TuringLang/DynamicPPL.jl

svaksha · Oct 28, 2021 · 3bc00de · 3bc00de
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diff --git a/Probability-Statistics.md b/Probability-Statistics.md
@@ -1,6 +1,9 @@
-+ [PROBABILITY](#probability)
-   + [PROGRAMMING](#programming)
-   + [STOCHASTICS](#stochastics)
++ [§1. PROBABILITY](#1-PROBABILITY)
+   + [§1.1. Probabilistic Programming](#1-1-Probabilistic-Programming)
+   + [§1.2. STOCHASTICS](#1-2-stochastics)
+        + [§1.2.1. Bayesian](#1-2-1-Bayesian)
+        + [§1.2.2. Gaussian](#1-2-2-Gaussian)
+        + [§1.2.3. Markovian)(#1-2-3-Markovian)
 + [STATISTICS](#statistics)
    + [REGRESSION](#regression)
    + [DENSITIES](#densities)
@@ -16,36 +19,40 @@
 
 ----
 
-# [PROBABILITY](https://en.wikipedia.org/wiki/Probability_theory)
 
-## [PROGRAMMING](https://en.wikipedia.org/wiki/Probabilistic_programming)
+# §1. [PROBABILITY](https://en.wikipedia.org/wiki/Probability_theory) <span id="1-PROBABILITY"><span>
+
+## §1.1. [Probabilistic Programming](https://en.wikipedia.org/wiki/Probabilistic_programming) <span id="1-1-Probabilistic-Programming"><span>
+
++ [DynamicPPL.jl](https://github.com/TuringLang/DynamicPPL.jl) :: Implementation of domain-specific language (DSL) for dynamic probabilistic programming 
 + [Gen.jl](https://github.com/probcomp/Gen) :: Probabilistic programming with programmable inference.
 + [Omega.jl](https://github.com/zenna/Omega.jl) ::  Causal, Higher-Order, Probabilistic Programming.
 + [Soss.jl](https://github.com/cscherrer/Soss.jl) :: A library for probabilistic programming.
 + [Stan.jl](https://github.com/StanJulia/Stan.jl) :: A Julia wrapper for the Stan language.
 + [Stheno.jl](https://github.com/willtebbutt/Stheno.jl) :: Probabilistic programming with Gaussian processes in Julia.
 + [Turing.jl](https://github.com/TuringLang/Turing.jl) :: A Turing complete probabilistic programming language.
 
-## [STOCHASTICS](https://en.wikipedia.org/wiki/Stochastic_process)
-
-### Markovian
-[Markov Logic Network](https://en.wikipedia.org/wiki/Markov_logic_network)
-+ [POMDPs.jl](https://github.com/JuliaPOMDP/POMDPs.jl) :: A Julia framework for solving Markov decision processes.
-+ [POMDPToolbox.jl](https://github.com/JuliaPOMDP/POMDPToolbox.jl) :: Support tools for solving `POMDPs`.
-+ [HMMBase.jl](https://github.com/maxmouchet/HMMBase.jl) :: A lightweight abstraction for hidden Markov models in Julia.
-
-### Gaussian
-+ [GaussianMixtures.jl](https://github.com/davidavdav/GaussianMixtures.jl) :: Julia modules for Gaussian Mixture Models.
-+ [GaussianProcesses.jl](https://github.com/STOR-i/GaussianProcesses.jl) :: A Julia package for Gaussian Processes.
+## §1.2. [STOCHASTICS](https://en.wikipedia.org/wiki/Stochastic_process) <span id="1-2-STOCHASTICS"><span>
 
