chore: Update README

Removing README.qmd, as it is no longer used

Author: mhovd

README.md

@@ -2,50 +2,67 @@
 
 # Pmetrics <a href="https://lapkb.github.io/Pmetrics/"><img src="man/figures/Pmetrics_logo.png" align="right" height="100" width = "100" alt="Pmetrics" /></a>
 
-> [!WARNING]
->
-> This is a development branch of Pmetrics using a new backend written
-> in Rust. The repository for the current stable release is
-> [LAPKB/Pmetrics](https://github.com/LAPKB/Pmetrics).
-
-Thank you for your interest in Pmetrics, created by the [Laboratory of
+Thank you for your interest in `Pmetrics`, created by the [Laboratory of
 Applied Pharmacokinetics and Bioinformatics](http://www.lapk.org).
-Pmetrics is a library package for R to perform non-parametric and
+`Pmetrics` is a library package for R to perform non-parametric and
 parametric pharmacokinetic-pharmacodynamic population and individual
 modeling and simulation. It is primarily designed for pharmacometric
 researchers.
 
-Pmetrics is based on over 40 years of research by our laboratory and is
-the most mature non-parametric method available. Nevertheless, Pmetrics
+`Pmetrics` is based on over 40 years of research by our laboratory and is
+the most mature non-parametric method available. Nevertheless, `Pmetrics`
 is dynamically evolving. Best of all, it is SHAREWARE with only a
 suggested donation.
 
-## Source code
-
-The open source code for the Pmetrics R package is hosted here on
-Github. LAPKB has developed two other packages,
-[PMcore](https://github.com/LAPKB/PMcore) and
-[pharmsol](https://github.com/LAPKB/pharmsol), which implement the core
-algorithms used by Pmetrics. These packages are also open source and
-available on Github.
 
 ## Installation
 
-To install and use Pmetrics, you will need **R**, **Rust**, and the
-**Pmetrics** package appropriate for your system.
+### R (required)
+
+You can download and install [R](https://r-project.org) from the
+[Comprehensive R Archive Network (CRAN)](https://cran.r-project.org/).
+
+### Rust (required)
+
+The simulation engine for `Pmetrics` is written in `Rust`, which is required to fit models.
+
+Follow the instructions on the [Rust
+website](https://www.rust-lang.org/tools/install) to install Rust on
+your system.
+
+### Pmetrics
+
+`Pmetrics` is distributed on [r-universe](https://lapkb.r-universe.dev/Pmetrics), and built for Windows, MacOS, and Linux. To install, you must specify `r-universe` as the repository using
+
+```r
+install.packages("Pmetrics", repos = "https://lapkb.r-universe.dev")
+```
+
+For updating the package and for easier future installations, you can run the following command
+to add the `r-universe` repository to your `R.profile`
 
-<a href="https://r-project.org"><img src="man/figures/Rlogo.png" align="left" height="40" width="40" alt="R" /></a><br><br>
-You can download and install **R** from the [Comprehensive R Archive
-Network (CRAN)](https://cran.r-project.org/). In addition, we *strongly*
-recommend a third-party integrated development environment (IDE) to use
-R and Pmetrics rather than the rudimentary IDE that comes with R. We use
-all the IDEs below when developing and working with Pmetrics.
+```r
+write('options(repos = c(CRAN = "https://cloud.r-project.org", LAPKB = "https://lapkb.r-universe.dev"))', "~/.Rprofile", append = TRUE)
+```
+
+With this setup, you can install or update Pmetrics using the
+standard command `install.packages("Pmetrics")` without specifying
+the repository each time.
+
+
+### IDE (optional)
+
+In addition, we *strongly* recommend a third-party integrated
+development environment (IDE) to use R and Pmetrics rather than the
+rudimentary IDE that comes with R. We use all the IDEs below when
+developing and working with Pmetrics.
 
 - [RStudio](https://posit.co/download/rstudio-desktop/) is the oldest
   and most stable IDE, developed by [Posit](https://posit.co). Most
   users who only program in R use Rstudio. It has a simple interface
   with many R-specific buttons and menus. It is relatively easy to learn
   and use, but does not support other programming languages.
+
 - [Positron](https://positron.posit.co) is a newer alternative also from
   Posit. Posit are now mostly developing Positron rather than Rstudio.
   Positron primarily supports users who work in R and Python. However,
@@ -56,121 +73,25 @@ all the IDEs below when developing and working with Pmetrics.
   Rstudio, but has a steeper learning curve and currently fewer
   R-specific buttons and menus. VS Code users will find Positron
   familiar.
+
 - [VS Code](https://code.visualstudio.com) itself can be used for R, but
   it is best suited for experienced coders who also use other
   programming languages.
 
