updated readme

zhenkewu · Dec 21, 2023 · 2c136d6 · 2c136d6
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diff --git a/CRAN-SUBMISSION b/CRAN-SUBMISSION
@@ -1,3 +1,3 @@
 Version: 1.0.2
-Date: 2023-12-19 05:51:51 UTC
-SHA: 5190ba7362467caafdab0944dcefc58b5394649e
+Date: 2023-12-20 20:05:15 UTC
+SHA: 5096733c107dda4f39e0666f56312c458031ea48
diff --git a/LICENSE b/LICENSE
@@ -1,2 +1,2 @@
-YEAR: 2014-2022
+YEAR: 2014-2024
 COPYRIGHT HOLDER: Zhenke Wu
diff --git a/README.Rmd b/README.Rmd
@@ -36,11 +36,13 @@ knitr::opts_chunk$set(
 
 **Maintainer**: Zhenke Wu, zhenkewu@umich.edu
 
+**Source Code**: Please click [here](https://github.com/zhenkewu/baker) for source code on GitHub.
+
 **Issues**: Please click [here](https://github.com/zhenkewu/baker/issues) to report reproducible issues.
 
-**Vignette**: Please click [here](https://zhenkewu.com/assets/html/baker_vignette.html) to read the latest vignette.
+**Vignette**: Please click [here](https://zhenkewu.com/assets/html/baker_vignette.html) to read the latest long-version vignette; a short version can be found [here](https://zhenkewu.com/baker/articles/baker_demo.html).
 
-**Package website:** Please click [here](https://zhenkewu.com/baker/) for a website generated by `pkgdown`, which contains html format of the package manual.
+**Package website:** Please click [here](https://zhenkewu.com/baker/) for a website generated by `pkgdown`, which contains html format of the package manual ("Refence").
 
 **References**: If you are using **baker** for population and individual estimation from case-control data, please cite the following papers:
 
@@ -154,12 +156,12 @@ maintainer or chat by clicking the `gitter` button at the top of this README fil
 
 <div id='id-section8'/>
 
-Connect `R` to `JAGS`/`WinBUGS`
+Connect `R` to `JAGS`
 ---------------------------------
-#### Mac OSX 10.11 El Capitan
+#### Mac OSX (10.11+)
 
 1. Use [Just Another Gibbs Sampler (JAGS)](https://mcmc-jags.sourceforge.io/)
-2. Install JAGS 4.2.0; Download [here](https://sourceforge.net/projects/mcmc-jags/files/JAGS/4.x/Mac%20OS%20X/)
+2. Install JAGS 4.3.2 (or 4.2.0 - currently it is slightly slower for 4.3.2, which was updated to be compatible with R 4.3.x); Download [here](https://sourceforge.net/projects/mcmc-jags/files/JAGS/4.x/Mac%20OS%20X/)
 3. Install `R`; Download from [here](https://cran.r-project.org/)
 4. Fire up `R`, run `R` command `install.packages("rjags")`
 5. Run `R` command `library(rjags)` in R console; If the installations are successful, you'll see some notes like this:
@@ -182,6 +184,7 @@ Here we use [JHPCE](https://jhpce.jhu.edu/) as an example. [The complete install
 extra information. 
 
 1. Download source code for [JAGS 4.2.0](https://sourceforge.net/projects/mcmc-jags/files/JAGS/4.x/Source/JAGS-4.2.0.tar.gz/download);
+The workflow would be similar for later versions of `JAGS`.
 
