---
title: "Exploratory Regression Shiny App"
author: "Catherine B. Hurley"
date: "`r Sys.Date()`"
output: rmarkdown::html_vignette
vignette: >
  %\VignetteIndexEntry{Exploratory Regression Shiny App}
  %\VignetteEngine{knitr::rmarkdown}
  \usepackage[utf8]{inputenc}
---

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

The Exploratory Regression Shiny App (ERSA) package consists of a collection of functions for displaying the
results of a regression calculation, which are then packaged together as a shiny app function.

To use ERSA first do
```{r}
library(ERSA)
```
Then construct a regression model of your choice.
```{r eval=F}
f <- lm(Fertility ~ . , data = swiss)
exploreReg(f,swiss)
```
Here is a screen shot of the result:

```{r echo=FALSE, out.width='100%'}
knitr::include_graphics('swiss1.png')
```

## The summary or drop1 display
The app display consists of four panels. In the top left corner is a display of the model summary
t-statistics, from
```{r}
f <- lm(Fertility ~ . , data = swiss)
summary(f)
```
This display (Plot1) shows the magnitude of each t-statistic. The red dashed line
shows the 5% significance level. There are a few other options for this display.
The display may be switched to "CI", which shows parameter confidence intervals or
"CI stdX" for confidence intervals in standard X units. If the model contains
factors with more than two levels, then better choices are "F stat" or "Adj. SS".
These give the summaries from the Sum of Sq or F stat columns of the drop1 results:
```{r}
drop1(f, test="F")
```
Clicking on this display removes the closest predictor, clicking again adds it 
in. Once a predictor is added or dropped, this change is also reflected in the other
ERSA displays.

When  FixedScales box near Plot1 is ticked, the axes on Plot1 remain unchanged as predictors
are added or dropped. Sometimes the extent on the x-axis is not large enough, or is too large,
in this case untick the FixedScales box and the x-axis will vary to accomodate
the included predictors.

## The anova display
The second panel in the top right shows the results of
```{r}
anova(f)
```
as Plot2. Each predictor of this output is represented by a coloured slice, whose height
represents the sum of squares. These sums of squares depend on the order in
which predictors were entered into the model fit. The second barchart (Plot3) represents
the anova table obtained by reversing the predictor order.
The dropdown menus give other choices. Forwards and backwards give the
order of predictors as visited by the forwards and backwards selection algorithms.
By choosing order "Random", a user can click on a slice to move it up one position,
or double click to move it down. 

## The Parallel coordinates plot display

The lower part of the app has a parallel coordinate plot on the lower right,
and a control panel on the left.
The user can choose to show either (i) Variables (ii) Residuals, (iii) Hatvalues
and (iv) CooksD.
Each axis is assigned to a variable, using the order from Plot1, Plot2 and Plot3.
The residuals and hatvalues are obtained by leaving out one predictor at a time, if the
selected order is Plot1, or by adding predictors in sequence if the order is Plot2 or Plot3.
When residuals are plotted, the Difference option when selected shows the difference

Specifically, let $e$ denote the vector of residuals from the full model and let
$e^{-j}$ denote the residual vector from the fit using all  predictors except the $j$th.
When residuals are selected, using order from Plot1,
the PCP  shows $e^{-j}$ on the $j$th axis, or $e^{-j} - e$ when the Difference button is selected
in Residual options. Let $e^{j}$ be the residuals from the model including the first $j$ predictors.
When Residuals are selected, using order from Plot2 or Plot3, the PCP  shows $e^{j}$ on the $j$th axis, or $e^{j} - e^{j-1}$ when the Difference button is selected
in Residual options.
For any of the Plot orders, when the Absolute button is selected,
either absolute residuals or absolute residual differences are plotted.

Dragging a brush over the PCP axes will highlight cases and print information for the selected cases.
Clicking on Remove Brushed will remove the highlighted cases from view. All regression models
are recalculated and the displays are updated. Clicking the All Cases buttom
will update all displays to use the complete dataset.
Double clicking on the PCP itself will un-highlight all cases.

## Individual plots

There are functions to construct static plot versions of all the plots in the Exploratory
Regression shiny app.

For the Plot1 displays use
```{r fig.width=4, fig.height=4, fig.align='center'}
plottStats(f)
cols <- termColours(f)
plottStats(f, cols)
```

or 
```{r eval=F}
plotCIStats(f,cols)
plotCIStats(f, cols,stdunits=TRUE)
plotAnovaStats(f, cols,type="F")
plotAnovaStats(f, cols,type="SS")
```

For the Plot2 displays use
```{r fig.width=6, fig.height=4}
fr <- revPredOrder(f, swiss)
plotSeqSS(list(f,fr), cols,legend=TRUE)
```

Other orders are
```{r eval=F}
fselOrder(f)
bselOrder(f)
randomPredOrder(f)
regsubsetsOrder(f)
```

To plot the PCP display of the data use:
```{r fig.width=7,fig.height=4, fig.align='center'}
pcpPlot(swiss, f)
```
Cases are automatically coloured by the magnitude of the response.


To plot a PCP display of the residuals leaving out one predictor at
a time use
```{r fig.width=7,fig.height=4,fig.align='center'}
pcpPlot(swiss, f, type="Residuals")
```

In residual, hatvalue and CooksD plots cases are automatically coloured by the magnitude of full model residuals.
Using the option sequential=T gives the residuals adding model terms in sequence,
as they appear in the supplied fit f.

Swapping "Residuals" with "Hatvalues"  shows the fit hat values,
similarly "CooksD".
```{r fig.width=7, fig.height=4,fig.align='center'}
pcpPlot(swiss, f, type="Hatvalues", sequential=T)
```