-### Bayesian
+### §1.2.1. Bayesian <span id="1-2-1-Bayesian"><span>
 + [ArviZ.jl](https://github.com/arviz-devs/ArviZ.jl) :: A Julia interface to the [ArviZ](https://arviz-devs.github.io/arviz/") package for exploratory analysis of Bayesian models, with functions for posterior analysis, model checking, comparison and diagnostics.
 + [BayesNets.jl](https://github.com/sisl/BayesNets.jl) :: Bayesian Networks for Julia.
 + [BayesianDataFusion.jl](https://github.com/jaak-s/BayesianDataFusion.jl) :: Implementation of data fusion methods.
 + [BayesEstDiffusion.jl](https://github.com/mschauer/BayesEstDiffusion.jl) :: Bayesian estimation of diffusion processes.
 + [BayesianNonparametrics.jl](https://github.com/OFAI/BayesianNonparametrics.jl) :: Bayesian nonparametrics in Julia.
 
 
+### §1.2.2. Gaussian <span id="1-2-2-Gaussian"><span>
++ [GaussianMixtures.jl](https://github.com/davidavdav/GaussianMixtures.jl) :: Julia modules for Gaussian Mixture Models.
++ [GaussianProcesses.jl](https://github.com/STOR-i/GaussianProcesses.jl) :: A Julia package for Gaussian Processes.
+
+
+### §1.2.3. Markovian <span id="1-2-3-Markovian"><span>
+The [Markov Logic Network](https://en.wikipedia.org/wiki/Markov_logic_network)
++ [POMDPs.jl](https://github.com/JuliaPOMDP/POMDPs.jl) :: A Julia framework for solving Markov decision processes.
++ [POMDPToolbox.jl](https://github.com/JuliaPOMDP/POMDPToolbox.jl) :: Support tools for solving `POMDPs`.
++ [HMMBase.jl](https://github.com/maxmouchet/HMMBase.jl) :: A lightweight abstraction for hidden Markov models in Julia.
+
 
 ----
 
@@ -116,12 +123,12 @@
 + [RecombinatorKMeans.jl](https://github.com/carlobaldassi/RecombinatorKMeans.jl) :: An implementation of the recombinator-k-means method.
 + [StableDQMC.jl](https://github.com/crstnbr/StableDQMC.jl                   ) :: Numerical stabilization routines for determinant quantum Monte Carlo.
 
-## [TESTS]()
+## TESTS
 + [HypothesisTests.jl](https://github.com/JuliaStats/HypothesisTests.jl) :: T-tests, Wilcoxon rank sum (Mann-Whitney U), signed rank, and circular statistics in Julia.
 + [RobustStats.jl](https://github.com/mrxiaohe/RobustStats.jl) :: A collection of robust statistical tests based on the R package WRS (R-Forge repository) by Rand Wilcox.
 
 ## UNCLASSIFIED
-+ [BloomFilters.jl](https://github.com/johnmyleswhite/BloomFilters.jl) :: are a probabilistic data structur e that can be used to test the inclusion and exclusion of items in a list.
++ [BloomFilters.jl](https://github.com/johnmyleswhite/BloomFilters.jl) :: are a probabilistic data structure that can be used to test the inclusion and exclusion of items in a list.
 + [AdaGram.jl](https://github.com/sbos/AdaGram.jl) :: Adaptive Skip-gram implementation.
 + [Civecm.jl](https://github.com/andreasnoackjensen/Civecm.jl) :: Cointegration in Vector Error Correction Models in Julia.
 + [CTDE.jl](https://github.com/adolgert/CTDE.jl) :: Continuous time, discrete event system in Julia.

diff --git a/README.md b/README.md
@@ -2,10 +2,10 @@
 
 [Julia.jl](http://svaksha.github.io/Julia.jl) aggregates and curates decibans of knowledge resources for programming in [Julia](https://github.com/JuliaLang), an all-purpose programming language that addresses the needs of high-performance numerical analysis and computational science.
 
