Fixed the notebook startup part. Updated README accordingly.

Author: goedman

README.md

@@ -33,6 +33,18 @@ To use the demonstration Pluto notebooks, you can add:
   [c3e4b0f8] Pluto v0.12.18
   [7f904dfe] PlutoUI v0.6.11
 ```
+
+To run the notebooks, I typically use an `alias`:
+```
+alias pluto="clear; j -i -e 'using Pkg; import Pluto; Pluto.run()'"
+```
+and then do:
+```
+$ cd ~/.julia/dev/ParetoSmoothedImportanceSampling
+$ pluto
+```
+to start Pluto from within that directory. 
+
 The cars WAIC example requires RDatasets.jl to be installed and functioning.
 
 ### Included functions

notebooks/arsenic.jl

@@ -5,24 +5,22 @@ using Markdown
 using InteractiveUtils
 
 # ╔═╡ 8183b318-5ebb-11eb-1cd8-a96e8704a378
-using Pkg, DrWatson, ParetoSmoothedImportanceSampling
+using Pkg, DrWatson
 
-# ╔═╡ d4f7a39c-5ebb-11eb-0a37-4b8499832108
+# ╔═╡ 686dac30-5ebb-11eb-00f1-434980dba906
 begin
+	@quickactivate "ParetoSmoothedImportanceSamplng"
+	using ParetoSmoothedImportanceSampling
 	using StanSample, StatsFuns, StatsPlots
-	using JSON
+	using DataFrames, CSV, JSON
+end
 
+# ╔═╡ 923212a8-630d-11eb-390f-75d21be80011
+begin
 	ProjDir = joinpath(psis_path, "..", "examples", "arsenic")
 	include(joinpath(ProjDir, "cvit.jl"))
 end;
 
-# ╔═╡ 686dac30-5ebb-11eb-00f1-434980dba906
-begin
-	cd(psis_path)
-	@quickactivate "ParetoSmoothedImportanceSampling"
-	pkg"instantiate"
-end
-
 # ╔═╡ ca0d916e-5ebe-11eb-3af1-0993bf5b82c8
 md" ### Psis_loo."
 
@@ -125,6 +123,9 @@ begin
 	sm3 = SampleModel("arsenic_logistic_t", model_str_2)
 end;
 
+# ╔═╡ d83916ba-6309-11eb-309b-474efacd9f85
+md" ##### Be patient... 10 cross Validations."
+
 # ╔═╡ e70f73aa-5eb8-11eb-1960-bf6731681898
 begin
 	cvitr, cvitst = cvit(n, 10, true)
@@ -160,7 +161,7 @@ end
 # ╔═╡ Cell order:
 # ╠═8183b318-5ebb-11eb-1cd8-a96e8704a378
 # ╠═686dac30-5ebb-11eb-00f1-434980dba906
-# ╠═d4f7a39c-5ebb-11eb-0a37-4b8499832108
+# ╠═923212a8-630d-11eb-390f-75d21be80011
 # ╟─ca0d916e-5ebe-11eb-3af1-0993bf5b82c8
 # ╟─2ee71b16-5ebd-11eb-3a7d-4553f2f22274
 # ╠═37f06bc2-5ebd-11eb-31f6-65bfa74ea9cf
@@ -177,5 +178,6 @@ end
 # ╟─98d7208e-5ebd-11eb-3a64-e568c1ceebc0
 # ╟─e86ee35c-5ebd-11eb-1932-ffbde638f11e
 # ╠═e86f0ab2-5ebd-11eb-1a0b-6958db3a7435
+# ╟─d83916ba-6309-11eb-309b-474efacd9f85
 # ╠═e70f73aa-5eb8-11eb-1960-bf6731681898
 # ╠═1bf8d5a2-5ebe-11eb-12b3-2501e2f9d288

notebooks/cars.jl

@@ -5,27 +5,22 @@ using Markdown
 using InteractiveUtils
 
 # ╔═╡ b9fc511c-6007-11eb-0c6b-1f6871a40710
-using Pkg, DrWatson, ParetoSmoothedImportanceSampling
+using Pkg, DrWatson
 
-# ╔═╡ 20d3ad36-6008-11eb-2f2a-d379b234b0e9
+# ╔═╡ 20d377b2-6008-11eb-364a-617b6934ecb2
 begin
+	@quickactivate "ParetoSmoothedImportanceSamplng"
+	using ParetoSmoothedImportanceSampling
 	using StanSample, StatsFuns, StatsPlots
-	using DataFrames, RDatasets
-end;
+	using DataFrames, CSV, RDatasets
+end
 
 # ╔═╡ af6b0b20-6008-11eb-2fa1-2f61145ab7db
 md"
 !!! note
 
 	This script assumes that RDatasets.jl is loaded. RDatasets.jl is not included in the dependencies of PSIS.jl (as it would require R to be installed)."
 
-# ╔═╡ 20d377b2-6008-11eb-364a-617b6934ecb2
-begin
-	cd(psis_path)
-	@quickactivate "ParetoSmoothedImportanceSampling"
-	pkg"instantiate"
-end
-
 # ╔═╡ 20d43cda-6008-11eb-09f0-53489a26110d
 df = RDatasets.dataset("datasets", "cars");
 
@@ -110,7 +105,6 @@ pk_plot(pk)
 # ╟─af6b0b20-6008-11eb-2fa1-2f61145ab7db
 # ╠═b9fc511c-6007-11eb-0c6b-1f6871a40710
 # ╠═20d377b2-6008-11eb-364a-617b6934ecb2
-# ╠═20d3ad36-6008-11eb-2f2a-d379b234b0e9
 # ╠═20d43cda-6008-11eb-09f0-53489a26110d
 # ╠═20e22570-6008-11eb-1565-f13541b41861
 # ╠═20e2ebb6-6008-11eb-34f5-61f1ec3d024c

notebooks/roaches.jl

@@ -5,19 +5,14 @@ using Markdown
 using InteractiveUtils
 
 # ╔═╡ dcb4d418-5ec2-11eb-29d8-214f38b4d3ae
-using Pkg, DrWatson, ParetoSmoothedImportanceSampling
-
-# ╔═╡ c9e1486c-5e9f-11eb-08ed-671b762dd075
-begin
-  using StanSample, StatsFuns, StatsPlots
-  using DataFrames
-end
+using Pkg, DrWatson
 
 # ╔═╡ d20c24f8-5ec2-11eb-3d45-d97fedebee8e
 begin
-	cd(psis_path)
 	@quickactivate "ParetoSmoothedImportanceSamplng"
-	pkg"instantiate"
+	using ParetoSmoothedImportanceSampling
+	using StanSample, StatsFuns, StatsPlots
+	using DataFrames, CSV
 end
 
 # ╔═╡ e3552750-5e9f-11eb-324b-8df36d671c79
@@ -165,7 +160,6 @@ pk_plot(pk2; title="PSIS diagnostic plot for neg-binomial model.", leg=:topright
 # ╔═╡ Cell order:
 # ╠═dcb4d418-5ec2-11eb-29d8-214f38b4d3ae
 # ╠═d20c24f8-5ec2-11eb-3d45-d97fedebee8e
-# ╠═c9e1486c-5e9f-11eb-08ed-671b762dd075
 # ╠═e3552750-5e9f-11eb-324b-8df36d671c79
 # ╠═e3691972-5e9f-11eb-20b2-a766ef562598
 # ╠═e371fde4-5e9f-11eb-39ad-8d25ac3034fc