---
title: "condTruncMVN: Conditional Truncated Multivariate Normal Distribution"
author: "Paul M. Hargarten"
date: "`r Sys.Date()`"
keywords: 
geometry: margin=1in
preamble: >
  \usepackage{indentfirst}
  \usepackage{amsmath}
  \usepackage{graphicx}
output: 
   rmarkdown::html_vignette: 
       toc: true
vignette: >
  %\VignetteIndexEntry{condTruncMVN: Conditional Truncated Multivariate Normal Distribution}
  %\VignetteEngine{knitr::rmarkdown}
  %\VignetteEncoding{UTF-8}
link-citations: true
citation_package: biblatex
bibliography: mnvignette.bib
csl: multidisciplinary-digital-publishing-institute.csl 
# csl: /Users/Shared/Zotero/styles/multidisciplinary-digital-publishing-institute.csl
---


```{r, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,  # If TRUE, all output would be in the code chunk.
  comment = "#>",
  fig.path = "man/figures/README-",
  out.width = "100%",
  results = "markup",
  prompt = TRUE,
  strip.white = TRUE,
  tidy = TRUE,
  tidy.opts = list(width.cutoff = 90), # options for tidy to remove blank lines [blank = FALSE] and set the approximate line width to be 80.
  fig.show = "asis",
  fig.height = 4.5,  # inches
  fig.width = 4.5   # inches
)
library("formatR")
```


<!-- 

Note on Function Names: 4/2/20
I decided to use \*cmvtruncnorm instead of \*cmvtnorm for clarity. THe difference between \*cmvtnorm and \*cmvnorm (absence of t) is confusing between the different packages. So:
pcmvtruncnorm()  , not pcmvtnorm()
dcmvtruncnorm()  , not dcmvtnorm()
rcmvtruncnorm()  , not rcmvtnorm()
And changed condtMVN() to condtruncMVN() for consistency. 
--->

The goal of condTruncMVN is to find densities, probabilities, and samples from a conditional truncated multivariate normal distribution. Suppose that **Z = (X,Y)** is from a fully-joint multivariate normal distribution of dimension *n* with **mean** $\boldsymbol\mu$ and covariance matrix **sigma** ( _$\Sigma$_ ) truncated between **lower** and **upper**. Then, Z has the density
$$
f_Z(\textbf{z}, \boldsymbol\mu, \Sigma, \textbf{lower}, \textbf{upper})=
\frac{exp(-\frac{1}{2}*(\textbf{z}-\boldsymbol\mu)^T \Sigma^{-1} (\textbf{z}-\boldsymbol\mu))}
{\int_{\textbf{lower}}^{\textbf{upper}} 
exp(-\frac{1}{2}*(\textbf{z}-\boldsymbol\mu)^T \Sigma^{-1} (\textbf{z}-\boldsymbol\mu)) d\textbf{z}}
$$
for all **z** in [**lower**, **upper**] in $\mathbb{R^{n}}$.


This package computes the conditional truncated multivariate normal distribution of Y|X. The conditional distribution follows a truncated multivariate normal [@horraceResultsMultivariateTruncated2005]. Specifically, the functions are arranged such that

$$  Y = Z[ , dependent.ind]  $$
$$  X = Z[ , given.ind] $$
$$  Y|X = X.given \sim  MVN(mean, sigma, lower, upper) $$
  The [d,p,r]cmvtnorm() functions create a list of parameters used in truncated conditional normal and then passes the parameters to the source function below. 

    
| Function Name  | Description | Source Function | Univariate Case| Additional Parameters
|----------      | ------------| ----------      | ------------ |  --------------------- |  
| condtMVN  | List of parameters used in truncated conditional normal.| condMVNorm:: condMVN() |  |  |
| dcmvtnorm | Calculates the density f(Y=y\| X = X.given) up to a constant. The integral of truncated distribution is not computed. |  tmvtnorm:: dtmvnorm() | truncnorm:: dtruncnorm() | y, log |
| pcmvtnorm | Calculates the probability that Y\|X is between lowerY and upperY given the parameters. |  tmvtnorm:: ptmvnorm() | truncnorm:: ptruncnorm() |  lowerY, upperY, maxpts, abseps, releps |
| rcmvtnorm | Generate random sample. | tmvmixnorm:: rtmvn() |  truncnorm:: rtruncnorm()  | n, init, burn, thin |