-+ [INDEX](#index)
-+ [LICENSE](#license)
-   + [ODbL and AGPLv3](#odbl-and-agplv3)
-   + [Mirrors](#mirrors)
++ [§1. INDEX](#1-INDEX)
++ [§2. LICENSE](#2-LICENSE)
+   + [§2.1. ODbL and AGPLv3](#2-1-ODbL-and-AGPLv3)
+   + [§2.2. Mirrors](#2-2-Mirrors)
 + [CONTRIBUTE](#contribute)
    + [Guidelines](#guidelines)
    + [BugReport-PullRequest](#bugreport-pullrequest)
@@ -14,7 +14,7 @@
 
 ----
 
-# INDEX
+# §1. INDEX <span id="1-INDEX"><span>
 
 + [AI](https://github.com/svaksha/Julia.jl/blob/master/AI.md) :: Algorithms, DataMining, Data Structures, HMM, ML, NLP, ...
 + [Actuarial Science](https://github.com/svaksha/Julia.jl/blob/master/ActuarialScience.md) :: Software related to the subcategories of econometrics, finance, etc.
@@ -46,20 +46,24 @@
 
 ----
 
-# LICENSE
+# §2. LICENSE <span id="2-LICENSE"><span>
 
 + COPYRIGHT © 2012-Now [SVAKSHA](http://svaksha.com/pages/Bio), herewith dual-licensed for the data (ODbL-v1.0+) and the software (AGPLv3+), respectively.
 
-## [ODbL](https://opendatacommons.org/licenses/odbl/1-0/) and [AGPLv3](http://www.gnu.org/licenses/agpl-3.0.html)
+   + [§2.1. ODbL and AGPLv3](#2-1-ODbL-and-AGPLv3)
+
+
+## §2.1. AGPLv3 and ODbL <span id="2-1-AGPLv3-and-ODbL"><span>
+This repo uses multiple licences for data and code, viz. [ODbL](https://opendatacommons.org/licenses/odbl/1-0/) and [AGPLv3](http://www.gnu.org/licenses/agpl-3.0.html)
 
 + The __data__ (aggregated and curated decibans of knowledge resources for Julia language) in this repository (`Julia.jl`) is released under the [Open Database License](https://opendatacommons.org/licenses/odbl/1-0/) (ODbL-v1.0). The Open Database License (ODbL) grants anyone the freedom to share, create and adapt the data or database with proper __credit attribution__ as specified in the license and __offer any new work under the same terms__, and __release a public copy if using the new work for commercial purposes__.
 + The __software__ used in `Julia.jl` is released under the [AGPLv3 License](http://www.gnu.org/licenses/agpl-3.0.html), and above, as detailed in the [LICENSE-AGPLv3.md](https://github.com/svaksha/Julia.jl/blob/master/LICENSE-AGPLv3.md) file.
 + ALL copies and forks of this work must retain the Copyright, respective Licence files for program code (AGPLv3) and data (ODbL) along with this permission notice in all copies or substantial portions of the new work.
 
 The motivation for this change is to make it easier for people to re-use this data as a knowledge resource within a database. For example, [julia-observer](https://juliaobserver.com) is a visual tool for browsing through packages that pulls data from `Julia.jl`, `General` and various sources. By releasing the website code [publicly](https://github.com/djsegal/julia_observer) are an example on how one can build upon or transform the data to benefit the community.
 
+## §2.2. Mirrors <span id="2-2-Mirrors"><span>
 
-## Mirrors
 + [Bitbucket](https://bitbucket.org/svaksha/Julia.jl) :: git clone [email protected]:svaksha/Julia.jl.git
 + [GitLab](https://gitlab.com/svaksha/Julia.jl) :: git clone [email protected]:svaksha/Julia.jl.git
 

