---
title: "Introduction to condvis2"
author: "Catherine B. Hurley"
date: "`r Sys.Date()`"
output: rmarkdown::html_vignette
vignette: >
  %\VignetteIndexEntry{Introduction to condvis2}
  %\VignetteEncoding{UTF-8}
  %\VignetteEngine{knitr::rmarkdown}
editor_options: 
  chunk_output_type: console
---

```{r setup, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.width=5, fig.height=5 ,fig.align="center"
)
fpath <- "vignettefigs/"
```


This vignette is an introduction to condvis2. This package constructs shiny-based interactive
visualisations of prediction models.


## Ozone data

We will use the airquality data built in to R.

```{r}
ozone <- na.omit(airquality)
```

The first fit we consider uses Wind only to predict ozone. 
Here we construct the fit and plot the results.
```{r }
fit1 <- loess(Ozone~Wind, data=ozone)
plot(Ozone~Wind, data=ozone, xlim=c(1.5, 21), ylim=c(-5,175))
wind <- seq(min(ozone$Wind),  max(ozone$Wind), length.out=30)
lines(wind, predict(fit1, data.frame(Wind=wind)))
```


If we add in a second predictor, we can either move to plotting the surface,
or plot how the fit relates to one predictor, for a fixed value of another.

```{r fig.width=7.3, fig.height=2.7}
fit2 <- loess(Ozone~Wind+Solar.R, data=ozone)
par(mfrow=c(1,3))
par(mar=c(5,5,3,1))
for (s in quantile(ozone$Solar.R, c(.25,.5,.75))){
plot(Ozone~Wind, data=subset(ozone, Solar.R <= s+20 & Solar.R >= s-20),
     xlim=c(1.5, 21),ylim=c(-5,175), main=paste0("Solar.R=",s))
lines(wind, predict(fit2, data.frame(Wind=wind, Solar.R= s)))
}
```

Notice in the above plots we are only plotting observations where Solar.R values are
close to the value used for prediction.

These plots can be constructed interactively in `condvis2`:

```{r eval=F}
suppressMessages(library(condvis2))
condvis(ozone, fit2,sectionvars="Wind", conditionvars="Solar.R")
```

This gives the following display:

```{r echo=FALSE, out.width='100%'}
knitr::include_graphics(paste0(fpath, "ozone.png"))
```

- The histogram on the right shows the values for Solar.R.
- The selected value of Solar.R is 207. By clicking on the histogram,
you can change this selection.
- The main display (on the left) shows the predicted values of Ozone, varying Wind
and fixing Solar.R at $f_2 =207$.
- Only observations which have Solar.R values near 207 are shown,i.e.,
observations whose $d_i = |x_{i,2} - f_2|<1$, where Solar.R values  are measured
in standard units.
- The nearness required can be increased or decreased from 1 by moving the Similarity Threshold
slider. 
- Also, point colours
fade to reflect the distances $d_i$, so points very near or on the section are dark blue,
with colour fading as distance increases.
- You can exchange the roles of Solar.R and Wind by choosing Solar.R in the `Choose a sectionvar` menu.

In this way we can see how well the curve fits to observations in its section.

If we include another predictor in the fit

```{r }
fit3 <- loess(Ozone~Wind+Solar.R+Temp, data=ozone)
```

and invoke condvis

```{r eval=F}
condvis(ozone, fit3, sectionvars="Wind", conditionvars=c("Solar.R", "Temp"))
```
the result is  shown in the screenshot below.

```{r echo=FALSE, out.width='100%'}
knitr::include_graphics(paste0(fpath, "ozone1.png"))
```

- The plot on the right shows the values for Solar.R and Temp. By clicking
on this plot, you can change the selected values.
- The main display (on the left) shows the predicted values of Ozone, varying Wind
and fixing Solar.R and Temp.
- Only observations which have Solar.R and Temp values near the pink
cross are shown.The distance is calculated as
\[ d_i = max(|x_{i,2} - f_2|, |x_{i,3} - f_3|)<1,\]
where $f_2$ and $f_3$ are the fixed values
of Solar.R and Temp, and $(x_{i,2}, x_{i,3})$ are the observation coordinates (all standardised).
- Again, point colours
fade to reflect the distances $d_i$.
- The plot on the right shows all the observations, but points near the pink cross
(those visible in the main plot) are slightly larger with a dark outline.

