+
+This standardized approach to how a scientific project is structured
+helps ensure that the final code and documents are fairly modular,
+self-contained, easy to share and make public, and be as reproducible as
+possible. The structure also makes use of the existing and established
+applications and workflows ([RStudio](https://www.rstudio.com/),
+[devtools](https://CRAN.R-project.org/package=devtools), and
+[usethis](https://CRAN.R-project.org/package=usethis)).
## Installation
-You can install the released version of prodigenr from [CRAN] with:
+You can install the released version of prodigenr from
+[CRAN](https://cran.r-project.org) with:
``` r
install.packages("prodigenr")
@@ -57,17 +57,17 @@ install.packages("prodigenr")
And the development version from [GitHub](https://github.com/) with:
``` r
-# install.packages("remotes")
-remotes::install_github("rostools/prodigenr")
+# install.packages("pak")
+pak::pak("rostools/prodigenr")
```
## Usage
-There are two ways of creating a new project: using the R console or using the
-RStudio "New Project" menu option.
+There are two ways of creating a new project: using the R console or
+using the RStudio "New Project" menu option.
-Through the console, use the `setup_project()` command. So, for instance, if you
-want a manuscript project, type out:
+Through the console, use the `setup_project()` command. So, for
+instance, if you want a manuscript project, type out:
``` r
library(prodigenr)
@@ -75,20 +75,22 @@ setup_project("~/Desktop/DiseaseDiet")
```
This then creates a directory tree, with template files for starting
-your analysis! Open the newly created project via the `.Rproj` file. For the
-RStudio approach, go to "File -> New Project", then "New directory" and find the
-prodigenr project in the list:
+your analysis! Open the newly created project via the `.Rproj` file. For
+the RStudio approach, go to "File -\> New Project", then "New directory"
+and find the prodigenr project in the list:
-
+
-Once in the project, you can add a manuscript R Markdown file using:
+Once in the project, you can add a manuscript/report
+[Quarto](https://quarto.org/) file using:
``` r
-create_manuscript()
+create_report()
```
-The main secondary function is the `template_list` command, which lists the
-available template files (submit a PR if you want another template included!):
+The main secondary function is the `template_list` command, which lists
+the available template files:
```{r, include=FALSE}
library(prodigenr)
@@ -98,39 +100,35 @@ library(prodigenr)
template_list
```
-
-
For a more detailed tutorial, see the introduction vignette:
-```r
+``` r
vignette('prodigenr', 'prodigenr')
```
## Related packages or projects
-There are several existing packages for creating projects, each of which has
-it's own pros and cons. Check out the last section of the `vignette("prodigenr")`
-for more details. Try them out and see which you like!
+There are several existing packages for creating projects, each of which
+has it's own pros and cons. Check out the last section of the
+`vignette("prodigenr")` for more details. Try them out and see which you
+like!
-prodigenr tries to use ideas from R packages/[devtools] while still being as simple
-as possible and to be more specific to academic researchers primarily in
-biomedical/non-computer science fields. However, it can always improve! I
-welcome any suggestions, just submit a
+prodigenr tries to use ideas from R
+packages/[devtools](https://CRAN.R-project.org/package=devtools) while
+still being as simple as possible and to be more specific to academic
+researchers primarily in biomedical/non-computer science fields.
+However, it can always improve! I welcome any suggestions, just submit a
[GitHub issue](https://github.com/rostools/prodigenr/issues).
## Interested in contributing?
-See the [contributing documentation](https://rostools.github.io/prodigenr/CONTRIBUTING.html) for information on how to
-contribute. Please note that this project is released with a
-[Contributor Code of Conduct](https://rostools.github.io/prodigenr/CODE_OF_CONDUCT.html). By participating in this project you
-agree to abide by its terms.
+See the [contributing
+documentation](https://rostools.github.io/prodigenr/CONTRIBUTING.html)
+for information on how to contribute. Please note that this project is
+released with a [Contributor Code of
+Conduct](https://rostools.github.io/prodigenr/CODE_OF_CONDUCT.html). By
+participating in this project you agree to abide by its terms.
-[R]: https://cran.r-project.org
-[RStudio]: https://www.rstudio.com/
-[devtools]: https://CRAN.R-project.org/package=devtools
-[usethis]: https://CRAN.R-project.org/package=usethis
-[CRAN]: https://cran.r-project.org
-[rostools-github]: https://github.com/rostools
-[rostools-manifesto]: https://rostools.gitlab.io/manifesto
+Special thanks to [\@zsemnani](https://twitter.com/zsemnani?lang=en) for
+creating the logo!
-Special thanks to [@zsemnani](https://twitter.com/zsemnani?lang=en) for creating the logo!
diff --git a/README.md b/README.md
index 24a56c7..4050d6c 100644
--- a/README.md
+++ b/README.md
@@ -1,7 +1,7 @@
-# Project creation with prodigenr: A component of reproducible and open scientific projects
+# Project creation with prodigenr: A component of reproducible and open scientific projects
@@ -11,28 +11,19 @@ Badge](http://www.r-pkg.org/badges/version/prodigenr)](https://cran.r-project.or
[](https://lifecycle.r-lib.org/articles/stages.html)
[](https://www.r-pkg.org:443/pkg/prodigenr)
-
-This [R](https://cran.r-project.org) package is part of a
-[series](https://github.com/rostools) of (planned) packages that are
-aimed at creating a toolkit for doing reproducible and open science.
-Many researchers (especially in biomedicine, medicine, or health, which
-is my area of research) have little to no knowledge on what open science
-is or what reproducibility is, let alone how to do it. Our goal is
-create an [(opinionated) toolkit](https://rostools.gitlab.io/manifesto)
-to automate and simplify the process of doing open and reproducible
-science.
+
This package has a simple aim of being a *pro*ject *di*rectory
*gen*erato*r* (prodigenr), with a simple focus on:
1. Creating a standardized project folder structure with a few template
- files needed for beginning a data analysis project
+ files needed for beginning a data analysis project.
2. Following a “one project, one (main) output” principle, such as a
report/manuscript in the case of scientific output or a book or
- website for things like courses or workshops
+ website for things like courses or workshops.
3. Adhering to established best practices that make it easier for the
- project to be reproducible and open
+ project to be reproducible and open.
This standardized approach to how a scientific project is structured
helps ensure that the final code and documents are fairly modular,
@@ -54,8 +45,8 @@ install.packages("prodigenr")
And the development version from [GitHub](https://github.com/) with:
``` r
-# install.packages("remotes")
-remotes::install_github("rostools/prodigenr")
+# install.packages("pak")
+pak::pak("rostools/prodigenr")
```
## Usage
@@ -76,26 +67,28 @@ your analysis! Open the newly created project via the `.Rproj` file. For
the RStudio approach, go to “File -\> New Project”, then “New directory”
and find the prodigenr project in the list:
-
+
+
+Creating a prodigenr project in
+RStudio
+
-Once in the project, you can add a manuscript R Markdown file using:
+Once in the project, you can add a manuscript/report
+[Quarto](https://quarto.org/) file using:
``` r
-create_manuscript()
+create_report()
```
The main secondary function is the `template_list` command, which lists
-the available template files (submit a PR if you want another template
-included!):
+the available template files:
``` r
template_list
#> [1] "report" "slides"
```
-
-
For a more detailed tutorial, see the introduction vignette:
``` r
+
+# Project creation with prodigenr: A component of reproducible and open scientific projects