-<a href="https://rust-lang.org"><img src="man/figures/rust-logo-64x64.png" align="left" height="40" width = "40" alt="Rust" /></a><br><br>
-**Rust** is the language used by pharmsol for the backend of Pmetrics
-and all the heavy “number crunching”. Rust is modern, fast, reliable,
-widely used, and extremely well supported. It works on all major
-operating systems.
-
-Follow the instructions on the [Rust
-website](https://www.rust-lang.org/tools/install) to install Rust on
-your system.
-
-<img src="man/figures/Pmetrics_logo.png" align="left" height="40" width = "40" alt="Pmetrics" /><br><br>
-The compiled versions of **Pmetrics** for MacOS, Windows and Linux are
-hosted on [r-universe](https://lapkb.r-universe.dev/Pmetrics). Follow
-these easy steps to install the correct version for your system.
-
-1.  Add the LAPKB r-universe repository to your list of repositories by
-    adding this code to your `.Rprofile` script, which ensures that R
-    will always include the LAPKB repository when installing or updating
-    packages, even after you restart or update R.
-
-    ``` r
-    options(repos = c(
-        CRAN = "https://cloud.r-project.org",
-        LAPKB = "https://lapkb.r-universe.dev"
-    ))
-    ```
-
-    If you don’t have an `.Rprofile` script, you can create one in your
-    home directory. This only needs to be done once.
-
-    <details>
-
-    <summary>
-
-    Mac
-
-    </summary>
-
-    You can create or edit the `.Rprofile` file using TextEdit or any
-    text editor. Make sure to save it as a plain text file named
-    `.Rprofile` in your home directory, i.e.,
-    `/Users/yourusername/.Rprofile`. Do not add a `.txt` extension. To
-    open/edit your `.Rprofile` later, type `open -e ~/.Rprofile` in the
-    Terminal.
-
-    </details>
-
-    <details>
-
-    <summary>
-
-    Windows
-
-    </summary>
-
-    You can create or edit the `.Rprofile` file using Notepad or any
-    text editor. Make sure to save it as a plain text file named
-    `.Rprofile` in your home directory, i.e.,
-    `C:\Users\yourusername\.Rprofile`. Do not add a `.txt` extension. To
-    open/edit your `.Rprofile` later, type
-    `notepad %USERPROFILE%\.Rprofile` in the Command Prompt.
-
-    </details>
-
-    <details>
-
-    <summary>
-
-    Linux
-
-    </summary>
-
-    You can create or edit the `.Rprofile` file using any text editor,
-    such as `nano` or `vim`. Make sure to save it as a plain text file
-    named `.Rprofile` in your home directory, i.e.,
-    `/home/yourusername/.Rprofile`. To open/edit your `.Rprofile` later,
-    type `nano ~/.Rprofile` or `vim ~/.Rprofile` in the terminal.
-
-    </details>
-
-2.  After you have run the above command once, you can install or update
-    previously installed Pmetrics by running this command in R:
-
-    ``` r
-    install.packages("Pmetrics")
-    ```
-
-    This command is the same as for any other R package hosted on CRAN.
-    By having the LAPKB repository in your list of repositories, R will
-    automatically find and install/update the correct version of
-    Pmetrics for your system.
-
-    <details>
 
-    <summary>
+## Related projects
 
-    What if I couldn’t add the LAPKB repository to my .Rprofile?
+The LAPKB has developed two packages in `Rust` to power `Pmetrics`.
 
-    </summary>
+[`pharmsol`](https://github.com/LAPKB/pharmsol) is a Rust library for defining and solving pharmacokinetic models.
 
-    You can still install Pmetrics by specifying the repository directly
-    in the `install.packages` function like this:
+[`PMcore`](https://github.com/LAPKB/PMcore) depends on `pharmsol` to fit models to data, and implements the different algorithms which are made available in `Pmetrics`.
 
-    ``` r
-    install.packages("Pmetrics", repos = "https://lapkb.r-universe.dev")
-    ```
+Pmetrics and the code that powers it is provided as open-source code.
 
-    However, you will need to include the `repos` argument each time you
-    want to install or update Pmetrics.
+## Contributing
 
-    </details>
+We welcome contributions in the form of feature requests, raising issues, or writing code.
 
 ## Documentation