## Two section variables

You can also pick a second section variable, to see how the fitted surface looks as a function
of two variables, while the third is modified interactively.

```{r echo=FALSE, out.width='100%'}
knitr::include_graphics(paste0(fpath, "ozone4.png"))
```
The image shows  fitted surface levels as a function of two predictors. The points shown
are near the fixed conditioning values. 
For an image plot, the point colour represents
the observed response, coloured in the same way as the fitted surface.
Here we convey the distance of an observations condition values to the
fixed condition levels by size. You will see some points in the main display
whose colour does not match the image colour, for example,
the two darker points around Wind=10, with low Solar.R. As the points are large,
they are near the conditioning values which are poorly fit.

There is very little data at low Temp, and none of these observations
have a Wind value below 7. So the steep incline at the left hand side of the
main plot is not supported by the data. Prediction in this area is extrapolation.


```{r echo=FALSE, out.width='100%'}
knitr::include_graphics(paste0(fpath, "ozone3.png"))
```

Alternatively, the relationship between Ozone and (Wind, Solar.R) for fixed Temp
may be displayed as a 3-d surface. The points near the selected value of Temp are
dark blue, lightening in colour as the distance increases. The residual sizes are
shown via line segments.

## Comparing two fits

We could fit a second fit to the same data and compare the results.

```{r eval=F}
library(e1071)
fit4 <- svm(Ozone~Wind+Solar.R+Temp, data=ozone)
condvis(ozone, list(loess=fit3,svm=fit4), sectionvars="Wind", conditionvars=c("Solar.R", "Temp"))
```

```{r echo=FALSE, out.width='100%'}
knitr::include_graphics(paste0(fpath, "ozone5.png"))
```

We see big differences between the fits, especially for low Wind.

Note: condvis uses CVpredict to extract predictions from fitted models. By default
CVpredict uses predict, but there are customised versions of CVpredict for many fit
types. (See the help page.)

## Confidence intervals


Condvis2  supports confidence intervals, for fits that offer them.

Use

```{r eval=F}
fit5 <- lm(Ozone~Wind+Solar.R+Temp, data=ozone)
condvis(ozone, fit5, 
        sectionvars="Wind", conditionvars=c("Solar.R", "Temp"), predictArgs=list(list(pinterval="confidence")))

```

The loess fit does not provide confidence intervals but it does
offer standard errors, which can be used for confidence bounds:

```{r eval=F}
fitu <- fit3
class(fitu)<- c("upper", class(fitu))

CVpredict.upper <- function(f, newdata, ...){
  p <- predict(f, newdata, se=T)
  p$fit+ 2*p$se.fit
}

fitl <- fit3
class(fitl)<- c("lower", class(fitu))

CVpredict.lower <- function(f, newdata, ...){
  p <- predict(f, newdata, se=T)
  p$fit- 2*p$se.fit
}

condvis(ozone, list(loess=fit3,lower=fitl,upper=fitu), 
        sectionvars="Wind", conditionvars=c("Solar.R", "Temp"), 
        linecols=c("red", "blue","blue"))
```




```{r echo=FALSE, out.width='100%'}
knitr::include_graphics(paste0(fpath, "ozone6.png"))
```


## Tour controls

As the conditioning dimension increases, it might be easier to view sections that are
automatically chosen. The tour controls offer various controls.

- The simplest method chooses random observations in conditioning space
to form the sections.
-  Click on the arrow below `Tour Step` to watch.
- You can increase the number of random points via the `Tour Length` slider.
- If you want a smoother appearance to the tour, increase `Interp steps` from 0.