 2. Suppose you've downloaded it in `~/local/jags/4.2.0`. Follow the bash commands below:
 
@@ -261,12 +264,12 @@ date
 <div id='id-section10'/>
 #### Windows 
 
-- JAGS 4.2.0
+- JAGS 4.2.0 (also applicable to later versions)
 1. Install `R`; Download from [here](https://cran.r-project.org/)
 2. Install [JAGS 4.2.0](https://sourceforge.net/projects/mcmc-jags/files/JAGS/4.x/Windows/); Add the path to JAGS 4.2.0 into the environmental variable (essential for R to find the jags program). See [this](https://superuser.com/questions/949560/how-do-i-set-system-environment-variables-in-windows-10) for setting environmental variables;
 - alternatives are `brew install -v jags` for OSX, `sudo apt-get install jags` for Ubuntu/Debian
 3. Fire up `R`, run `R` command `install.packages("rjags")`
-4. Install [`Rtools`](https://cran.r-project.org/bin/windows/Rtools/) (for building and installing R pacakges from source); Add the path to `Rtools` (e.g., `C:\Rtools\`) into your environmental variables so that R knows where to find it. 
+4. Install [`Rtools`](https://cran.r-project.org/bin/windows/Rtools/) (for building and installing R packages from source); Add the path to `Rtools` (e.g., `C:\Rtools\`) into your environmental variables so that R knows where to find it. 
 
 <!-- - [WinBUGS 1.4.3](http://www.mrc-bsu.cam.ac.uk/software/bugs/the-bugs-project-winbugs/) -->
 <!--     1. Install the [patch](http://www.mrc-bsu.cam.ac.uk/software/bugs/the-bugs-project-winbugs/the-bugs-project-winbugs-patches/) -->

diff --git a/README.md b/README.md
@@ -20,17 +20,21 @@ status](https://github.com/zhenkewu/baker/actions/workflows/R-CMD-check.yaml/bad
 
 **Maintainer**: Zhenke Wu, <zhenkewu@umich.edu>
 
+**Source Code**: Please click [here](https://github.com/zhenkewu/baker)
+for source code on GitHub.
+
 **Issues**: Please click
 [here](https://github.com/zhenkewu/baker/issues) to report reproducible
 issues.
 
 **Vignette**: Please click
 [here](https://zhenkewu.com/assets/html/baker_vignette.html) to read the
-latest vignette.
+latest long-version vignette; a short version can be found
+[here](https://zhenkewu.com/baker/articles/baker_demo.html).
 
 **Package website:** Please click [here](https://zhenkewu.com/baker/)
 for a website generated by `pkgdown`, which contains html format of the
-package manual.
+package manual (“Refence”).
 
 **References**: If you are using **baker** for population and individual
 estimation from case-control data, please cite the following papers:
@@ -172,13 +176,14 @@ You will get a dynamic figure. A snapshot is below:
 
 <div id='id-section8'/>
 
-## Connect `R` to `JAGS`/`WinBUGS`
+## Connect `R` to `JAGS`
 
-#### Mac OSX 10.11 El Capitan
+#### Mac OSX (10.11+)
 
 1.  Use [Just Another Gibbs Sampler
     (JAGS)](https://mcmc-jags.sourceforge.io/)
-2.  Install JAGS 4.2.0; Download
+2.  Install JAGS 4.3.2 (or 4.2.0 - currently it is slightly slower for
+    4.3.2, which was updated to be compatible with R 4.3.x); Download
     [here](https://sourceforge.net/projects/mcmc-jags/files/JAGS/4.x/Mac%20OS%20X/)
 3.  Install `R`; Download from [here](https://cran.r-project.org/)
 4.  Fire up `R`, run `R` command `install.packages("rjags")`
@@ -210,6 +215,7 @@ offers extra information.
 
 1.  Download source code for [JAGS
     4.2.0](https://sourceforge.net/projects/mcmc-jags/files/JAGS/4.x/Source/JAGS-4.2.0.tar.gz/download);
+    The workflow would be similar for later versions of `JAGS`.
 
 2.  Suppose you’ve downloaded it in `~/local/jags/4.2.0`. Follow the
     bash commands below:
@@ -294,7 +300,7 @@ date
 
 #### Windows
 
-- JAGS 4.2.0
+- JAGS 4.2.0 (also applicable to later versions)
 
 1.  Install `R`; Download from [here](https://cran.r-project.org/)
 2.  Install [JAGS
@@ -309,7 +315,7 @@ date
 
 3.  Fire up `R`, run `R` command `install.packages("rjags")`
 4.  Install [`Rtools`](https://cran.r-project.org/bin/windows/Rtools/)
-    (for building and installing R pacakges from source); Add the path
+    (for building and installing R packages from source); Add the path
     to `Rtools` (e.g., `C:\Rtools\`) into your environmental variables
     so that R knows where to find it.