diff --git a/db.csv b/db.csv
@@ -1830,22 +1830,23 @@ Physics,[Thermodynamics](http://en.wikipedia.org/wiki/Category:Thermodynamics),P
 Physics,[Thermodynamics](http://en.wikipedia.org/wiki/Category:Thermodynamics),ThermodynamicsTable.jl,https://github.com/DANA-Laboratory/ThermodynamicsTable.jl,"Thermodynamics table for critical values, heat capacity, etc.."
 Physics,[Thermodynamics](http://en.wikipedia.org/wiki/Category:Thermodynamics),WaveToy.jl,https://github.com/eschnett/WaveToy.jl,Julia WaveToy.
 Physics,Miscellaneous,fys,https://github.com/jhlq/fys,Physics and misc unmaintained Julia code.
-Probability-Statistics,[PROGRAMMING](https://en.wikipedia.org/wiki/Probabilistic_programming),Gen.jl,https://github.com/probcomp/Gen,Probabilistic programming with programmable inference.
-Probability-Statistics,[PROGRAMMING](https://en.wikipedia.org/wiki/Probabilistic_programming),Omega.jl,https://github.com/zenna/Omega.jl," Causal, Higher-Order, Probabilistic Programming."
-Probability-Statistics,[PROGRAMMING](https://en.wikipedia.org/wiki/Probabilistic_programming),Soss.jl,https://github.com/cscherrer/Soss.jl,A library for probabilistic programming.
-Probability-Statistics,[PROGRAMMING](https://en.wikipedia.org/wiki/Probabilistic_programming),Stan.jl,https://github.com/StanJulia/Stan.jl,A Julia wrapper for the Stan language.
-Probability-Statistics,[PROGRAMMING](https://en.wikipedia.org/wiki/Probabilistic_programming),Stheno.jl,https://github.com/willtebbutt/Stheno.jl,Probabilistic programming with Gaussian processes in Julia.
-Probability-Statistics,[PROGRAMMING](https://en.wikipedia.org/wiki/Probabilistic_programming),Turing.jl,https://github.com/TuringLang/Turing.jl,A Turing complete probabilistic programming language.
-Probability-Statistics,Markovian,POMDPs.jl,https://github.com/JuliaPOMDP/POMDPs.jl,A Julia framework for solving Markov decision processes.
-Probability-Statistics,Markovian,POMDPToolbox.jl,https://github.com/JuliaPOMDP/POMDPToolbox.jl,Support tools for solving `POMDPs`.
-Probability-Statistics,Markovian,HMMBase.jl,https://github.com/maxmouchet/HMMBase.jl,A lightweight abstraction for hidden Markov models in Julia.
-Probability-Statistics,Gaussian,GaussianMixtures.jl,https://github.com/davidavdav/GaussianMixtures.jl,Julia modules for Gaussian Mixture Models.
-Probability-Statistics,Gaussian,GaussianProcesses.jl,https://github.com/STOR-i/GaussianProcesses.jl,A Julia package for Gaussian Processes.
-Probability-Statistics,Bayesian,ArviZ.jl,https://github.com/arviz-devs/ArviZ.jl,"A Julia interface to the [ArviZ](https://arviz-devs.github.io/arviz/"") package for exploratory analysis of Bayesian models, with functions for posterior analysis, model checking, comparison and diagnostics."
-Probability-Statistics,Bayesian,BayesNets.jl,https://github.com/sisl/BayesNets.jl,Bayesian Networks for Julia.
-Probability-Statistics,Bayesian,BayesianDataFusion.jl,https://github.com/jaak-s/BayesianDataFusion.jl,Implementation of data fusion methods.
-Probability-Statistics,Bayesian,BayesEstDiffusion.jl,https://github.com/mschauer/BayesEstDiffusion.jl,Bayesian estimation of diffusion processes.
-Probability-Statistics,Bayesian,BayesianNonparametrics.jl,https://github.com/OFAI/BayesianNonparametrics.jl,Bayesian nonparametrics in Julia.
