---
author: "Metodiev Martin"
date: "`r Sys.Date()`"
output: rmarkdown::html_vignette
vignette: >
  %\VignetteEngine{knitr::knitr}
  %\VignetteIndexEntry{univmixtures}
  %\usepackage[UTF-8]{inputenc}
---

```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = FALSE)
library(mvtnorm)
library(scov)
```

## Modelling the data

In this example, the correlation matrix of the data is a linear combination
of the following covariates:

1. The intercept

```{r intercept}
intercept = matrix(1,ncol=4,nrow=4)
corrplot::corrplot(intercept,method = "square")
mtext("intercept", side = 2, line = 0, cex = 1)
```
2. X1

```{r X1}
X1 = rbind(c(1,1,1,0),c(1,1,1,0),c(1,1,1,0),c(0,0,0,1))
corrplot::corrplot(X1,method = "square")
mtext("X1", side = 2, line = 0, cex = 1)
```
2. X2

```{r X2}
X2 = rbind(c(1,0,0,0),c(0,1,1,1),c(0,1,1,1),c(0,1,1,1))
corrplot::corrplot(X2,method = "square")
mtext("X2", side = 2, line = 0, cex = 1)
```

3. The interaction between X1 and X2

```{r interaction}
corrplot::corrplot(X2*X1,method = "square")
mtext("interaction between X1 and X2", side = 2, line = 0, cex = 1)
```
Let's combine all these covariates into a list.

```{r covariate list}
covar_mats = list(intercept=intercept,X1=X1,X2=X2)
```

4. There is also a spatial effect, which has the following adjacency matrix:

```{r spatial}
adj_matrix = rbind(c(0,1,0,0),c(1,0,0,0),c(0,0,0,1),c(0,0,1,0))
corrplot::corrplot(adj_matrix,method = "square")
mtext("adjacency matrix", side = 2, line = 0, cex = 1)
```

## Preparing the data

We simulate data from the standard normal distribution:

```{r load data}
mean = rep(0,4)
sigma = 0.05*intercept+0.2*X1+0.2*X2+0.1*X2*X1+0.4*(diag(4) + adj_matrix)
diag(sigma) = 1
num_observations = 100
dataset = mvtnorm::rmvnorm(num_observations,mean=mean,sigma=sigma)
```

The correlation matrix of this distribution is a weighted sum of the covariates:

```{r show sigma}
corrplot::corrplot(sigma,method = "square")
mtext("correlation matrix", side = 2, line = 0, cex = 1)
```

## Computing the WSCE, SCE and IVE

The SCE estimates the linear coefficients of the covariates to estimate the
correlation matrix. Notice how the squares representing different covariates 
have different sizes and colors.

```{r compute sce}
sce = scov::scov(covar_mats, dataset, adj_matrix,
                 interaction_effects=list(c("X1","X2")),
                 ncores=1,parallelize=FALSE,verbose=FALSE)
corrplot::corrplot(sce$corrmat_estim,method = "square")
mtext("SCE", side = 2, line = 0, cex = 1)
```

Suppose that one suspects that the data does not follow a normal distribution.
In that case, one should use our semiparamteric estimator, the IVE.

Let's initialize the data from a different distribution,

```{r initialize non-normal data}
dataset = mvtnorm::rmvt(num_observations,sigma=sigma,df=2) + matrix(runif(4*num_observations,max=10001,min=10000),nrow=num_observations,ncol=4)
```

and compute the IVE:

```{r compute ive}
ive = scov::scov(covar_mats, dataset, adj_matrix,
                 interaction_effects=list(c("X1","X2")),
                 semiparametric=TRUE,
                 ncores=1,parallelize=FALSE)
corrplot::corrplot(ive$corrmat_estim,method = "square")
mtext("IVE", side = 2, line = 0, cex = 1)
```
One might also be worried about the model not being specified correctly.
For example, one of the covariates could be unknown. In this case, one should
use the WSCE.

Let us, e.g., suppose that we do not know that interactions are present. Let
us simulate the data from the same normal distribution,

```{r load data 2}
mean = rep(0,4)
sigma = 0.05*intercept+0.2*X1+0.2*X2+0.1*X2*X1+0.4*(diag(4) + adj_matrix)
diag(sigma) = 1
dataset = mvtnorm::rmvnorm(num_observations,mean=mean,sigma=sigma)
```

but compute the WSCE without X2 (NOTE: a lot faster if parallelize=TRUE and ncores>1):

```{r compute wsce}
covar_mats = list(intercept=intercept,X1=X1)
wsce = scov::scov(list(X1=X1), dataset, adj_matrix,
                  misspecification = TRUE,
                  parallelize = FALSE,
                  ncores=1,verbose=FALSE)
corrplot::corrplot(wsce$corrmat_estim,method = "square")
mtext("WSCE", side = 2, line = 0, cex = 1)
```
Notice that the parameter lambda is far away from 1, indicating
that the model is misspecified.

```{r show lambda}
paste0("lambda: ",wsce$lambda)
```