## Installation

You can install the released version of condTruncMVN from [CRAN](https://CRAN.R-project.org) with `install.packages("condTruncMVN")`.  You can load the package by:
```{r}
library("condTruncMVN")
```

And the development version from [GitHub](https://github.com/) with:

<!--
```{r, include=FALSE}
# install.packages("devtools")
#  devtools::install_github("phargarten2/ggplot2")
```
-->

## Example

Suppose $X2,X3,X5|X1 = 1,X4 = -1 \sim N_3(1, Sigma, -10, 10)$. The following code finds the parameters of the distribution, calculates the density, probability, and finds random variates from this distribution.

```{r example}
library(condTruncMVN)
d <- 5
rho <- 0.9
Sigma <- matrix(0, nrow = d, ncol = d)
Sigma <- rho^abs(row(Sigma) - col(Sigma))
Sigma
```


First, we find the conditional Truncated Normal Parameters. 
```{r}
condtMVN(mean  = rep(1, d),
  sigma = Sigma,
  lower = rep(-10, d),
  upper = rep(10, d),
  dependent.ind = c(2, 3, 5),
  given.ind = c(1, 4), X.given = c(1, -1)
)
```

Find the log-density when X2,X3,X5 all equal $0$:
```{r}
dcmvtruncnorm(
  rep(0, 3),
  mean  = rep(1, 5),
  sigma = Sigma,
  lower = rep(-10, 5),
  upper = rep(10, d),
  dependent.ind = c(2, 3, 5),
  given.ind = c(1, 4), X.given = c(1, -1),
  log = TRUE
)
```

Find $P( -0.5 < X2,X3,X5 < 0 | X1 = 1,X4 = -1)$: 
```{r}
pcmvtruncnorm(
  rep(-0.5, 3), rep(0, 3),
  mean = rep(1, d),
  sigma = Sigma,
  lower = rep(-10, d),
  upper = rep(10, d),
  dependent.ind = c(2, 3, 5),
  given.ind = c(1, 4), X.given = c(1, -1)
)
```

Generate two random numbers from the distribution.
```{r}
set.seed(2342)
rcmvtruncnorm(2,
  mean = rep(1, d),
  sigma = Sigma,
  lower = rep(-10, d),
  upper = rep(10, d),
  dependent.ind = c(2, 3, 5),
  given.ind = c(1, 4), X.given = c(1, -1)
)
```

Another Example: To find the probability that $X1|X2, X3, X4, X5 \sim N(**1**, Sigma, **-10**, **10**)$
is between -0.5 and 0: 
```{r}
pcmvtruncnorm(-0.5, 0,
  mean  = rep(1, d),
  sigma = Sigma,
  lower = rep(-10, d),
  upper = rep(10, d),
  dependent.ind = 1,
  given.ind = 2:5, X.given = c(1, -1, 1, -1)
)
```


If I want to generate 2 random variates from $X1|X2, X3, X4, X5 \sim N(**1**, Sigma, **-10**, **10**)$: 
```{r}
set.seed(2342)
rcmvtruncnorm(2,
  mean  = rep(1, d),
  sigma = Sigma,
  lower = rep(-10, d),
  upper = rep(10, d),
  dependent.ind = 1,
  given.ind = 2:5, X.given = c(1, -1, 1, -1)
)
```




## Computational Details

This vignette is successfully processed using the following. 
```{r echo=FALSE}
# sessioninfo::session_info() # makes a mess! Instead

cat(" -- Session info ---------------------------------------------------")
sessioninfo::platform_info()
cat("--  Packages -------------------------------------------------------")
tmp.df <- sessioninfo::package_info(
  c("condMVNorm", "matrixNormal", "tmvmixnorm", "tmvtnorm", "truncnorm"),
  dependencies = FALSE
)
print(tmp.df)
```

## Final Notes

Please note that the 'condTruncMVN' package is released with a ![Contributor Code of Conduct](../CODE_OF_CONDUCT.md). By contributing to this project, you agree to abide by its terms.

<!-- badges: start 
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[![CRAN status](https://www.r-pkg.org/badges/version/condTruncMVN)](https://CRAN.R-project.org/package=condTruncMVN)

## References