+Probability-Statistics,"§1.1.[ProbabilisticProgramming](https://en.wikipedia.org/wiki/Probabilistic_programming)<spanid=""1-1-Probabilistic-Programming""><span>",DynamicPPL.jl,https://github.com/TuringLang/DynamicPPL.jl,Implementation of domain-specific language (DSL) for dynamic probabilistic programming
+Probability-Statistics,"§1.1.[ProbabilisticProgramming](https://en.wikipedia.org/wiki/Probabilistic_programming)<spanid=""1-1-Probabilistic-Programming""><span>",Gen.jl,https://github.com/probcomp/Gen,Probabilistic programming with programmable inference.
+Probability-Statistics,"§1.1.[ProbabilisticProgramming](https://en.wikipedia.org/wiki/Probabilistic_programming)<spanid=""1-1-Probabilistic-Programming""><span>",Omega.jl,https://github.com/zenna/Omega.jl," Causal, Higher-Order, Probabilistic Programming."
+Probability-Statistics,"§1.1.[ProbabilisticProgramming](https://en.wikipedia.org/wiki/Probabilistic_programming)<spanid=""1-1-Probabilistic-Programming""><span>",Soss.jl,https://github.com/cscherrer/Soss.jl,A library for probabilistic programming.
+Probability-Statistics,"§1.1.[ProbabilisticProgramming](https://en.wikipedia.org/wiki/Probabilistic_programming)<spanid=""1-1-Probabilistic-Programming""><span>",Stan.jl,https://github.com/StanJulia/Stan.jl,A Julia wrapper for the Stan language.
+Probability-Statistics,"§1.1.[ProbabilisticProgramming](https://en.wikipedia.org/wiki/Probabilistic_programming)<spanid=""1-1-Probabilistic-Programming""><span>",Stheno.jl,https://github.com/willtebbutt/Stheno.jl,Probabilistic programming with Gaussian processes in Julia.
+Probability-Statistics,"§1.1.[ProbabilisticProgramming](https://en.wikipedia.org/wiki/Probabilistic_programming)<spanid=""1-1-Probabilistic-Programming""><span>",Turing.jl,https://github.com/TuringLang/Turing.jl,A Turing complete probabilistic programming language.
+Probability-Statistics,"§1.2.1.Bayesian<spanid=""1-2-1-Bayesian""><span>",ArviZ.jl,https://github.com/arviz-devs/ArviZ.jl,"A Julia interface to the [ArviZ](https://arviz-devs.github.io/arviz/"") package for exploratory analysis of Bayesian models, with functions for posterior analysis, model checking, comparison and diagnostics."
+Probability-Statistics,"§1.2.1.Bayesian<spanid=""1-2-1-Bayesian""><span>",BayesNets.jl,https://github.com/sisl/BayesNets.jl,Bayesian Networks for Julia.
+Probability-Statistics,"§1.2.1.Bayesian<spanid=""1-2-1-Bayesian""><span>",BayesianDataFusion.jl,https://github.com/jaak-s/BayesianDataFusion.jl,Implementation of data fusion methods.
+Probability-Statistics,"§1.2.1.Bayesian<spanid=""1-2-1-Bayesian""><span>",BayesEstDiffusion.jl,https://github.com/mschauer/BayesEstDiffusion.jl,Bayesian estimation of diffusion processes.
+Probability-Statistics,"§1.2.1.Bayesian<spanid=""1-2-1-Bayesian""><span>",BayesianNonparametrics.jl,https://github.com/OFAI/BayesianNonparametrics.jl,Bayesian nonparametrics in Julia.
+Probability-Statistics,"§1.2.2.Gaussian<spanid=""1-2-2-Gaussian""><span>",GaussianMixtures.jl,https://github.com/davidavdav/GaussianMixtures.jl,Julia modules for Gaussian Mixture Models.
+Probability-Statistics,"§1.2.2.Gaussian<spanid=""1-2-2-Gaussian""><span>",GaussianProcesses.jl,https://github.com/STOR-i/GaussianProcesses.jl,A Julia package for Gaussian Processes.
