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Last updated: 2022-04-26

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Knit directory: fiveMinuteStats/analysis/

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File	Version	Author	Date	Message
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html	a5a03a1	Matthew Stephens	2020-03-01	Build site.
Rmd	66fc13f	Matthew Stephens	2020-03-01	gaussian_process.Rmd
html	5f62ee6	Matthew Stephens	2019-03-31	Build site.
Rmd	0cd28bd	Matthew Stephens	2019-03-31	workflowr::wflow_publish(all = TRUE)
html	dbcff1f	stephens999	2019-01-23	Build site.
Rmd	7a0ba80	stephens999	2019-01-23	workflowr::wflow_publish(“analysis/index.Rmd”)
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Rmd	e8e0399	stephens999	2018-05-17	wflow_publish(“analysis/index.Rmd”)
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Rmd	5530e01	stephens999	2018-05-03	workflowr::wflow_publish(“analysis/index.Rmd”)
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Rmd	1077c97	stephens999	2018-04-23	workflowr::wflow_publish(c(“analysis/index.Rmd”, “analysis/MH_intro.Rmd”,
html	30630b2	stephens999	2018-04-23	Build site.
Rmd	5c310c2	stephens999	2018-04-23	MH_intro.Rmd
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Rmd	a7ec7b7	stephens999	2018-04-23	workflowr::wflow_publish(c(“analysis/index.Rmd”,
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Rmd	9e15ba0	stephens999	2018-04-23	workflowr::wflow_publish(c(“analysis/index.Rmd”,
html	d41d022	stephens999	2017-04-24	Build site.
Rmd	f012c1d	stephens999	2017-04-24	Files commited by wflow_commit.
html	c1d0c3f	stephens999	2017-04-17	update index
Rmd	72ef4ea	stephens999	2017-04-17	Files commited by wflow_commit.
html	c7e182b	stephens999	2017-04-17	Build site.
Rmd	9f09eca	stephens999	2017-04-17	Files commited by wflow_commit.
html	34bcc51	John Blischak	2017-03-06	Build site.
Rmd	2aa70fe	John Blischak	2017-03-06	Manually udpate some Rmd files.
html	8e61683	Marcus Davy	2017-03-03	rendered html using wflow_build(all=TRUE)
html	fffe50c	stephens999	2017-02-20	Build site.
Rmd	92d7daa	stephens999	2017-02-20	Files commited by wflow_commit.
html	20c6639	stephens999	2017-02-19	Build site.
Rmd	d20b048	stephens999	2017-02-19	Files commited by wflow_commit.
html	9778b49	stephens999	2017-02-19	Build site.
Rmd	592db57	stephens999	2017-02-19	Files commited by wflow_commit.
html	48bf85f	stephens999	2017-01-28	Build site.
Rmd	ca3b3b6	stephens999	2017-01-28	Files commited by wflow_commit.
html	fbfa018	stephens999	2017-01-28	Build site.
Rmd	2c4f22e	stephens999	2017-01-28	Files commited by wflow_commit.
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Rmd	fc0336e	stephens999	2017-01-24	Files commited by wflow_commit.
html	c3b365a	John Blischak	2017-01-02	Build site.
Rmd	ae24830	stephens999	2016-09-04	add example of computing LR on different data
Rmd	966d6f6	stephens999	2016-05-17	Merge branch ‘gh-pages’ of https://github.com/jhmarcus/fiveMinuteStats into jhmarcus-gh-pages
Rmd	6bb4560	stephens999	2016-05-12	add gibbs sampling example
Rmd	a72861e	stephens999	2016-05-02	add integral
Rmd	153e684	stephens999	2016-05-02	add IS
Rmd	8466ce3	stephens999	2016-05-02	add gibbs sampling example
Rmd	47f75ca	stephens999	2016-04-20	add BF and p value comparison
Rmd	c5e07f5	Xiao Nan	2016-04-13	add shiny conjugate normal app link to index
Rmd	ed83285	jhmarcus	2016-04-07	added popgen section to index and wright_fisher tutorials
Rmd	f1dd5fc	stephens999	2016-04-04	update index
Rmd	106d322	mbonakda	2016-02-24	add new notes to index
Rmd	294d219	stephens999	2016-02-16	add normal markov chain example
Rmd	be2da01	stephens999	2016-02-15	add multivariate normal
Rmd	0ba385e	mbonakda	2016-02-06	update index
Rmd	d1b8aae	jnovembre	2016-02-05	Changed sub-headings
Rmd	dce7ece	jnovembre	2016-02-05	modified index.html to add Poisson process and fix typo
Rmd	1187afb	mbonakda	2016-02-02	fix typos
Rmd	ac0ba21	mbonakda	2016-02-02	add to index
Rmd	313901b	jnovembre	2016-01-31	Modified index and added html
Rmd	ad8b7b5	mbonakda	2016-01-30	update names
Rmd	4e0c4fd	mbonakda	2016-01-30	update index
Rmd	4335247	mbonakda	2016-01-23	fix index typo
Rmd	9d4269b	mbonakda	2016-01-23	add simulating discrete chains to index
Rmd	b0339a9	stephens999	2016-01-19	update index
Rmd	9156677	stephens999	2016-01-19	add multiclass example
Rmd	ff6b857	mbonakda	2016-01-12	add asymptotic normality of MLE and wilks
Rmd	3ee2cf4	stephens999	2016-01-12	add likelihood function
Rmd	d6f4bea	stephens999	2016-01-12	add examples
Rmd	6feeb2e	stephens999	2016-01-11	update index
Rmd	8b7278d	stephens999	2016-01-11	add LR for continuous data
Rmd	93476ef	stephens999	2016-01-07	update LR to make clear it is for discrete data
Rmd	8f61232	stephens999	2016-01-07	add simple LR example
Rmd	f1b8c7c	stephens999	2016-01-05	add likelihood and loglikelihood
Rmd	90df5f8	stephens999	2016-01-05	tidy up material related to ashlar by removing much of it
Rmd	d3c8f4e	jhsiao999	2015-12-12	fix typo
Rmd	10bba89	jhsiao999	2015-12-12	add tutorial
Rmd	99f4499	jhsiao999	2015-12-12	add a Rmarkdown example
Rmd	1b891a0	jhsiao999	2015-12-12	first commit

