Rel 4.4.5 - Minor shuffling between require and main src dir

Author: goedman

docs/src/references.md

@@ -10,7 +10,9 @@ There is no shortage of additional good books on Bayesian statistics. A few of m
 
 3. [Bolstad: Understanding Computational Bayesian Statistics](http://www.wiley.com/WileyCDA/WileyTitle/productCd-0470046090.html)
 
-4. [Gelman, Hill: Data Analysis Using Regression and Multilevel/Hierarchical Models](http://www.stat.columbia.edu/~gelman/arm/)
+4.a [Gelman, Hill: Data Analysis Using Regression and Multilevel/Hierarchical Models](http://www.stat.columbia.edu/~gelman/arm/)
+
+4.b [Gelman, Hill, Vehtari: Rgression and other stories](https://www.cambridge.org/highereducation/books/regression-and-other-stories/DD20DD6C9057118581076E54E40C372C#overview)
 
 5. [Kruschke: Doing Bayesian Data Analysis](https://sites.google.com/site/doingbayesiandataanalysis/what-s-new-in-2nd-ed)
 
@@ -21,3 +23,5 @@ There is no shortage of additional good books on Bayesian statistics. A few of m
 8. [Causal Inference in Statistics - A Primer](https://www.wiley.com/en-us/Causal+Inference+in+Statistics%3A+A+Primer-p-9781119186847)
 
 9. [Betancourt: A Conceptual Introduction to Hamiltonian Monte Carlo](https://arxiv.org/abs/1701.02434)
+
+10. [Pearl, Mackenzie: The Book of Why](https://www.basicbooks.com/titles/judea-pearl/the-book-of-why/9780465097616/)

src/StatisticalRethinking.jl

@@ -29,10 +29,7 @@ using DocStringExtensions: SIGNATURES, FIELDS, TYPEDEF
 
 function __init__()
   @require Turing="fce5fe82-541a-59a6-adf8-730c64b5f9a0" include("require/turing/turing.jl")
-  #@require Optim="429524aa-4258-5aef-a3af-852621145aeb" include("require/turing/turing_optim_sample.jl")
-
   @require StanSample="c1514b29-d3a0-5178-b312-660c88baa699" include("require/stan/stan.jl")
-
   @require LogDensityProblems="6fdf6af0-433a-55f7-b3ed-c6c6e0b8df7c" include("require/dhmc/dhmc.jl")
 
   #@require MCMCChains="c7f686f2-ff18-58e9-bc7b-31028e88f75d" include("require/mcmcchains/mcmcchains.jl")
@@ -90,6 +87,7 @@ include("hmc.jl")
 include("pk_qualify.jl")
 include("quap.jl")
 include("dataframe.jl")
+#include("particles_mcmcchains.jl")
 
 export
   sr_path,

src/pluto_helpers.jl

@@ -4,3 +4,14 @@ PRECIS(df::DataFrame) = Text(precis(df; io=String))
 
 export
     PRECIS
+
+CHNS(chns::MCMCChains.Chains) = Text(sprint(show, "text/plain", chns))
+
+# Pluto helpers for MCMCChains
+
+HPD(chns::MCMCChains.Chains) = Text(sprint(show, "text/plain", hpd(chns)))
+
+export
+    HPD,
+    CHNS
+

src/require/mcmcchains/particles.jl

@@ -1,10 +1 @@
 
-CHNS(chns::MCMCChains.Chains) = Text(sprint(show, "text/plain", chns))
-
-# Pluto helpers for MCMCChains
-
-HPD(chns::MCMCChains.Chains) = Text(sprint(show, "text/plain", hpd(chns)))
-
-export
-    HPD,
-    CHNS

src/require/mcmcchains/pluto_helpers.jl

@@ -6,7 +6,7 @@ using Test
 tests = ["srtools", "link", "simulate", "lppd"]
 stan_tests = ["wd-loo-compare",]
 
-stan_exists()::Bool = "JULIA_CMDSTAN_HOME" in keys(ENV) || "CMDSTAN" in keys(ENV)
+stan_exists()::Bool = ("JULIA_CMDSTAN_HOME" in keys(ENV) || "CMDSTAN" in keys(ENV))
 
 
 for t ∈ tests