+Probability-Statistics,"§1.2.3.Markovian<spanid=""1-2-3-Markovian""><span>",POMDPs.jl,https://github.com/JuliaPOMDP/POMDPs.jl,A Julia framework for solving Markov decision processes.
+Probability-Statistics,"§1.2.3.Markovian<spanid=""1-2-3-Markovian""><span>",POMDPToolbox.jl,https://github.com/JuliaPOMDP/POMDPToolbox.jl,Support tools for solving `POMDPs`.
+Probability-Statistics,"§1.2.3.Markovian<spanid=""1-2-3-Markovian""><span>",HMMBase.jl,https://github.com/maxmouchet/HMMBase.jl,A lightweight abstraction for hidden Markov models in Julia.
 Probability-Statistics,[REGRESSION](https://en.wikipedia.org/wiki/Regression_analysis),CovarianceMatrices.jl,https://github.com/gragusa/CovarianceMatrices.jl,Covariance Matrix Estimation in Julia.
 Probability-Statistics,[REGRESSION](https://en.wikipedia.org/wiki/Regression_analysis),CurveFit.jl,https://github.com/pjabardo/CurveFit.jl,Simple least squares and curve fitting functions.
 Probability-Statistics,[REGRESSION](https://en.wikipedia.org/wiki/Regression_analysis),FixedEffectModels.jl,https://github.com/FixedEffects/FixedEffectModels.jl,Fast estimation of linear models with IV and high dimensional categorical variables.
@@ -1891,9 +1892,9 @@ Probability-Statistics,[SAMPLING](),MonteCarloMeasurements.jl,https://github.com
 Probability-Statistics,[SAMPLING](),PSIS.jl,https://github.com/alvaro1101/PSIS.jl,Pareto smoothed importance sampling (PSIS) and PSIS leave-one-out cross-validation for Julia.
 Probability-Statistics,[SAMPLING](),RecombinatorKMeans.jl,https://github.com/carlobaldassi/RecombinatorKMeans.jl,An implementation of the recombinator-k-means method.
 Probability-Statistics,[SAMPLING](),StableDQMC.jl,https://github.com/crstnbr/StableDQMC.jl                   ,Numerical stabilization routines for determinant quantum Monte Carlo.
-Probability-Statistics,[TESTS](),HypothesisTests.jl,https://github.com/JuliaStats/HypothesisTests.jl,"T-tests, Wilcoxon rank sum (Mann-Whitney U), signed rank, and circular statistics in Julia."
-Probability-Statistics,[TESTS](),RobustStats.jl,https://github.com/mrxiaohe/RobustStats.jl,A collection of robust statistical tests based on the R package WRS (R-Forge repository) by Rand Wilcox.
-Probability-Statistics,UNCLASSIFIED,BloomFilters.jl,https://github.com/johnmyleswhite/BloomFilters.jl,are a probabilistic data structur e that can be used to test the inclusion and exclusion of items in a list.
+Probability-Statistics,TESTS,HypothesisTests.jl,https://github.com/JuliaStats/HypothesisTests.jl,"T-tests, Wilcoxon rank sum (Mann-Whitney U), signed rank, and circular statistics in Julia."
+Probability-Statistics,TESTS,RobustStats.jl,https://github.com/mrxiaohe/RobustStats.jl,A collection of robust statistical tests based on the R package WRS (R-Forge repository) by Rand Wilcox.
+Probability-Statistics,UNCLASSIFIED,BloomFilters.jl,https://github.com/johnmyleswhite/BloomFilters.jl,are a probabilistic data structure that can be used to test the inclusion and exclusion of items in a list.
 Probability-Statistics,UNCLASSIFIED,AdaGram.jl,https://github.com/sbos/AdaGram.jl,Adaptive Skip-gram implementation.
 Probability-Statistics,UNCLASSIFIED,Civecm.jl,https://github.com/andreasnoackjensen/Civecm.jl,Cointegration in Vector Error Correction Models in Julia.
 Probability-Statistics,UNCLASSIFIED,CTDE.jl,https://github.com/adolgert/CTDE.jl,"Continuous time, discrete event system in Julia."