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Inference

Likelihood Ratio and Likelihood

• Likelihood Ratio for fully specified models, discrete data
• Likelihood Ratio for fully specified models, continuous data
• Likelihood Ratios: Examples and Pitfalls
  • Examples and Pitfalls
  • Example: LRs must be computed on same data
• Likelihood Ratios: how big is convincing?
• Likelihood Ratios: Wilks’s Theorem
• The Likelihood Function
• Asymptotic Normality of MLE

Bayesian Inference

• Bayesian inference for comparing two fully-specified models
• Bayesian inference for comparing multiple fully-specified models
• Bayesian inference for a continuous parameter: analytic calculation
• Bayesian inference for a continuous parameter: summarizing the posterior
• Bayesian inference for a continuous parameter: conjugacy
• Bayesian inference for a normal mean
• Bayesian inference for a normal mean (shiny app illustration)
• Bayesian inference for multiple independent parameters

Empirical Bayes

• The Empirical Bayes Normal Means problem

Frequentist vs Bayesian Inference

• The difficulty calibrating p values
• Relationship between Bayes Factor and p value
• Conditional coverage of a standard normal CI

Decision Theory

• Making a decision under uncertainty: the two class problem
• Brief introduction to decision theory for prediction problems

Mixture Models

• Introduction to Mixture Models

• Introduction to the EM algorithm

• A variational view of the EM algorithm

• EM for Gaussian Mixture Models

• Archive: Alternative Introduction to Mixture Models

Bayesian Computation

• Every Bayesian computation is an integral (or a sum)
• Importance sampling

Markov Chain Monte Carlo

• The Metropolis–Hastings algorithm
• The Metropolis–Hastings algorithm 2
• Simple examples of Metropolis–Hastings algorithm
• Introduction to Gibbs Sampling
• Gibbs Sampling for a univariate normal mixture
• Gibbs Sampling for a mixture of product-bernoullis

Hidden Markov Models

• Forwards Backwards calculation example

Distributions

• The Beta Distribution
• The Dirichlet Distribution
• The Pólya–Gamma Distribution

Stochastic Processes

Discrete-Time Markov Chains

• Discrete-Time Markov Chains: Introduction
• Discrete-Time Markov Chains: Finding the Stationary Distribution via solution of the global balance equations
• Discrete-Time Markov Chains: Finding the Stationary Distribution via eigendecomposition
• Simulating Discrete-Time Markov Chains: An Introduction
• Simulating Discrete-Time Markov Chains: Limiting Distributions

Poisson Processes

• Poisson Processes: Thinning with time-dependent probabilities
• Poisson Process: The Limiting Case of the Bernoulli Process

Methods for sampling non-standard distributions

• Inverse Transform Sampling

Multivariate Normal

• A key property of univariate normal
• Bivariate normal distribution
• Multivariate Normal
• The precision matrix
• Interpreting \(N(\mu,\Sigma)\) via eigen-decomposition of \(\Sigma\)

Gaussian Process

• Introduction to Gaussian Processes

Population Genetics

• Simulating from a simple genetic mixture model
• Wright-Fisher Model
• Wright-Fisher Model Approximations

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