---
title: "Introduction"
output: rmarkdown::html_vignette
vignette: >
  %\VignetteEngine{knitr::rmarkdown}
  %\VignetteIndexEntry{Introduction}
  \usepackage[utf8]{inputenc}
---

```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE, eval = TRUE)
options(rmarkdown.html_vignette.check_title = FALSE)
```

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This R-package `moewishart` provides maximum likelihood estimation (MLE) and Bayesian estimation for the **Wishart mixture model** and the **Wishart mixture-of-experts** (**MoE-Wishart**) model. 
It implements four different inference algorithms for the two model:

- mixture model of Wishart distributions:
    - EM algorithm for finding the MLE;
    - Bayesian approach using Gibbs-within-MH sampling algorithm.
- Mixture-of-Expert model, in which the gating probabilities depend on covariates:
   - EM-MoE algorithm for finding the MLE;
   - Bayesian-MoE approach using a Gibbs-within-MH sampling algorithm.  


## Installation

Install the latest released version from [CRAN](https://CRAN.R-project.org/package=moewishart):

```{r eval=FALSE}
install.packages("BayesSUR")
```

Install the latest development version from [GitHub](https://github.com/zhizuio/moewishart):

```{r eval=FALSE}
# library("devtools")
devtools::install_github("zhizuio/moewishart")
```

## Example


<br> 

Data simulation from a MoE-Wishart model:

- Sample size $n = 200$
- Dimension of the Wishart distribution $p = 2$
- Number of latent components $K = 3$
- $q=3$ gating covariates $\mathbf X = [x_{ij}] \in \mathbb R^{n\times q}$, $x_{ij}\sim\text{N}(0,1)$, $i=1,...,n$, $j=1,...,q$
- Fixed covariate effects $\boldsymbol\beta=[\boldsymbol\beta_1,...,\boldsymbol\beta_K] \in \mathbb R^{q\times K}$, with $\boldsymbol\beta_{K}=0$
- Probabilities of subpopulations $\boldsymbol\pi = [\pi_{ik}] \in \mathbb R^{n\times q}$, $\pi_{ik} = \exp(\mathbf X_i\boldsymbol\beta_k) / \sum_{l=1}^K\exp(\mathbf X_i\boldsymbol\beta_l)$, $k=1,...,K$
- Degrees of freedom $\boldsymbol\nu = (\nu_1,\nu_2,\nu_3) = (8, 12, 3)$
- Scale matrices of the Wishart distribution $\Sigma_1$, $\Sigma_2$, $\Sigma_3 \in \mathbb R^{p\times p}$
- Data $S_i \sim \pi_{i1}\text{Wishart}(\nu_1, \Sigma_1) + \pi_{i2}\text{Wishart}(\nu_2, \Sigma_2) + \pi_{i3}\text{Wishart}(\nu_3, \Sigma_3)$


### 1. Working model: Bayesian MoE-Wishart model

```{r, results='hide'}
library(moewishart)

n <- 200 # number of subjects
p <- 2 # dimension of covariance matrix
set.seed(123) # fix coefficients of underlying MoE model
Xq <- 3
K <- 3
betas <- matrix(runif(Xq * K, -2, 2), nrow = Xq, ncol = K)
betas[, K] <- 0

# simulate data
dat <- simData(n, p,
  Xq = 3, K = 3, betas = betas,
  pis = c(0.35, 0.40, 0.25),
  nus = c(8, 12, 3)
)

# fit Bayesian MoE-Wishart model
set.seed(123)
fit <- moewishart(
  dat$S,
  X = cbind(1, dat$X), K = 3,
  mh_sigma = c(0.2, 0.1, 0.2), # RW-MH variances (length K)
  mh_beta = c(0.3, 0.3), # RW-MH variances (length K-1)
  niter = 3000, burnin = 1000
)
```

<br> 

Posterior means for degrees of freedom (DoF) of Wishart distributions:

```{r}
burnin <- 1000
nu_mcmc <- fit$nu[-c(1:burnin), ]
colMeans(nu_mcmc)
```

<br> 
True DoF:

```{r}
dat$nu # true nu
```

<br> 
Posterior means for scale matrices of Wishart distributions:

```{r}
MoE_Sigma <- Reduce("+", fit$Sigma) / length(fit$Sigma)
MoE_Sigma
```

<br> 
Posterior means for gating coefficients:

```{r}
beta_mcmc <- fit$Beta_samples[-c(1:burnin), , ]
apply(beta_mcmc, c(2, 3), mean)
```


### 2. Working model: Bayesian Wishart mixture model

```{r, results='hide'}
# fit Bayesian Wishart mixture model
set.seed(123)
fit2 <- mixturewishart(
  dat$S,
  K = 3,
  mh_sigma = c(0.2, 0.1, 0.2), # RW-MH variances
  niter = 3000, burnin = 1000
)
```

<br> 
Posterior means for subpopulation probabilities:

```{r}
colMeans(fit2$pi[-c(1:burnin), ])
```

<br> 

Posterior means for DoF of Wishart distributions:

```{r}
colMeans(fit2$nu[-c(1:burnin), ])
```


### 3. Working model: MoE-Wishart model via EM algorithm

```{r}
# fit MoE-Wishart model via EM alg.
set.seed(123)
fit3 <- moewishart(
  dat$S,
  X = cbind(1, dat$X), K = 3,
  method = "em",
  niter = 3000
)
```

<br> 

EM estimates for DoF of Wishart distributions:

```{r}
fit3$nu
```

<br> 
EM estimates for Wishart scale matrices:

```{r}
fit3$Sigma
```

<br> 
EM estimates for gating coefficients:

```{r}
fit3$Beta
```


### 4. Working model: Wishart mixture model via EM algorithm

```{r}
# fit Wishart mixture model via EM alg.
set.seed(123)
fit4 <- mixturewishart(
  dat$S,
  K = 3,
  method = "em",
  niter = 3000
)
```

<br> 
EM estimates for DoF of Wishart distributions:

```{r}
fit4$nu
```

<br> 
EM estimate for Wishart scale matrices:

```{r}
fit4$Sigma
```



