Rel 4.5.0 - README updates

Author: goedman

README.md

@@ -7,8 +7,6 @@ SR2TuringPluto is a Julia project that uses Pluto notebooks for this purpose. Ea
 
 This Julia project uses Turing as the underlying mcmc implementation.  A companion project ( [SR2StanPluto.jl](https://github.com/StatisticalRethinkingJulia/SR2StanPluto.jl) ) uses Stan.
 
-**Note: A new version (v5.0.0) is under development. This is a breaking version. Probably safe to stick with tagged version 4.0.3 until then.**
-
 ## Installation
 
 To (locally) reproduce and use this project, do the following:
@@ -25,23 +23,12 @@ If you want a specific tagged version, use:
 ```
 $ git tag -l # To see available tags, followed by:
 $ git checkout tags/<tag_name> # or simply:
-$ git checkout v4.0.3
+$ git checkout v4.5.0
 ```
 
-and in the Julia REPL:
-
-```
-julia> ]                           # Actvate Pkg mode
-(@v1.8) pkg> activate .            # Activate pkg in .
-(SR2TuringPluto) pkg> instantiate  # Install in pkg environment
-(SR2TuringPluto) pkg> <delete>     # Exit package mode
-```
-
-If above procedure fails, if present, try to delete the Manifest.toml file and repeat above steps. **These steps are only needed the first time.**
-
 The next step assumes your Julia setup includes at least `Pkg`, `DrWatson`, `Pluto` and `PlutoUI`.
 
-2. Start a Pluto notebook server.
+2. Start a Pluto notebook server in the Julia REPL:
 ```
 $ julia
 
@@ -53,16 +40,14 @@ julia> Pluto.run()
 
 ## Usage
 
-Note: *SR2TuringPluto v4 requires StatisticalRethinking.jl v 4.*
+Note: *SR2TuringPluto v4 requires StatisticalRethinking.jl v4.*
 
 Select a notebook in the `open a file` entry box, e.g. type `./` and step to `./notebooks/TuringGuide.jl`.
 
 SR2TuringPluto.jl is a DrWatson project, with some added/re-purposed subdirectories,
 
 The `data` directory, in DrWatson accessible through `datadir()`, can be used for locally generated data, exercises, etc. All "rethinking" data files are stored and maintained in StatisticalRethinking.jl and can be accessed via `sr_datadir(...)`.
 
-The scripts in the `scripts` subdirectory are directly generated from the notebooks and thus adhere to Pluto's programming restrictions.
-
 This leads to a typical set of opening lines in each notebook:
 ```
 using Pkg, DrWatson
@@ -85,7 +70,7 @@ df = df[df.age .>= 18, :]
 
 ## Naming of models and results:
 
-1. ppl5_1 or m5_1    : Turing model
+1. ppl5_1            : Turing model
 1. m5_1t             : The instantiated Turing model (includes data)
 
 Chain(s):
@@ -101,27 +86,38 @@ Results as a DataFrame:
 
 As before, the `t` at the end of the model number indicates Turing.
 
+**Note**: Naming is not yet consistent through all notebooks. Work in progress!
+
 ## Status
 
 SR2TuringPluto.jl is compatible with the 2nd edition of the book.
 
 StructuralCausalModels.jl and ParetoSmoothedImportanceSampling.jl are included as experimental dependencies in the StatisticalRethinking.jl v3 package. Definitely work in progress!
 
+Max Lapan added a package Dagitty.jl which coversoptions similar as available in StructuralCausalModels.jl. There is also a new package, ParetoSmooth.jl which overlaps with ParetoSmoothedImportanceSampling.jl.
+As terminology differs from the terminology used in the Statistical Rethinking book, I have not used this package in the notebooks (yet?).
+
+**Note: A new version (v5.0.0) is under development. This is a breaking version. Probably safe to stick with tagged version 4.0.3 until then.**
+
 Any feedback is appreciated. Please open an issue.
 
 ## Acknowledgements
 
 Of course, without the excellent textbook by Richard McElreath, this package would not have been possible. The author has also been supportive of this work and gave permission to use the datasets.
 
-This repository and format is derived from work by Max Lapan, Karajan, previous and Stan versions of StatisticalRethinking.jl and many other contributors.
+This repository is derived from work by Max Lapan, Karajan, previous and current Stan versions of StatisticalRethinking.jl. It has been improved through comments and suggestions of many other contributors.
 
 ## Versions
 
 ### Version 5.0.0 (Under development, will take time)
 
 1. Complete overhaul.likely using Makie.jl, Graphs.jl and more.
 2. Larger notebooks.
-3. Dropped additional figures in early chapters.    r
+3. Dropped additional figures in early chapters.
+
+### Version 4.5.0
+
+1. Adapted chapters 5 to 14 to an initial Pluto format.
 
 ### Version 4.0.5